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Transcriptome variation along bud development in grapevine (Vitis vinifera L.)

Transcriptome variation along bud development in grapevine (Vitis vinifera L.) | Plant Genomics | Scoop.it

Abstract (provisional)

Background

Vegetative buds provide plants in temperate environments the possibility for growth and reproduction when environmental conditions are favorable. In grapevine, crucial developmental events take place within buds during two growing seasons in consecutive years. The first season, the shoot apical meristem within the bud differentiates all the basic elements of the shoot including flowering transition in lateral primordia and development of inflorescence primordia. These events practically end with bud dormancy. The second season, buds resume shoot growth associated to flower formation and development. Gene expression has been previously monitored at specific stages of bud development but has never been followed along the two growing seasons.

Results

Gene expression changes were analyzed along the bud annual cycle at eight different time points. Principal Components Analysis (PCA) revealed that the main factors explaining the global gene expression differences were the processes of bud dormancy and active growth as well as stress responses. Accordingly, non dormant buds showed an enrichment in functional categories typical of actively proliferating and growing cells together with the over abundance of transcripts belonging to stress response pathways. Differential expression analyses performed between consecutive time points indicated that major transcriptional changes were associated to para/endodormancy, endo/ecodormancy and ecodormancy/bud break transitions. Transcripts encoding key regulators of reproductive development were grouped in three major expression clusters corresponding to: (i) transcripts associated to flowering induction, (ii) transcripts associated to flower meristem specification and initiation and (iii) transcripts putatively involved in dormancy. Within this cluster, a MADS-box gene (VvFLC2) and other transcripts with similar expression patterns could participate in dormancy regulation.

Conclusions

This work provides a global view of major transcriptional changes taking place along bud development in grapevine, highlighting those molecular and biological functions involved in the main events of bud development. As reported in other woody species, the results suggest that genes regulating flowering could also be involved in dormancy regulatory pathways in grapevine.

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Proteomic Validation of Transcript Isoforms, Including Those Assembled from RNA-Seq Data

Proteomic Validation of Transcript Isoforms, Including Those Assembled from RNA-Seq Data | Plant Genomics | Scoop.it
Human proteome analysis now requires an understanding of protein isoforms. We recently published the PG Nexus pipeline, which facilitates high confidence validation of exons and splice junctions by integrating genomics and proteomics data. Here we comprehensively explore how RNA-seq transcriptomics data, and proteomic analysis of the same sample, can identify protein isoforms. RNA-seq data from human mesenchymal (hMSC) stem cells were analyzed with our new TranscriptCoder tool to generate a database of protein isoform sequences. MS/MS data from matching hMSC samples were then matched against the TranscriptCoder-derived database, along with Ensembl and the neXtProt database. Querying the TranscriptCoder-derived or Ensembl database could unambiguously identify ∼450 protein isoforms, with isoform-specific proteotypic peptides, including candidate hMSC-specific isoforms for the genes DPYSL2 and FXR1. Where isoform-specific peptides did not exist, groups of nonisoform-specific proteotypic peptides could specifically identify many isoforms. In both the above cases, isoforms will be detectable with targeted MS/MS assays. Unfortunately, our analysis also revealed that some isoforms will be difficult to identify unambiguously as they do not have peptides that are sufficiently distinguishing. We covisualize mRNA isoforms and peptides in a genome browser to illustrate the above situations. Mass spectrometry data is available via ProteomeXchange (PXD001449).
Biswapriya Biswavas Misra's insight:

Human proteome analysis now requires an understanding of protein isoforms. We recently published the PG Nexus pipeline, which facilitates high confidence validation of exons and splice junctions by integrating genomics and proteomics data. Here we comprehensively explore how RNA-seq transcriptomics data, and proteomic analysis of the same sample, can identify protein isoforms. RNA-seq data from human mesenchymal (hMSC) stem cells were analyzed with our new TranscriptCoder tool to generate a database of protein isoform sequences. MS/MS data from matching hMSC samples were then matched against the TranscriptCoder-derived database, along with Ensembl and the neXtProt database. Querying the TranscriptCoder-derived or Ensembl database could unambiguously identify ∼450 protein isoforms, with isoform-specific proteotypic peptides, including candidate hMSC-specific isoforms for the genes DPYSL2 and FXR1. Where isoform-specific peptides did not exist, groups of nonisoform-specific proteotypic peptides could specifically identify many isoforms. In both the above cases, isoforms will be detectable with targeted MS/MS assays. Unfortunately, our analysis also revealed that some isoforms will be difficult to identify unambiguously as they do not have peptides that are sufficiently distinguishing. We covisualize mRNA isoforms and peptides in a genome browser to illustrate the above situations. Mass spectrometry data is available via ProteomeXchange (PXD001449).

 
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De Novo Assembly and Characterization of the Transcriptome of the Chinese Medicinal Herb, Gentiana rigescens

De Novo Assembly and Characterization of the Transcriptome of the Chinese Medicinal Herb, Gentiana rigescens | Plant Genomics | Scoop.it
Gentiana rigescens is an important medicinal herb in China. The main validated medicinal component gentiopicroside is synthesized in shoots, but is mainly found in the plant’s roots. The gentiopicroside biosynthetic pathway and its regulatory control remain to be elucidated. Genome resources of gentian are limited. Next-generation sequencing (NGS) technologies can aid in supplying global gene expression profiles. In this study we present sequence and transcript abundance data for the root and leaf transcriptome of G. rigescens, obtained using the Illumina Hiseq2000. Over fifty million clean reads were obtained from leaf and root libraries. This yields 76,717 unigenes with an average length of 753 bp. Among these, 33,855 unigenes were identified as putative homologs of annotated sequences in public protein and nucleotide databases. Digital abundance analysis identified 3306 unigenes differentially enriched between leaf and root. Unigenes found in both tissues were categorized according to their putative functional categories. Of the differentially expressed genes, over 130 were annotated as related to terpenoid biosynthesis. This work is the first study of global transcriptome analyses in gentian. These sequences and putative functional data comprise a resource for future investigation of terpenoid biosynthesis in Gentianaceae species and annotation of the gentiopicroside biosynthetic pathway and its regulatory mechanisms.
Biswapriya Biswavas Misra's insight:
Gentiana rigescens is an important medicinal herb in China. The main validated medicinal component gentiopicroside is synthesized in shoots, but is mainly found in the plant’s roots. The gentiopicroside biosynthetic pathway and its regulatory control remain to be elucidated. Genome resources of gentian are limited. Next-generation sequencing (NGS) technologies can aid in supplying global gene expression profiles. In this study we present sequence and transcript abundance data for the root and leaf transcriptome of G. rigescens, obtained using the Illumina Hiseq2000. Over fifty million clean reads were obtained from leaf and root libraries. This yields 76,717 unigenes with an average length of 753 bp. Among these, 33,855 unigenes were identified as putative homologs of annotated sequences in public protein and nucleotide databases. Digital abundance analysis identified 3306 unigenes differentially enriched between leaf and root. Unigenes found in both tissues were categorized according to their putative functional categories. Of the differentially expressed genes, over 130 were annotated as related to terpenoid biosynthesis. This work is the first study of global transcriptome analyses in gentian. These sequences and putative functional data comprise a resource for future investigation of terpenoid biosynthesis in Gentianaceae species and annotation of the gentiopicroside biosynthetic pathway and its regulatory mechanisms. 
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Comparative Analysis of Anther Transcriptome Profiles of Two Different Rice Male Sterile Lines Genotypes under Cold Stress.

