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BMC Genomics | Abstract

BMC Genomics | Abstract | Plant Genomics | Scoop.it

Plant mitochondrial genome has unique features such as large size, frequent recombination and incorporation of foreign DNA. Cytoplasmic male sterility (CMS) is caused by rearrangement of the mitochondrial genome, and a novel chimeric open reading frame (ORF) created by shuffling of endogenous sequences is often responsible for CMS. The Ogura-type male-sterile cytoplasm is one of the most extensively studied cytoplasms in Brassicaceae. Although the gene orf138 has been isolated as a determinant of Ogura-type CMS, no homologous sequence to orf138 has been found in public databases. Therefore, how orf138 sequence was created is a mystery. In this study, we determined the complete nucleotide sequence of two radish mitochondrial genomes, namely, Ogura- and normal-type genomes, and analyzed them to reveal the origin of the gene orf138.

Results

Ogura- and normal-type mitochondrial genomes were assembled to 258,426-bp and 244,036-bp circular sequences, respectively. Normal-type mitochondrial genome contained 33 protein-coding and three rRNA genes, which are well conserved with the reported mitochondrial genome of rapeseed. Ogura-type genomes contained same genes and additional atp9. As for tRNA, normal-type contained 17 tRNAs, while Ogura type contained 17 tRNAs and one additional trnfM. The gene orf138 was specific to Ogura-type mitochondrial genome, and no sequence homologous to it was found in normal-type genome. Comparative analysis of the two genomes revealed that radish mitochondrial genome consists of 11 syntenic regions (length >3kb, similarity >99.9%). It was shown that short repeats and overlapped repeats present in the edge of syntenic regions were involved in recombination events during evolution to interconvert two types of mitochondrial genome. Ogura-type mitochondrial genome has four unique regions (2,803 bp, 1,601 bp, 451 bp and 15,255 bp in size) that are non-syntenic to normal-type genome, and the gene orf138 was found to be located at the edge of the largest unique region. Blast analysis performed to assign the unique regions showed that about 80% of the region was covered by short homologous sequences to the mitochondrial sequences of normal-type radish or other reported Brassicaceae species, although no homology was found for the remaining 20% of sequences.

Conclusions

Ogura-type mitochondrial genome was highly rearranged compared with the normal-type genome by recombination through one large repeat and multiple short repeats. The rearrangement has produced four unique regions in Ogura-type mitochondrial genome, and most of the unique regions are composed of known Brassicaceae mitochondrial sequences. This suggests that the regions unique to the Ogura-type genome were generated by integration and shuffling of pre-existing mitochondrial sequences during the evolution of Brassicaceae, and novel genes such as orf138 could have been created by the shuffling process of mitochondrial genome.

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gFeatMiner 0.1.3 | Software Review and download link

gFeatMiner 0.1.3 gives you much convenience with this useful framework for dealing with genomic data using a request based system.
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Molecular Genetics and Genomics, Online First™ - SpringerLink

In a previous study, we selected a high tryptophan (Trp)-accumulating rice (Oryza sativa L.) mutant line by in vitro mutagenesis using gamma rays. To obtain detailed information about the Trp biosynthetic pathway during the grain-filling in rice, we investigated the gene expression profiles in the wild-type (cv. Dongan) and the high-level Trp-accumulating mutant line (MRVII-33) at five different grain-filling stages using microarray analysis. The mutant line showed approximately 6.3-fold higher Trp content and 2.3-fold higher amino acids compared with the original cultivar at the final stage (stage V). The intensity of gene expression was analyzed and compared between the wild-type and mutant line at each of the five grain-filling stages using the Rice 4 × 44K oligo DNA microarray. Among the five stages, stage III showed the highest gene expression changes for both up- and down-regulated genes. Among the Trp biosynthesis-related genes, trpG showed high expression in the mutant line during stages I to IV and trpE showed higher at stage III. Gene clustering was performed based on the genes of KEGG’s amino acid metabolism, and a total of 276 genes related to amino acid metabolism were placed into three clusters. The functional annotation enrichment analysis of the genes classified into the three clusters was also conducted using ClueGO. It was found that cluster 3 uniquely included biological processes related to aromatic amino acid metabolism. These results suggest that gene analysis based on microarray data is useful for elucidating the biological mechanisms of Trp accumulation in high Trp-accumulating mutants at each of the grain-filling stages.