Comparative Analysis of Anther Transcriptome Profiles of Two Different Rice Male Sterile Lines Genotypes under Cold Stress. | Plant Genomics | Scoop.it
Rice is highly sensitive to cold stress during reproductive developmental stages, and little is known about the mechanisms of cold responses in rice anther. Using the HiSeq™ 2000 sequencing platform, the anther transcriptome of photo thermo sensitive genic male sterile lines (PTGMS) rice Y58S and P64S (Pei'ai64S) were analyzed at the fertility sensitive stage under cold stress. Approximately 243 million clean reads were obtained from four libraries and aligned against the oryza indica genome and 1497 and 5652 differentially expressed genes (DEGs) were identified in P64S and Y58S, respectively. Both gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were conducted for these DEGs. Functional classification of DEGs was also carried out. The DEGs common to both genotypes were mainly involved in signal transduction, metabolism, transport, and transcriptional regulation. Most of the DEGs were unique for each comparison group. We observed that there were more differentially expressed MYB (Myeloblastosis) and zinc finger family transcription factors and signal transduction components such as calmodulin/calcium dependent protein kinases in the Y58S comparison group. It was also found that ribosome-related DEGs may play key roles in cold stress signal transduction. These results presented here would be particularly useful for further studies on investigating the molecular mechanisms of rice responses to cold stress.
Biswapriya Biswavas Misra's insight:

Rice is highly sensitive to cold stress during reproductive developmental stages, and little is known about the mechanisms of cold responses in rice anther. Using the HiSeq™ 2000 sequencing platform, the anther transcriptome of photo thermo sensitive genic male sterile lines (PTGMS) rice Y58S and P64S (Pei'ai64S) were analyzed at the fertility sensitive stage under cold stress. Approximately 243 million clean reads were obtained from four libraries and aligned against the oryza indica genome and 1497 and 5652 differentially expressed genes (DEGs) were identified in P64S and Y58S, respectively. Both gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were conducted for these DEGs. Functional classification of DEGs was also carried out. The DEGs common to both genotypes were mainly involved in signal transduction, metabolism, transport, and transcriptional regulation. Most of the DEGs were unique for each comparison group. We observed that there were more differentially expressed MYB (Myeloblastosis) and zinc finger family transcription factors and signal transduction components such as calmodulin/calcium dependent protein kinases in the Y58S comparison group. It was also found that ribosome-related DEGs may play key roles in cold stress signal transduction. These results presented here would be particularly useful for further studies on investigating the molecular mechanisms of rice responses to cold stress.

  
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Transcriptome analysis of the compatible interaction of tomato with Verticillium dahliae using RNA-sequencing

Tomato Verticillium wilt is a soil-borne vascular disease caused by the necrotrophic fungus Verticillium dahliae. Although some understanding of plant defense mechanisms against V. dahliae infection has been gained for incompatible interactions, including identification of inducible resistant genes and defense signaling pathways, the genes and signaling pathways involved in the compatible interaction remain unclear. To investigate the molecular basis of the compatible interaction between tomato and V. dahliae, transcriptomes of V. dahliae infected tomatoes were compared to those of a control group. A total of approximately 25 million high-quality reads were generated by means of the RNA sequencing (RNA-seq) method. The sequence reads were aligned to the tomato reference genome and analyzed to measure gene expression levels, and to identify alternative splicing events. Comparative analysis between the two samples revealed 1,953 significantly differentially expressed genes (DEGs), including 1,281 up-regulated and 672 down-regulated genes. The RNA-Seq output was confirmed using RT-qPCR for ten selected genes. The Nr, Swiss-Prot, GO, COG and KEGG databases were used to annotate DEG functions. Of the 1,953 DEGs identified, 1,953, 1,579, 1,739, 862, and 380 were assigned by Nr, Swiss-Prot, GO, COG, and KEGG, respectively. The important functional groups identified via GO and COG enrichment were those responsible for fundamental biological regulation, secondary metabolism, and signal transduction. Of DEGs assigned to 87 KEGG pathways, most were associated with phenylpropanoid metabolism and plant-pathogen interaction pathways. Most of the DEGs involved in these two pathways were up-regulated, and may be involved in regulating the tomato-V. dahliae compatible interaction. The results will help to identify key susceptible genes and contribute to a better understanding of the mechanisms of tomato susceptible response to V. dahliae.
Biswapriya Biswavas Misra's insight:

Tomato Verticillium wilt is a soil-borne vascular disease caused by the necrotrophic fungus Verticillium dahliae. Although some understanding of plant defense mechanisms against V. dahliae infection has been gained for incompatible interactions, including identification of inducible resistant genes and defense signaling pathways, the genes and signaling pathways involved in the compatible interaction remain unclear. To investigate the molecular basis of the compatible interaction between tomato and V. dahliae, transcriptomes of V. dahliae infected tomatoes were compared to those of a control group. A total of approximately 25 million high-quality reads were generated by means of the RNA sequencing (RNA-seq) method. The sequence reads were aligned to the tomato reference genome and analyzed to measure gene expression levels, and to identify alternative splicing events. Comparative analysis between the two samples revealed 1,953 significantly differentially expressed genes (DEGs), including 1,281 up-regulated and 672 down-regulated genes. The RNA-Seq output was confirmed using RT-qPCR for ten selected genes. The Nr, Swiss-Prot, GO, COG and KEGG databases were used to annotate DEG functions. Of the 1,953 DEGs identified, 1,953, 1,579, 1,739, 862, and 380 were assigned by Nr, Swiss-Prot, GO, COG, and KEGG, respectively. The important functional groups identified via GO and COG enrichment were those responsible for fundamental biological regulation, secondary metabolism, and signal transduction. Of DEGs assigned to 87 KEGG pathways, most were associated with phenylpropanoid metabolism and plant-pathogen interaction pathways. Most of the DEGs involved in these two pathways were up-regulated, and may be involved in regulating the tomato-V. dahliae compatible interaction. The results will help to identify key susceptible genes and contribute to a better understanding of the mechanisms of tomato susceptible response to V. dahliae.

   
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Tales from the crypt: genome mining from fungarium specimens improves resolution of the mushroom tree of life

Tales from the crypt: genome mining from fungarium specimens improves resolution of the mushroom tree of life | Plant Genomics | Scoop.it
Biswapriya Biswavas Misra's insight:

The enormity of the breadth and depth of specimens held within the world's biological collections offers unparalleled opportunities to capture genomic data from across the entire range of known biological diversity. Such a task would take many lifetimes to complete if we could rely only on fresh samples. High-throughput sequencing provides a technical solution to the long-term problems of recalcitrant and degraded DNA typical of museum specimens, suggesting that we may be on the verge of a major collections-based revolution. Although the potential is great, the feasibility of using preserved collections for large-scale, taxonomically comprehensive phylogenomic studies remains unknown. In the present study, we demonstrate the continued relevance of fungarium collections in the genomic era by analyzing a genomic dataset composed of 39 genomes representing 26 family-level clades, including 14 newly generated draft genomes derived from short-read shotgun sequencing of preserved specimens, frozen and freeze-dried material, representing most of the known families of Agaricales. We predicted homologues of 210 putative single copy genes in the newly generated draft genome assemblies, of which 208 were used for phylogenetic reconstruction. Our analyses resulted in a robust and, for the first time, fully supported phylogeny of the Agaricales, enabling the recognition of seven suborders and providing a resource for testing hypotheses of the evolution of mushrooms. Our analysis of optimal combinations of ranked genes using an information theory-based method provides guidance on gene selection for future studies, enabling efficient application of high-throughput sequencing techniques toward unlocking the potential of collections-based research in the genomic era.