 

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Positionally-biased gene loss after whole genome ... [Genome Res. 2012] - PubMed - NCBI

Whole genome duplication (WGD) has made a significant contribution to many eukaryotic genomes including yeast, plants and vertebrates. Following WGD, some ohnologs (WGD paralogs) remain in the genome arranged in blocks of conserved gene order and content (paralogons). However the most common outcome is loss of one of the ohnolog pair. It is unclear what factors, if any, govern gene loss from paralogons. Recent studies have reported physical clustering (genetic linkage) of functionally linked (interacting) genes in the human genome and propose a biological significance for the clustering of interacting genes such as co-expression or preservation of epistatic interactions. Here we conduct a novel test of a hypothesis that functionally linked genes in the same paralogon are preferentially retained in cis after WGD. We compare the number of protein-protein interactions (PPIs) between linked singletons within a paralogon (defined as cis-PPIs) with that of PPIs between singletons across paralogon pairs (defined as trans-PPIs). We find that paralogons in which the number of cis-PPIs is greater than that of trans-PPIs are significantly enriched in human and yeast. The trend is similar in plants, but it is difficult to assess statistical significance due to multiple, overlapping WGD events. Interestingly, human singletons participating in cis-PPIs tend to be classified into "response to stimulus". We uncover strong evidence of biased gene loss after WGD which further supports the hypothesis of biologically significant gene clusters in eukaryotic genomes. These observations give us new insight for understanding the evolution of genome structure and of protein interaction networks.

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Predictive network modeling of the high-resolution dynamic plant transcriptome in response to nitrate

Predictive network modeling of the high-resolution dynamic plant transcriptome in response to nitrate | Plant Genomics | Scoop.it

Background

Nitrate, acting as both a nitrogen source and a signaling molecule, controls many aspects of plant development. However, gene networks involved in plant adaptation to fluctuating nitrate environments have not yet been identified.

Results

Here we use time-series transcriptome data to decipher gene relationships and consequently to build core regulatory networks involved in Arabidopsis root adaptation to nitrate provision. The experimental approach has been to monitor genome-wide responses to nitrate at 3, 6, 9, 12, 15 and 20 minutes using Affymetrix ATH1 gene chips. This high-resolution time course analysis demonstrated that the previously known primary nitrate response is actually preceded by a very fast gene expression modulation, involving genes and functions needed to prepare plants to use or reduce nitrate. A state-space model inferred from this microarray time-series data successfully predicts gene behavior in unlearnt conditions.

Conclusions

The experiments and methods allow us to propose a temporal working model for nitrate-driven gene networks. This network model is tested both in silico and experimentally. For example, the over-expression of a predicted gene hub encoding a transcription factor induced early in the cascade indeed leads to the modification of the kinetic nitrate response of sentinel genes such as NIR, NIA2, and NRT1.1, and several other transcription factors. The potential nitrate/hormone connections implicated by this time-series data are also evaluated.

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Opuntia-phylogeny

P remise of the study: The opuntias (nopales, prickly pears) are not only culturally, ecologically, economically, and medicinally
important, but are renowned for their taxonomic diffi culty due to interspecifi c hybridization, polyploidy, and morphological
variability. Evolutionary relationships in these stem succulents have been insuffi ciently studied; thus, delimitation of Opuntia
s.s. and major subclades, as well as the biogeographic history of this enigmatic group, remain unresolved.
• M ethods: We sequenced the plastid intergenic spacers atpB-rbcL, ndhF-rpl32 , psbJ-petA , and trnL-trnF , the plastid genes
matK and ycf1 , the nuclear gene ppc , and ITS to reconstruct the phylogeny of tribe Opuntieae, including Opuntia s.s. We used
phylogenetic hypotheses to infer the biogeographic history, divergence times, and potential reticulate evolution of Opuntieae.
• K ey results: Within Opuntieae, a clade of T acinga , O puntia lilae , B rasiliopuntia , and O . schickendantzii is sister to a
well-supported Opuntia s.s., which includes Nopalea . Opuntia s.s. originated in southwestern South America (SA) and then
expanded to the Central Andean Valleys and the desert region of western North America (NA). Two major clades evolved in
NA, which subsequently diversifi ed into eight subclades. These expanded north to Canada and south to Central America and
the Caribbean, eventually returning back to SA primarily via allopolyploid taxa. Dating approaches suggest that most of the
major subclades in Opuntia s.s. originated during the Pliocene.
• C onclusions: Opuntia s.s. is a well-supported clade that includes N opalea . The clade originated in southwestern SA, but the
NA radiation was the most extensive, resulting in broad morphological diversity and frequent species formation through reticulate
evolution and polyploidy

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Global transcriptome analysis reveals distinct expression among duplicated ... - 7thSpace Interactive (press release)

Global transcriptome analysis reveals distinct expression among duplicated ...7thSpace Interactive (press release)Global transcriptome analysis reveals distinct expression among duplicated genes during sorghum-Bipolarissorghicola interaction.
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Plants to express human proteins - Phys.Org

Plants to express human proteins - Phys.Org | Plant Genomics | Scoop.it
Plants to express human proteinsPhys.OrgThe information generated during the Plastomics project enhanced our understanding of the processes underlying the insertion and removal of foreign genes into the plastid genome of plants.
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A complete mitochondrial genome sequence of Ogura-type male-sterile ... - 7thSpace Interactive (press release)

A complete mitochondrial genome sequence of Ogura-type male-sterile ...7thSpace Interactive (press release)Plant mitochondrial genome has unique features such as large size, frequent recombination and incorporation of foreign DNA.
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Comparative transcriptome analysis of cadmium responses in Solanum nigrum and Solanum torvum - Xu - 2012 - New Phytologist - Wiley Online Library

Comparative transcriptome analysis of cadmium responses in Solanum nigrum and Solanum torvum - Xu - 2012 - New Phytologist - Wiley Online Library | Plant Genomics | Scoop.it

Solanum nigrum is a cadmium (Cd) accumulator, whereas Solanum torvum is a low Cd-accumulating plant. The molecular mechanisms that are responsible for differential cadmium (Cd) accumulation in the two Solanum species are poorly understood.

•Here, grafting experiments confirmed that increased Cd loading into the root xylem was responsible for the differential Cd accumulation in the two Solanum species. An iron (Fe) supply assay indicated that low Fe accumulation in S. torvum leaves is related to its Cd sensitivity.

•Transcriptome analyses revealed higher expression of the genes that encode several metal transporters as well as antioxidant-related genes, and several organic and amino acid biosynthesis/metabolism-related genes in Cd-treated S. nigrum. Our data also indicated that the different responsive mechanisms of the transporter genes to Fe deficiency might be responsible for differential uptake and redistribution of metals in the two Solanum species

•These results form a basis upon which to further explore the molecular mechanisms of Cd accumulation and tolerance, and provide an insight into novel strategies that can be used for phytoremediation and food safety.

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Recent Developments of Genomic Research in Soybean

Soybean is an important cash crop with unique and important traits such as the high seed protein and oil contents, and the ability to perform symbiotic nitrogen fixation. A reference genome of cultivated soybeans was established in 2010, followed by whole-genome re-sequencing of wild and cultivated soybean accessions. These efforts revealed unique features of the soybean genome and helped to understand its evolution. Mapping of variations between wild and cultivated soybean genomes were performed. These genomic variations may be related to the process of domestication and human selection. Wild soybean germplasms exhibited high genomic diversity and hence may be an important source of novel genes/alleles. Accumulation of genomic data will help to refine genetic maps and expedite the identification of functional genes. In this review, we summarize the major findings from the whole-genome sequencing projects and discuss the possible impacts on soybean researches and breeding programs. Some emerging areas such as transcriptomic and epigenomic studies will be introduced. In addition, we also tabulated some useful bioinformatics tools that will help the mining of the soybean genomic data.