 
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Dynamic evolution of resistance gene analogs in the orthologous genomic regions of powdery mildew resistance gene MlIW170 in Triticum dicoccoides and Aegilops tauschii

Dynamic evolution of resistance gene analogs in the orthologous genomic regions of powdery mildew resistance gene MlIW170 in Triticum dicoccoides and Aegilops tauschii | Plant Genomics | Scoop.it
Rapid evolution of powdery mildew resistance gene MlIW170 orthologous genomic regions in wheat subgenomes. Wheat is one of the most important staple grain crops in the world and also an excellent model for plant ploidy evolution research with different ploidy levels from diploid to hexaploid. Powdery mildew disease caused by Blumeria graminis f.sp. tritici can result in significant loss in both grain yield and quality in wheat. In this study, the wheat powdery mildew resistance gene MlIW170 locus located at the Triticum dicoccoides chromosome 2B short arm was further characterized by constructing and sequencing a BAC-based physical map contig covering a 0.3 cM genetic distance region (880 kb) and developing additional markers to delineate the resistance gene within a 0.16 cM genetic interval (372 kb). Comparative analyses of the T. dicoccoides 2BS region with the orthologous Aegilops tauschii 2DS region showed great gene colinearity, including the structure organization of both types of RGA1/2-like and RPS2-like resistance genes. Comparative analyses with the orthologous regions from Brachypodium and rice genomes revealed considerable dynamic evolutionary changes that have re-shaped this MlIW170 region in the wheat genome, resulting in a high number of non-syntenic genes including resistance-related genes. This result might reflect the rapid evolution in R-gene regions. Phylogenetic analysis on these resistance-related gene sequences indicated the duplication of these genes in the MlIW170 region, occurred before the separation of the wheat B and D genomes.
Biswapriya Biswavas Misra's insight:

Rapid evolution of powdery mildew resistance gene MlIW170 orthologous genomic regions in wheat subgenomes. Wheat is one of the most important staple grain crops in the world and also an excellent model for plant ploidy evolution research with different ploidy levels from diploid to hexaploid. Powdery mildew disease caused by Blumeria graminis f.sp. tritici can result in significant loss in both grain yield and quality in wheat. In this study, the wheat powdery mildew resistance gene MlIW170 locus located at the Triticum dicoccoides chromosome 2B short arm was further characterized by constructing and sequencing a BAC-based physical map contig covering a 0.3 cM genetic distance region (880 kb) and developing additional markers to delineate the resistance gene within a 0.16 cM genetic interval (372 kb). Comparative analyses of the T. dicoccoides 2BS region with the orthologous Aegilops tauschii 2DS region showed great gene colinearity, including the structure organization of both types of RGA1/2-like and RPS2-like resistance genes. Comparative analyses with the orthologous regions from Brachypodium and rice genomes revealed considerable dynamic evolutionary changes that have re-shaped this MlIW170 region in the wheat genome, resulting in a high number of non-syntenic genes including resistance-related genes. This result might reflect the rapid evolution in R-gene regions. Phylogenetic analysis on these resistance-related gene sequences indicated the duplication of these genes in the MlIW170 region, occurred before the separation of the wheat B and D genomes.

  
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Transcriptome Profiling of the Potato (Solanum tuberosum L.) Plant under Drought Stress and Water-Stimulus Conditions.

Transcriptome Profiling of the Potato (Solanum tuberosum L.) Plant under Drought Stress and Water-Stimulus Conditions. | Plant Genomics | Scoop.it
PLoS One. 2015 May 26;10(5):e0128041. doi: 10.1371/journal.pone.0128041. eCollection 2015.
Biswapriya Biswavas Misra's insight:

Drought stress can seriously affect tuberization, yield and quality of potato plant. However, the precise molecular mechanisms governing potato stolon's response to drought stress and water supply are not very well understood. In this work, a potato (Solanum tuberosum L.) variant, Ningshu 4, was subjected to severe drought stress treatment (DT) and re-watering treatment (RWT) at tuber bulking stage. Strand-specific cDNA libraries of stolon materials were constructed for paired-end transcriptome sequencing analyses and differentially expressed gene (DEG) examination. In comparison to untreated-control (CT) plants, 3189 and 1797 DEGs were identified in DT and RWT plants and 4154 solely expressed DEGs were screened out from these two comparison groups. Interestingly, 263 genes showed opposite expression patterns in DT and RWT plants. Among them, genes homologous to Protein Phosphatase 2C (PP2C), Aspartic protease in guard cell 1 (ASPG1), auxin-responsive protein, Arabidopsis pseudo response regualtor 2 (APRR2), GA stimulated transcripts in Arabidopsis 6 (GASA6), Calmodulin-like protein 19 (CML19), abscisic acid 8'-hydroxylases and calcium-transporting ATPase, et al. were related with drought-stress and water stimulus response. Sixteen DEGs involved in starch synthesis, accumulation and tuber formation exhibited significantly different expression upon re-watering. In addition, 1630, 1527 and 1596 transcription factor encoding genes were detected in CT, DT and RWT. DEGs of ERF, bHLH, MYB, NAC, WRKY, C2H2, bZIP and HD-ZIP families accounted for 50% in three comparison groups, respectively. Furthermore, characteristics of 565 gene ontology (GO) and 108 Kyoto Encyclopedia of Genes and Genomes pathways (KEGG) were analyzed with the 4154 DEGs. All these results suggest that the drought- and water-stimulus response could be implemented by the regulated expression of metabolic pathway DEGs, and these genes were involved in the endogenous hormone biosynthesis and signal transduction pathways. Our data provide more direct information for future study on the interaction between key genes involved in various metabolic pathways under drought stress in potato.

  
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De Novo Assembly and Characterization of the Transcriptome of the Chinese Medicinal Herb, Gentiana rigescens.

De Novo Assembly and Characterization of the Transcriptome of the Chinese Medicinal Herb, Gentiana rigescens. | Plant Genomics | Scoop.it
Int J Mol Sci. 2015 May 20;16(5):11550-73. doi: 10.3390/ijms160511550.
Biswapriya Biswavas Misra's insight:

Gentiana rigescens is an important medicinal herb in China. The main validated medicinal component gentiopicroside is synthesized in shoots, but is mainly found in the plant's roots. The gentiopicroside biosynthetic pathway and its regulatory control remain to be elucidated. Genome resources of gentian are limited. Next-generation sequencing (NGS) technologies can aid in supplying global gene expression profiles. In this study we present sequence and transcript abundance data for the root and leaf transcriptome of G. rigescens, obtained using the Illumina Hiseq2000. Over fifty million clean reads were obtained from leaf and root libraries. This yields 76,717 unigenes with an average length of 753 bp. Among these, 33,855 unigenes were identified as putative homologs of annotated sequences in public protein and nucleotide databases. Digital abundance analysis identified 3306 unigenes differentially enriched between leaf and root. Unigenes found in both tissues were categorized according to their putative functional categories. Of the differentially expressed genes, over 130 were annotated as related to terpenoid biosynthesis. This work is the first study of global transcriptome analyses in gentian. These sequences and putative functional data comprise a resource for future investigation of terpenoid biosynthesis in Gentianaceae species and annotation of the gentiopicroside biosynthetic pathway and its regulatory mechanisms.

  
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A proteomic approach to Physcomitrella patens rhizoid exudates.

A proteomic approach to Physcomitrella patens rhizoid exudates. | Plant Genomics | Scoop.it
The interaction between plants and the surrounding environment has been widely studied, specially the defence reactions and the plant-plant interactions. One of the most remarkable metabolic features of plant roots is the ability to secrete a vast array of compounds into the rhizosphere, not only of low molecular weight but also polysaccharides and proteins. Here, we took advantage of proteomics to study the rhizoid exudates of Physcomitrella patens at early and late development stages (7 and 28 days of culture in liquid medium). Samples were extracted, separated and detected with nanoLC-MALDI-TOF/TOF MS/MS, identifying 47 proteins at the development stage of 7 days, and 66 proteins at 28 days. Moreover, 21 proteins were common to the two analyzed periods. All the identified proteins were classified into 8 functional categories: response to stress, response to stimulus, oxido-reduction, cell wall modification, photosynthesis and carbohydrate metabolism, transport, DNA metabolic process and regulation/signalling. Our results show important differences in the protein expression profile along the development of P. patens, mainly at the level of regulation- and senescence-related proteins. Defence-related proteins, such as chitinases, thaumatins and peroxidases have a major role in the interaction of P. patens with the environment.
Biswapriya Biswavas Misra's insight:

The interaction between plants and the surrounding environment has been widely studied, specially the defence reactions and the plant-plant interactions. One of the most remarkable metabolic features of plant roots is the ability to secrete a vast array of compounds into the rhizosphere, not only of low molecular weight but also polysaccharides and proteins. Here, we took advantage of proteomics to study the rhizoid exudates of Physcomitrella patens at early and late development stages (7 and 28 days of culture in liquid medium). Samples were extracted, separated and detected with nanoLC-MALDI-TOF/TOF MS/MS, identifying 47 proteins at the development stage of 7 days, and 66 proteins at 28 days. Moreover, 21 proteins were common to the two analyzed periods. All the identified proteins were classified into 8 functional categories: response to stress, response to stimulus, oxido-reduction, cell wall modification, photosynthesis and carbohydrate metabolism, transport, DNA metabolic process and regulation/signalling. Our results show important differences in the protein expression profile along the development of P. patens, mainly at the level of regulation- and senescence-related proteins. Defence-related proteins, such as chitinases, thaumatins and peroxidases have a major role in the interaction of P. patens with the environment.

 
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What can we learn from the transcriptome of the resurrection plant Craterostigma plantagineum?

What can we learn from the transcriptome of the resurrection plant Craterostigma plantagineum? | Plant Genomics | Scoop.it
The desiccation transcriptome of the resurrection plant C. plantagineum is composed of conserved protein coding transcripts, taxonomically restricted transcripts and recently evolved non-protein coding transcripts. Research in resurrection plants has been hampered by the lack of genome sequence information, but recently introduced sequencing technologies overcome this limitation partially and provide access to the transcriptome of these plants. Transcriptome studies showed that mechanisms involved in desiccation tolerance are conserved in resurrection plants, seeds and pollen. The accumulation of protective molecules such as sugars and LEA proteins are major components in desiccation tolerance. Leaf folding, chloroplast protection and protection during rehydration must involve specific molecular mechanisms, but the basis of such mechanisms is mainly unknown. The study of regulatory regions of a desiccation-induced C. plantagineum gene suggests that cis-regulatory elements may be responsible for expression variations in desiccation tolerant and non-desiccation-tolerant plants. The analysis of the C. plantagineum transcriptome also revealed that part of it is composed of taxonomically restricted genes (TRGs) and non-protein coding RNAs (ncRNAs). TRGs are known to code for new traits required for the adaptation of organisms to particular environmental conditions. Thus the study of TRGs from resurrection plants should reveal species-specific functions related to the desiccation tolerance phenotype. Non-protein coding RNAs can regulate gene expression at epigenetic, transcriptional and post-transcriptional level and thus these RNAs may be key players in the rewiring of regulatory networks of desiccation-related genes in C. plantagineum.
Biswapriya Biswavas Misra's insight:

The desiccation transcriptome of the resurrection plant C. plantagineum is composed of conserved protein coding transcripts, taxonomically restricted transcripts and recently evolved non-protein coding transcripts. Research in resurrection plants has been hampered by the lack of genome sequence information, but recently introduced sequencing technologies overcome this limitation partially and provide access to the transcriptome of these plants. Transcriptome studies showed that mechanisms involved in desiccation tolerance are conserved in resurrection plants, seeds and pollen. The accumulation of protective molecules such as sugars and LEA proteins are major components in desiccation tolerance. Leaf folding, chloroplast protection and protection during rehydration must involve specific molecular mechanisms, but the basis of such mechanisms is mainly unknown. The study of regulatory regions of a desiccation-induced C. plantagineum gene suggests that cis-regulatory elements may be responsible for expression variations in desiccation tolerant and non-desiccation-tolerant plants. The analysis of the C. plantagineum transcriptome also revealed that part of it is composed of taxonomically restricted genes (TRGs) and non-protein coding RNAs (ncRNAs). TRGs are known to code for new traits required for the adaptation of organisms to particular environmental conditions. Thus the study of TRGs from resurrection plants should reveal species-specific functions related to the desiccation tolerance phenotype. Non-protein coding RNAs can regulate gene expression at epigenetic, transcriptional and post-transcriptional level and thus these RNAs may be key players in the rewiring of regulatory networks of desiccation-related genes in C. plantagineum.

  
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Transcriptomic landscape of Pueraria lobata demonstrates potential for phytochemical study

Pueraria lobata (Willd.) Ohwi has a long and broad application in the treatment of disease. However, in the US and EU, it is treated as a notorious weed. The information to be gained from decoding the deep transcriptome profile would facilitate further research on P. lobata. In this study, more than 93 million fastq format reads were generated by Illumina’s next-generation sequencing approach using five types of P. lobata tissue, followed by CLC de novo assembly methods, ultimately yielding about 83,041 contigs in total. Then BLASTx similarity searches against the NCBI NR database and UniProtKB database were conducted. Once the duplicates among BLASTx hits were eliminated, ID mapping against the UniProt database was conducted online to retrieve Gene Ontology information. In search of the putative genes relevant to essential biosynthesis pathways, all 1,348 unique enzyme commission numbers were used to map pathways against the Kyoto Encyclopedia of Genes and Genomes. Enzymes related to the isoflavonoid and flavonoid biosynthesis pathways were focused for detailed investigation and subsequently, qRT-PCR was conducted for biological validation. Metabolites of interest, puerarin and daidzin were studied by HPLC. The findings in this report may serve as a footstone for further research into this promising medicinal plant.
Biswapriya Biswavas Misra's insight:

Pueraria lobata (Willd.) Ohwi has a long and broad application in the treatment of disease. However, in the US and EU, it is treated as a notorious weed. The information to be gained from decoding the deep transcriptome profile would facilitate further research on P. lobata. In this study, more than 93 million fastq format reads were generated by Illumina’s next-generation sequencing approach using five types of P. lobata tissue, followed by CLC de novo assembly methods, ultimately yielding about 83,041 contigs in total. Then BLASTx similarity searches against the NCBI NR database and UniProtKB database were conducted. Once the duplicates among BLASTx hits were eliminated, ID mapping against the UniProt database was conducted online to retrieve Gene Ontology information. In search of the putative genes relevant to essential biosynthesis pathways, all 1,348 unique enzyme commission numbers were used to map pathways against the Kyoto Encyclopedia of Genes and Genomes. Enzymes related to the isoflavonoid and flavonoid biosynthesis pathways were focused for detailed investigation and subsequently, qRT-PCR was conducted for biological validation. Metabolites of interest, puerarin and daidzin were studied by HPLC. The findings in this report may serve as a footstone for further research into this promising medicinal plant.

   
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Landscape of the lipidome and transcriptome under heat stress in Arabidopsis thaliana

Landscape of the lipidome and transcriptome under heat stress in Arabidopsis thaliana | Plant Genomics | Scoop.it
Biswapriya Biswavas Misra's insight:

Environmental stress causes membrane damage in plants. Lipid studies are required to understand the adaptation of plants to climate change. Here, LC-MS-based lipidomic and microarray transcriptome analyses were carried out to elucidate the effect of short-term heat stress on the Arabidopsis thaliana leaf membrane. Vegetative plants were subjected to high temperatures for one day, and then grown under normal conditions. Sixty-six detected glycerolipid species were classified according to patterns of compositional change by Spearman’s correlation coefficient. Triacylglycerols, 36:4- and 36:5-monogalactosyldiacylglycerol, 34:2- and 36:2-digalactosyldiacylglycerol, 34:1-, 36:1- and 36:6-phosphatidylcholine, and 34:1-phosphatidylethanolamine increased by the stress and immediately decreased during recovery. The relative amount of one triacylglycerol species (54:9) containing α-linolenic acid (18:3) increased under heat stress. These results suggest that heat stress in Arabidopsis leaves induces an increase in triacylglycerol levels, which functions as an intermediate of lipid turnover, and results in a decrease in membrane polyunsaturated fatty acids. Microarray data revealed candidate genes responsible for the observed metabolic changes.