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CiteULike: Genetic Architecture of MicroRNA Expression: Implications for the Transcriptome and Complex Traits

We sought to comprehensively and systematically characterize the relationship between genetic variation, miRNA expression, and mRNA expression. Genome-wide expression profiling of samples of European and African ancestry identified in each population hundreds of miRNAs whose increased expression is correlated with correspondingly reduced expression of target mRNAs. We scanned 32 UTR SNPs with a potential functional effect on miRNA binding for cis-acting expression quantitative trait loci (eQTLs) for the corresponding proximal target genes. To extend sequence-based, localized analyses of SNP effect on miRNA binding, we proceeded to dissect the genetic basis of miRNA expression variation; we mapped miRNA expression levelsas quantitative traitsto loci in the genome as miRNA eQTLs, demonstrating that miRNA expression is under significant genetic control. We found that SNPs associated with miRNA expression are significantly enriched with those SNPs already shown to be associated with mRNA. Moreover, we discovered that many of the miRNA-associated genetic variations identified in our study are associated with a broad spectrum of human complex traits from the National Human Genome Research Institute catalog of published genome-wide association studies. Experimentally, we replicated miRNA-induced mRNA expression inhibition and the cis-eQTL relationship to the target gene for several identified relationships among SNPs, miRNAs, and mRNAs in an independent set of samples; furthermore, we conducted miRNA overexpression and inhibition experiments to functionally validate the miRNA-mRNA relationships. This study extends our understanding of the genetic regulation of the transcriptome and suggests that genetic variation might underlie observed relationships between miRNAs and mRNAs more commonly than has previously been appreciated.
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Lighting up the plant hormone 'command system' | e! Science News

Light is not only the source of a plant's energy, but also an environmental signal that instructs the growth behavior of plants. As a result, a plant's sensitivity to light is of great interest to scientists and their research on this issue could help improve crop yields down the road. Similarly understanding a plant's temperature sensitivity could also help improve agriculture and feed more people. Two new papers from Carnegie's Zhiyong Wang laboratory identify key aspects of the hormonal responses of plants to changes in light and heat in their environments. Their work is published online July 22 by Nature Cell Biology.

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Getting to the Root -- Unearthing the Plant-Microbe Quid Pro Quo - Science Daily (press release)

Getting to the Root -- Unearthing the Plant-Microbe Quid Pro Quo - Science Daily (press release) | Plant Genomics | Scoop.it
Howard Hughes Medical InstituteGetting to the Root -- Unearthing the Plant-Microbe Quid Pro QuoScience Daily (press release)Co-author Susannah Tringe, head of DOE JGI's Metagenome Program, said the microbiome can be viewed as an extension of the...
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heavy-tools.de » Blog Archive » Metal Toxicity in Plants: Perception ...

heavy-tools.de » Blog Archive » Metal Toxicity in Plants: Perception ... | Plant Genomics | Scoop.it
In recent years transcriptomic, proteomic and metabolomic studies have become very important tools for analyzing both the dynamics of changes in gene expression and the profiles of protein and metabolites under heavy ...
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Quantitative RNA-Seq analysis in non-model species: assessing transcriptome assemblies as a scaffold and the utility of evolutionary divergent genomic reference species

Abstract (provisional)

Background

How well does RNA-Seq data perform for quantitative whole gene expression analysis in the absence of a genome? This is one unanswered question facing the rapidly growing number of researchers studying non-model species. Using Homo sapiens data and resources, we compared the direct mapping of sequencing reads to predicted genes from the genome with mapping to de novo transcriptomes assembled from RNA-Seq data. Gene coverage and expression analysis was further investigated in the non-model context by using increasingly divergent genomic reference species to group assembled contigs by unique genes.

Results

Eight transcriptome sets, composed of varying amounts of Illumina and 454 data, were assembled and assessed. Hybrid 454/Illumina assemblies had the highest transcriptome and individual gene coverage. Quantitative whole gene expression levels were highly similar between using a de novo hybrid assembly and the predicted genes as a scaffold, although mapping to the de novo transcriptome assembly provided data on fewer genes. Using non-target species as reference scaffolds does result in some loss of sequence and expression data, and bias and error increase with evolutionary distance. However, within a 100 million year window these effect sizes are relatively small.