  
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The complete chloroplast genome sequence of the relict woody plant Metasequoia glyptostroboides Hu et Cheng | Plant Genetics and Genomics

Metasequoia glyptostroboides Hu et Cheng is the only species in the genus Metasequoia Miki ex Hu et Cheng, which belongs to the Cupressaceae family. There were around ten species in the Metasequoia genus, which were widely spread across the Northern Hemisphere during the Cretaceous of the Mesozoic and in the Cenozoic. M. glyptostroboides is the only remaining representative of this genus. Here, we report the complete chloroplast (cp) genome sequence and the cp genomic features of M. glyptostroboides. The M. glyptostroboides cp genome is 131,887 bp in length, with a total of 117 genes comprised of 82 protein-coding genes, 31 tRNA genes and four rRNA genes. In this genome, 11 forward repeats, nine palindromic repeats and 15 tandem repeats were detected. A total of 188 perfect microsatellites were detected through simple sequence repeat (SSR) analysis and these were distributed unevenly within the cp genome. Comparison of the cp genome structure and gene order to those of several other land plants indicated that a copy of the inverted repeat (IR) region, which was found to be IR region A (IRA), was lost in the M. glyptostroboides cp ge-nome. The five most divergent and five most conserved genes were determined and further phylogenetic analysis was performed among plant species, especially for relat-ed species in conifers. Finally, phylogenetic analysis demonstrated that M. glyptostro-boides is a sister species to Cryptomeria japonica (L. F.) D. Don and to Taiwania cryptomerioides Hayata. The complete cp genome sequence information of M. glyp-tostroboides will be great helpful for further investigations of this endemic relict woody plant and for in-depth understanding of the evolutionary history of the conif-erous cp genomes, especially for the position of M. glyptostroboides in plant systemat-ics and evolution.
Biswapriya Biswavas Misra's insight:

Metasequoia glyptostroboides Hu et Cheng is the only species in the genus Metasequoia Miki ex Hu et Cheng, which belongs to the Cupressaceae family. There were around ten species in the Metasequoia genus, which were widely spread across the Northern Hemisphere during the Cretaceous of the Mesozoic and in the Cenozoic. M. glyptostroboides is the only remaining representative of this genus. Here, we report the complete chloroplast (cp) genome sequence and the cp genomic features of M. glyptostroboides. The M. glyptostroboides cp genome is 131,887 bp in length, with a total of 117 genes comprised of 82 protein-coding genes, 31 tRNA genes and four rRNA genes. In this genome, 11 forward repeats, nine palindromic repeats and 15 tandem repeats were detected. A total of 188 perfect microsatellites were detected through simple sequence repeat (SSR) analysis and these were distributed unevenly within the cp genome. Comparison of the cp genome structure and gene order to those of several other land plants indicated that a copy of the inverted repeat (IR) region, which was found to be IR region A (IRA), was lost in the M. glyptostroboides cp ge-nome. The five most divergent and five most conserved genes were determined and further phylogenetic analysis was performed among plant species, especially for relat-ed species in conifers. Finally, phylogenetic analysis demonstrated that M. glyptostro-boides is a sister species to Cryptomeria japonica (L. F.) D. Don and to Taiwania cryptomerioides Hayata. The complete cp genome sequence information of M. glyp-tostroboides will be great helpful for further investigations of this endemic relict woody plant and for in-depth understanding of the evolutionary history of the conif-erous cp genomes, especially for the position of M. glyptostroboides in plant systemat-ics and evolution.

   
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GenoWAP: Post-GWAS Prioritization Through Integrated Analysis of Genomic Functional Annotation

bioRxiv - the preprint server for biology, operated by Cold Spring Harbor Laboratory, a research and educational institution
Biswapriya Biswavas Misra's insight:

Genome-wide association study (GWAS) has been a great success in the past decade. However, significant challenges still remain in both identifying new risk loci and interpreting results. Bonferroni-corrected significance level is known to be conservative, leading to insufficient statistical power when the effect size is moderate at risk locus. Complex structure of linkage disequilibrium also makes it challenging to separate causal variants from nonfunctional ones in large haplotype blocks. We describe GenoWAP, a post-GWAS prioritization method that integrates genomic functional annotation and GWAS test statistics. The effectiveness of GenoWAP is demonstrated through its applications to Crohn’s disease and schizophrenia using the largest studies available, where highly ranked loci show substantially stronger signals in the whole dataset after prioritization based on a subset of samples. At the single nucleotide polymorphism (SNP) level, top ranked SNPs after prioritization have both higher replication rates and consistently stronger enrichment of eQTLs. Within each risk locus, GenoWAP is also able to distinguish functional sites from groups of correlated SNPs. GenoWAP is freely available on the web at http://genocanyon.med.yale.edu/GenoWAP

 
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MS1 Peptide Ion Intensity Chromatograms in MS2 (SWATH) Data Independent Acquisitions. Improving Post Acquisition Analysis of Proteomic Experiments.

MS1 Peptide Ion Intensity Chromatograms in MS2 (SWATH) Data Independent Acquisitions. Improving Post Acquisition Analysis of Proteomic Experiments. | Plant Genomics | Scoop.it
Quantitative analysis of discovery-based proteomic workflows now relies on high-throughput large-scale methods for identification and quantitation of proteins and post-translational modifications. Advancements in label-free quantitative techniques, using either data-dependent or data-independent mass spectrometric acquisitions, have coincided with improved instrumentation featuring greater precision, increased mass accuracy, and faster scan speeds. We recently reported on a new quantitative method called MS1 Filtering (Schilling et al. (2012) Mol. Cell. Proteomics 11, 202-214) for processing data-independent MS1 ion intensity chromatograms from peptide analytes using the Skyline software platform. In contrast, data-independent acquisitions from MS2 scans, or SWATH, can quantify all fragment ion intensities when reference spectra are available. As each SWATH acquisition cycle typically contains an MS1 scan, these two independent label-free quantitative approaches can be acquired in a single experiment. Here, we have expanded the capability of Skyline to extract both MS1 and MS2 ion intensity chromatograms from a single SWATH data-independent acquisition (DIA) in an Integrated Dual Scan Analysis (IDSA) approach. The performance of both MS1 and MS2 data was examined in simple and complex samples using standard concentration curves. Cases of interferences in MS1 and MS2 ion intensity data were assessed, as were the differentiation and quantitation of phosphopeptide isomers in MS2 scan data. In addition, we demonstrated an approach for optimization of SWATH m/z window sizes to reduce interferences using MS1 scans as a guide. Finally, a correlation analysis was performed on both MS1 and MS2 ion intensity data obtained from SWATH acquisitions on a complex mixture using a linear model that automatically removes signals containing interferences. This work demonstrates the practical advantages of properly acquiring and processing MS1 precursor data in addition to MS2 fragment ion intensity data in a DIA (SWATH), and provides an approach to simultaneously obtain independent measurements of relative peptide abundance from a single experiment.
Biswapriya Biswavas Misra's insight:

Quantitative analysis of discovery-based proteomic workflows now relies on high-throughput large-scale methods for identification and quantitation of proteins and post-translational modifications. Advancements in label-free quantitative techniques, using either data-dependent or data-independent mass spectrometric acquisitions, have coincided with improved instrumentation featuring greater precision, increased mass accuracy, and faster scan speeds. We recently reported on a new quantitative method called MS1 Filtering (Schilling et al. (2012) Mol. Cell. Proteomics 11, 202-214) for processing data-independent MS1 ion intensity chromatograms from peptide analytes using the Skyline software platform. In contrast, data-independent acquisitions from MS2 scans, or SWATH, can quantify all fragment ion intensities when reference spectra are available. As each SWATH acquisition cycle typically contains an MS1 scan, these two independent label-free quantitative approaches can be acquired in a single experiment. Here, we have expanded the capability of Skyline to extract both MS1 and MS2 ion intensity chromatograms from a single SWATH data-independent acquisition (DIA) in an Integrated Dual Scan Analysis (IDSA) approach. The performance of both MS1 and MS2 data was examined in simple and complex samples using standard concentration curves. Cases of interferences in MS1 and MS2 ion intensity data were assessed, as were the differentiation and quantitation of phosphopeptide isomers in MS2 scan data. In addition, we demonstrated an approach for optimization of SWATH m/z window sizes to reduce interferences using MS1 scans as a guide. Finally, a correlation analysis was performed on both MS1 and MS2 ion intensity data obtained from SWATH acquisitions on a complex mixture using a linear model that automatically removes signals containing interferences. This work demonstrates the practical advantages of properly acquiring and processing MS1 precursor data in addition to MS2 fragment ion intensity data in a DIA (SWATH), and provides an approach to simultaneously obtain independent measurements of relative peptide abundance from a single experiment.

 
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Transcriptome diversity among rice root types during asymbiosis and interaction with arbuscular mycorrhizal fungi

Root systems consist of different root types (RTs) with distinct developmental and functional characteristics. RTs may be individually reprogrammed in response to their microenvironment to maximize adaptive plasticity. Molecular understanding of such specific remodeling—although crucial for crop improvement—is limited. Here, RT-specific transcriptomes of adult rice crown, large and fine lateral roots were assessed, revealing molecular evidence for functional diversity among individual RTs. Of the three rice RTs, crown roots displayed a significant enrichment of transcripts associated with phytohormones and secondary cell wall (SCW) metabolism, whereas lateral RTs showed a greater accumulation of transcripts related to mineral transport. In nature, arbuscular mycorrhizal (AM) symbiosis represents the default state of most root systems and is known to modify root system architecture. Rice RTs become heterogeneously colonized by AM fungi, with large laterals preferentially entering into the association. However, RT-specific transcriptional responses to AM symbiosis were quantitatively most pronounced for crown roots despite their modest physical engagement in the interaction. Furthermore, colonized crown roots adopted an expression profile more related to mycorrhizal large lateral than to noncolonized crown roots, suggesting a fundamental reprogramming of crown root character. Among these changes, a significant reduction in SCW transcripts was observed that was correlated with an alteration of SCW composition as determined by mass spectrometry. The combined change in SCW, hormone- and transport-related transcript profiles across the RTs indicates a previously overlooked switch of functional relationships among RTs during AM symbiosis, with a potential impact on root system architecture and functioning.

Via Christophe Jacquet
Biswapriya Biswavas Misra's insight:
Root systems consist of different root types (RTs) with distinct developmental and functional characteristics. RTs may be individually reprogrammed in response to their microenvironment to maximize adaptive plasticity. Molecular understanding of such specific remodeling—although crucial for crop improvement—is limited. Here, RT-specific transcriptomes of adult rice crown, large and fine lateral roots were assessed, revealing molecular evidence for functional diversity among individual RTs. Of the three rice RTs, crown roots displayed a significant enrichment of transcripts associated with phytohormones and secondary cell wall (SCW) metabolism, whereas lateral RTs showed a greater accumulation of transcripts related to mineral transport. In nature, arbuscular mycorrhizal (AM) symbiosis represents the default state of most root systems and is known to modify root system architecture. Rice RTs become heterogeneously colonized by AM fungi, with large laterals preferentially entering into the association. However, RT-specific transcriptional responses to AM symbiosis were quantitatively most pronounced for crown roots despite their modest physical engagement in the interaction. Furthermore, colonized crown roots adopted an expression profile more related to mycorrhizal large lateral than to noncolonized crown roots, suggesting a fundamental reprogramming of crown root character. Among these changes, a significant reduction in SCW transcripts was observed that was correlated with an alteration of SCW composition as determined by mass spectrometry. The combined change in SCW, hormone- and transport-related transcript profiles across the RTs indicates a previously overlooked switch of functional relationships among RTs during AM symbiosis, with a potential impact on root system architecture and functioning.
 
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Toward Whole-Transcriptome Editing with CRISPR-Cas9.

Toward Whole-Transcriptome Editing with CRISPR-Cas9. | Plant Genomics | Scoop.it
Targeted regulation of gene expression holds huge promise for biomedical research. In a series of recent publications (Gilbert et al., 2014; Konermann et al., 2015; Zalatan et al., 2015), sophisticated, multiplex-compatible transcriptional activator systems based on the CRISPR-Cas9 technology and genome-scale libraries advance the field toward whole-transcriptome control.
Biswapriya Biswavas Misra's insight:

Targeted regulation of gene expression holds huge promise for biomedical research. In a series of recent publications (Gilbert et al., 2014; Konermann et al., 2015; Zalatan et al., 2015), sophisticated, multiplex-compatible transcriptional activator systems based on the CRISPR-Cas9 technology and genome-scale libraries advance the field toward whole-transcriptome control.

 
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RNA-Seq Uncovers SNPs and Alternative Splicing Events in Asian Lotus ( Nelumbo nucifera )

RNA-Seq Uncovers SNPs and Alternative Splicing Events in Asian Lotus ( Nelumbo nucifera ) | Plant Genomics | Scoop.it
RNA-Seq is an efficient way to comprehensively identify single nucleotide polymorphisms (SNPs) and alternative splicing (AS) events from the expressed genes. In this study, we conducted transcriptome sequencing of four Asian lotus (Nelumbo nucifera) cultivars using Illumina HiSeq2000 platform to identify SNPs and AS events in lotus. A total of 505 million pair-end RNA-Seq reads were generated from four cultivars, of which 86% were mapped to the lotus reference genome. Using the four sets of data together, a total of 357,689 putative SNPs were identified with an average density of one SNP per 2.2 kb. These SNPs were located in 1,253 scaffolds and 15,016 expressed genes. A/G and C/T were the two major types of SNPs in the Asian lotus transcriptome. In parallel, a total of 177,540 AS events were detected in the four cultivars and were distributed in 64% of the expressed genes of lotus. The predominant type of AS events was alternative 5’ first exon, which accounted for 41.2% of all the observed AS events, and exon skipping only accounted for 4.3% of all AS. Gene Ontology analysis was conducted to analyze the function of the genes containing SNPs and AS events. Validation of selected SNPs and AS events revealed that 74% of SNPs and 80% of AS events were reliable, which indicates that RNA-Seq is an efficient approach to uncover gene-associated SNPs and AS events. A large number of SNPs and AS events identified in our study will facilitate further genetic and functional genomics research in lotus.
Biswapriya Biswavas Misra's insight:

RNA-Seq is an efficient way to comprehensively identify single nucleotide polymorphisms (SNPs) and alternative splicing (AS) events from the expressed genes. In this study, we conducted transcriptome sequencing of four Asian lotus (Nelumbo nucifera) cultivars using Illumina HiSeq2000 platform to identify SNPs and AS events in lotus. A total of 505 million pair-end RNA-Seq reads were generated from four cultivars, of which 86% were mapped to the lotus reference genome. Using the four sets of data together, a total of 357,689 putative SNPs were identified with an average density of one SNP per 2.2 kb. These SNPs were located in 1,253 scaffolds and 15,016 expressed genes. A/G and C/T were the two major types of SNPs in the Asian lotus transcriptome. In parallel, a total of 177,540 AS events were detected in the four cultivars and were distributed in 64% of the expressed genes of lotus. The predominant type of AS events was alternative 5’ first exon, which accounted for 41.2% of all the observed AS events, and exon skipping only accounted for 4.3% of all AS. Gene Ontology analysis was conducted to analyze the function of the genes containing SNPs and AS events. Validation of selected SNPs and AS events revealed that 74% of SNPs and 80% of AS events were reliable, which indicates that RNA-Seq is an efficient approach to uncover gene-associated SNPs and AS events. A large number of SNPs and AS events identified in our study will facilitate further genetic and functional genomics research in lotus.

  
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Proteomic analysis of crop plants under abiotic stress conditions: where to focus our research?

Approximately 80% of human food is composed of crops, which are dominated by cereals that collectively make up 50% of global food production (Langridge and Fleury, 2011). Among cereal crops, rice, wheat and maize provide approximately half of the calories consumed worldwide. Nevertheless, crop production is seriously hampered by influential abiotic stresses like drought, climate fluctuations, and salinity. It is estimated that up to 50–70% decline in crop productivity is attributed to abiotic stress (Mittler, 2006). Therefore, to ensure the security of global food production, it is essential to produce sustainable crop varieties that can adapt to climate variability, and to develop a broad spectrum of abiotic stress tolerant crops (Tester and Langridge, 2010). This has driven much research into the study of crop responses to abiotic stresses.
Biswapriya Biswavas Misra's insight:

Approximately 80% of human food is composed of crops, which are dominated by cereals that collectively make up 50% of global food production (Langridge and Fleury, 2011). Among cereal crops, rice, wheat and maize provide approximately half of the calories consumed worldwide. Nevertheless, crop production is seriously hampered by influential abiotic stresses like drought, climate fluctuations, and salinity. It is estimated that up to 50–70% decline in crop productivity is attributed to abiotic stress (Mittler, 2006). Therefore, to ensure the security of global food production, it is essential to produce sustainable crop varieties that can adapt to climate variability, and to develop a broad spectrum of abiotic stress tolerant crops (Tester and Langridge, 2010). This has driven much research into the study of crop responses to abiotic stresses.

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Whole-Transcriptome Analysis of Differentially Expressed Genes in the Vegetative Buds, Floral Buds and Buds of Chrysanthemum morifolium.

Whole-Transcriptome Analysis of Differentially Expressed Genes in the Vegetative Buds, Floral Buds and Buds of Chrysanthemum morifolium. | Plant Genomics | Scoop.it
PLoS One. 2015 May 26;10(5):e0128009. doi: 10.1371/journal.pone.0128009. eCollection 2015.
Biswapriya Biswavas Misra's insight:
AbstractBACKGROUND:

Chrysanthemum morifolium is an important floral crop that is cultivated worldwide. However, due to a lack of genomic resources, very little information is available concerning the molecular mechanisms of flower development in chrysanthemum.

RESULTS:

The transcriptomes of chrysanthemum vegetative buds, floral buds and buds were sequenced using Illumina paired-end sequencing technology. A total of 15.4 Gb of reads were assembled into 91,367 unigenes with an average length of 739 bp. A total of 43,137 unigenes showed similarity to known proteins in the Swissprot or NCBI non-redundant protein databases. Additionally, 25,424, 24,321 and 13,704 unigenes were assigned to 56 gene ontology (GO) categories, 25 EuKaryotic Orthologous Groups (KOG) categories, and 285 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, respectively. A total of 1,876 differentially expressed genes (DEGs) (1,516 up-regulated, 360 down-regulated) were identified between vegetative buds and floral buds, and 3,300 DEGs (1,277 up-regulated, 1,706 down-regulated) were identified between floral buds and buds. Many genes encoding important transcription factors (e.g., AP2, MYB, MYC, WRKY, NAC and CRT) as well as proteins involved in carbohydrate metabolism, protein kinase activity, plant hormone signal transduction, and the defense responses, among others, were considerably up-regulated in floral buds. Genes involved in the photoperiod pathway and flower organ determination were also identified. These genes represent important candidate genes for molecular cloning and functional analysis to study flowering regulation in chrysanthemum.

CONCLUSION:

This comparative transcriptome analysis revealed significant differences in gene expression and signaling pathway components between the vegetative buds, floral buds and buds of Chrysanthemum morifolium. A wide range of genes was implicated in regulating the phase transition from vegetative to reproductive growth. These results should aid researchers in the study of flower-time regulation, breeding and molecular biology in chrysanthemum.

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Physiological and transcriptomic characterization of submergence and reoxygenation responses in soybean seedlings.

Physiological and transcriptomic characterization of submergence and reoxygenation responses in soybean seedlings. | Plant Genomics | Scoop.it
Complete inundation at the early seedling stage is a common environmental constraint for soybean production throughout the world. As floodwaters subside, submerged seedlings are subsequently exposed to reoxygenation stress in the natural progression of a flood event. Here, we characterized the fundamental acclimation responses to submergence and reoxygenation in soybean at the seedling establishment stage. Approximately 90% of seedlings succumbed during 3 d of inundation under constant darkness, whereas 10 d of submergence were lethal to over 90% of seedlings under 12 h light/12 h dark cycles, indicating the significance of underwater photosynthesis in seedling survival. Submergence rapidly decreased the abundance of carbohydrate reserves and ATP in aerial tissue of seedlings although chlorophyll breakdown was not observed. The carbohydrate and ATP contents were recovered upon de-submergence, but sudden exposure to oxygen also induced lipid peroxidation, confirming that reoxygenation induced oxidative stress. Whole transcriptome analysis recognized genome-scale reconfiguration of gene expression that regulates various signalling and metabolic pathways under submergence and reoxygenation. Comparative analysis of differentially regulated genes in shoots and roots of soybean and other plants defines conserved, organ-specific and species-specific adjustments which enhance adaptability to submergence and reoxygenation through different metabolic pathways.
Biswapriya Biswavas Misra's insight:

Complete inundation at the early seedling stage is a common environmental constraint for soybean production throughout the world. As floodwaters subside, submerged seedlings are subsequently exposed to reoxygenation stress in the natural progression of a flood event. Here, we characterized the fundamental acclimation responses to submergence and reoxygenation in soybean at the seedling establishment stage. Approximately 90% of seedlings succumbed during 3 d of inundation under constant darkness, whereas 10 d of submergence were lethal to over 90% of seedlings under 12 h light/12 h dark cycles, indicating the significance of underwater photosynthesis in seedling survival. Submergence rapidly decreased the abundance of carbohydrate reserves and ATP in aerial tissue of seedlings although chlorophyll breakdown was not observed. The carbohydrate and ATP contents were recovered upon de-submergence, but sudden exposure to oxygen also induced lipid peroxidation, confirming that reoxygenation induced oxidative stress. Whole transcriptome analysis recognized genome-scale reconfiguration of gene expression that regulates various signalling and metabolic pathways under submergence and reoxygenation. Comparative analysis of differentially regulated genes in shoots and roots of soybean and other plants defines conserved, organ-specific and species-specific adjustments which enhance adaptability to submergence and reoxygenation through different metabolic pathways.

 
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Calibrating ChIP-Seq with Nucleosomal Internal Standards to Measure Histone Modification Density Genome Wide

Calibrating ChIP-Seq with Nucleosomal Internal Standards to Measure Histone Modification Density Genome Wide | Plant Genomics | Scoop.it
Highlights•

ICeChIP measures histone modification densities on a biologically meaningful scale

ICeChIP enables unbiased trans-experimental comparisons

ICeChIP provides in situ assessment of the immunoprecipitation specificity

ICeChIP reveals two distinct classes of bivalent genes in stem cells

Summary

Chromatin immunoprecipitation (ChIP) serves as a central experimental technique in epigenetics research, yet there are serious drawbacks: it is a relative measurement, which untethered to any external scale obscures fair comparison among experiments; it employs antibody reagents that have differing affinities and specificities for target epitopes that vary in abundance; and it is frequently not reproducible. To address these problems, we developed Internal Standard Calibrated ChIP (ICeChIP), wherein a native chromatin sample is spiked with nucleosomes reconstituted from recombinant and semisynthetic histones on barcoded DNA prior to immunoprecipitation. ICeChIP measures local histone modification densities on a biologically meaningful scale, enabling unbiased trans-experimental comparisons, and reveals unique insight into the nature of bivalent domains. This technology provides in situ assessment of the immunoprecipitation step, accommodating for many experimental pitfalls as well as providing a critical examination of untested assumptions inherent to conventional ChIP.


Via Christophe Jacquet
Biswapriya Biswavas Misra's insight:

Chromatin immunoprecipitation (ChIP) serves as a central experimental technique in epigenetics research, yet there are serious drawbacks: it is a relative measurement, which untethered to any external scale obscures fair comparison among experiments; it employs antibody reagents that have differing affinities and specificities for target epitopes that vary in abundance; and it is frequently not reproducible. To address these problems, we developed Internal Standard Calibrated ChIP (ICeChIP), wherein a native chromatin sample is spiked with nucleosomes reconstituted from recombinant and semisynthetic histones on barcoded DNA prior to immunoprecipitation. ICeChIP measures local histone modification densities on a biologically meaningful scale, enabling unbiased trans-experimental comparisons, and reveals unique insight into the nature of bivalent domains. This technology provides in situ assessment of the immunoprecipitation step, accommodating for many experimental pitfalls as well as providing a critical examination of untested assumptions inherent to conventional ChIP.

 
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The selective cytotoxic anti-cancer properties and proteomic analysis of Trigonella Foenum-Graecum.

Abstract
BACKGROUND:
There are a number of dietary components that may prove useful in the prevention and treatment of cancer. In some cultures, fenugreek seeds are used to treat cancer. The current study focuses on the anticancer properties and proteomic profiles of fenugreek seeds, and is prompted by the clinical profile of a case of primary CNS T cell lymphoma that responded to fenugreek treatment and resulted in tumor regression.
METHOD:
Various normal and cancer cell lines were exposed to fenugreek extract at differing concentrations (100 μg/ml, 200 μg/ml and 300 μg/ml) and at different time points (0, 24, 48, 72 and 96 hrs). Protein fingerprints of fenugreek grain/seed types, obtained from four different geographical regions, were analyzed by proteomic expression profiles.
RESULTS:
We observed selective cytotoxic effects of fenugreek extract in vitro to a panel of cancer cell lines, including T-cell lymphoma. Additionally, the cluster analysis of proteomics data showed that the protein profile of the particular fenugreek used by the patient is significantly different from three other regional subtypes of fenugreek extract.
CONCLUSION:
The in vitro effect of fenugreek as a substance with significant cytotoxicity to cancer cells points to the potential usefulness of fenugreek in the prevention and treatment of cancer.
Biswapriya Biswavas Misra's insight:
AbstractBACKGROUND:

There are a number of dietary components that may prove useful in the prevention and treatment of cancer. In some cultures, fenugreek seeds are used to treat cancer. The current study focuses on the anticancer properties and proteomic profiles of fenugreek seeds, and is prompted by the clinical profile of a case of primary CNS T cell lymphoma that responded to fenugreek treatment and resulted in tumor regression.

METHOD:

Various normal and cancer cell lines were exposed to fenugreek extract at differing concentrations (100 μg/ml, 200 μg/ml and 300 μg/ml) and at different time points (0, 24, 48, 72 and 96 hrs). Protein fingerprints of fenugreek grain/seed types, obtained from four different geographical regions, were analyzed by proteomic expression profiles.

RESULTS:

We observed selective cytotoxic effects of fenugreek extract in vitro to a panel of cancer cell lines, including T-cell lymphoma. Additionally, the cluster analysis of proteomics data showed that the protein profile of the particular fenugreek used by the patient is significantly different from three other regional subtypes of fenugreek extract.

CONCLUSION:

The in vitro effect of fenugreek as a substance with significant cytotoxicity to cancer cells points to the potential usefulness of fenugreek in the prevention and treatment of cancer.

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Signatures of host/symbiont genome coevolution in insect nutritional endosymbioses

The role of symbiosis in bacterial symbiont genome evolution is well understood, yet the ways that symbiosis shapes host genomes or more particularly, host/symbiont genome coevolution in the holobiont is only now being revealed. Here, we identify three coevolutionary signatures that characterize holobiont genomes. The first signature, host/symbiont collaboration, arises when completion of essential pathways requires host/endosymbiont genome complementarity. Metabolic collaboration has evolved numerous times in the pathways of amino acid and vitamin biosynthesis. Here, we highlight collaboration in branched-chain amino acid and pantothenate (vitamin B5) biosynthesis. The second coevolutionary signature is acquisition, referring to the observation that holobiont genomes acquire novel genetic material through various means, including gene duplication, lateral gene transfer from bacteria that are not their current obligate symbionts, and full or partial endosymbiont replacement. The third signature, constraint, introduces the idea that holobiont genome evolution is constrained by the processes governing symbiont genome evolution. In addition, we propose that collaboration is constrained by the expression profile of the cell lineage from which endosymbiont-containing host cells, called bacteriocytes, are derived. In particular, we propose that such differences in bacteriocyte cell lineage may explain differences in patterns of host/endosymbiont metabolic collaboration between the sap-feeding suborders Sternorrhyncha and Auchenorrhynca. Finally, we review recent studies at the frontier of symbiosis research that are applying functional genomic approaches to characterization of the developmental and cellular mechanisms of host/endosymbiont integration, work that heralds a new era in symbiosis research.


Via Pierre-Marc Delaux
Biswapriya Biswavas Misra's insight:

The role of symbiosis in bacterial symbiont genome evolution is well understood, yet the ways that symbiosis shapes host genomes or more particularly, host/symbiont genome coevolution in the holobiont is only now being revealed. Here, we identify three coevolutionary signatures that characterize holobiont genomes. The first signature, host/symbiont collaboration, arises when completion of essential pathways requires host/endosymbiont genome complementarity. Metabolic collaboration has evolved numerous times in the pathways of amino acid and vitamin biosynthesis. Here, we highlight collaboration in branched-chain amino acid and pantothenate (vitamin B5) biosynthesis. The second coevolutionary signature is acquisition, referring to the observation that holobiont genomes acquire novel genetic material through various means, including gene duplication, lateral gene transfer from bacteria that are not their current obligate symbionts, and full or partial endosymbiont replacement. The third signature, constraint, introduces the idea that holobiont genome evolution is constrained by the processes governing symbiont genome evolution. In addition, we propose that collaboration is constrained by the expression profile of the cell lineage from which endosymbiont-containing host cells, called bacteriocytes, are derived. In particular, we propose that such differences in bacteriocyte cell lineage may explain differences in patterns of host/endosymbiont metabolic collaboration between the sap-feeding suborders Sternorrhyncha and Auchenorrhynca. Finally, we review recent studies at the frontier of symbiosis research that are applying functional genomic approaches to characterization of the developmental and cellular mechanisms of host/endosymbiont integration, work that heralds a new era in symbiosis research.

 
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Identification of differentially expressed genes related to aphid resistance in cucumber (Cucumis sativus L.)

Identification of differentially expressed genes related to aphid resistance in cucumber (Cucumis sativus L.) | Plant Genomics | Scoop.it
Cucumber, a very important vegetable crop worldwide, is easily damaged by pests. Aphids (Aphis gossypii Glover) are among the most serious pests in cucumber production and often cause severe loss of yield and make fruit quality get worse. Identifying genes that render cucumbers resistant to aphid-induced damage and breeding aphid-resistant cucumber varieties have become the most promising control strategies. In this study, a Illumina Genome Analyzer platform was applied to monitor changes in gene expression in the whole genome of the cucumber cultivar ‘EP6392’ which is resistant to aphids. Nine DGE libraries were constructed from infected and uninfected leaves. In total, 49 differentially expressed genes related to cucumber aphid resistance were screened during the treatment period. These genes are mainly associated with signal transduction, plant-pathogen interactions, flavonoid biosynthesis, amino acid metabolism and sugar metabolism pathways. Eight of the 49 genes may be associated with aphid resistance. Finally, expression of 9 randomly selected genes was evaluated by qRT-PCR to verify the results for the tag-mapped genes. With the exception of 1-aminocyclopropane-1-carboxylate oxidase homolog 6, the expression of the chosen genes was in agreement with the results of the tag-sequencing analysis patterns.
Biswapriya Biswavas Misra's insight:

Cucumber, a very important vegetable crop worldwide, is easily damaged by pests. Aphids (Aphis gossypii Glover) are among the most serious pests in cucumber production and often cause severe loss of yield and make fruit quality get worse. Identifying genes that render cucumbers resistant to aphid-induced damage and breeding aphid-resistant cucumber varieties have become the most promising control strategies. In this study, a Illumina Genome Analyzer platform was applied to monitor changes in gene expression in the whole genome of the cucumber cultivar ‘EP6392’ which is resistant to aphids. Nine DGE libraries were constructed from infected and uninfected leaves. In total, 49 differentially expressed genes related to cucumber aphid resistance were screened during the treatment period. These genes are mainly associated with signal transduction, plant-pathogen interactions, flavonoid biosynthesis, amino acid metabolism and sugar metabolism pathways. Eight of the 49 genes may be associated with aphid resistance. Finally, expression of 9 randomly selected genes was evaluated by qRT-PCR to verify the results for the tag-mapped genes. With the exception of 1-aminocyclopropane-1-carboxylate oxidase homolog 6, the expression of the chosen genes was in agreement with the results of the tag-sequencing analysis patterns.

  
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