Conclusions

Predicted gene sets from sequenced genomes of related species can provide a powerful method for grouping RNA-Seq reads and annotating contigs. Gene expression results can be produced that are similar to results obtained using gene models derived from a high quality genome, though biased towards conserved genes. Our results demonstrate the power and limitations of conducting RNA-Seq in non-model species.

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PLoS ONE: De Novo Sequencing of Hypericum perforatum Transcriptome to Identify Potential Genes Involved in the Biosynthesis of Active Metabolites

PLoS ONE: De Novo Sequencing of Hypericum perforatum Transcriptome to Identify Potential Genes Involved in the Biosynthesis of Active Metabolites | Plant Genomics | Scoop.it
Background

Hypericum perforatum L. (St. John’s wort) is a medicinal plant with pharmacological properties that are antidepressant, anti-inflammatory, antiviral, anti-cancer, and antibacterial. Its major active metabolites are hypericins, hyperforins, and melatonin. However, little genetic information is available for this species, especially that concerning the biosynthetic pathways for active ingredients.

Methodology/Principal Findings

Using de novo transcriptome analysis, we obtained 59,184 unigenes covering the entire life cycle of these plants. In all, 40,813 unigenes (68.86%) were annotated and 2,359 were assigned to secondary metabolic pathways. Among them, 260 unigenes are involved in the production of hypericin, hyperforin, and melatonin. Another 2,291 unigenes are classified as potential Type III polyketide synthase. Our BlastX search against the AGRIS database reveals 1,772 unigenes that are homologous to 47 known Arabidopsis transcription factor families. Further analysis shows that 10.61% (6,277) of these unigenes contain 7,643 SSRs.

Conclusion

We have identified a set of putative genes involved in several secondary metabolism pathways, especially those related to the synthesis of its active ingredients. Our results will serve as an important platform for public information about gene expression, genomics, and functional genomics in H. perforatum.
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Genome-wide analysis of plant nat-siRNAs reveals insights into their distribution, biogenesis and function

Genome-wide analysis of plant nat-siRNAs reveals insights into their distribution, biogenesis and function | Plant Genomics | Scoop.it
Genome-wide analysis of plant nat-siRNAs reveals insights into their distribution, biogenesis and function - Science Alerts Social Network (Top #tweeted story in #bioscience: Genome-wide analysis of plant nat-siRNAs reveals ins…
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Phytochemistry In The Genomics And Post-genomics Eras

xxsurl.com Phytochemistry In The Genomics And Post-genomics Eras This monograph series is commissioned by the Phytochemical Society of North ...youtube.com...
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Molecular Techniques In Crop Improvement

xxsurl.com Molecular Techniques In Crop Improvement Preface.-- A. Plant Breeding in the genomics era:1.QTL analysis for plant breeding; Maria J. Asins, Guillermo P. Bernet, Irene Villalta and Emilio A.
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Effects of Drought on Gene Expression in Maize Revealed by RNA ...

Effects of Drought on Gene Expression in Maize Revealed by RNA ... | Plant Genomics | Scoop.it
Researchers at Virginia Tech University studied the maize (Zea mays) drought transcriptome using RNA-Seq analysis to compare drought treated and well-watered fertilized ovary and basal leaf meristem tissue.
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The In Planta Transcriptome of Ralstonia solanacearum: Conserved Physiological and Virulence Strategies during Bacterial Wilt of Tomato

Plant xylem fluid is considered a nutrient-poor environment, but the bacterial wilt pathogen Ralstonia solanacearum is well adapted to it, growing to 108 to 109 CFU/g tomato stem. To better understand how R. solanacearum succeeds in this habitat, we analyzed the transcriptomes of two phylogenetically distinct R. solanacearum strains that both wilt tomato, strains UW551 (phylotype II) and GMI1000 (phylotype I). We profiled bacterial gene expression at ~6 × 108 CFU/ml in culture or in plant xylem during early tomato bacterial wilt pathogenesis. Despite phylogenetic differences, these two strains expressed their 3,477 common orthologous genes in generally similar patterns, with about 12% of their transcriptomes significantly altered in planta versus in rich medium. Several primary metabolic pathways were highly expressed during pathogenesis. These pathways included sucrose uptake and catabolism, and components of these pathways were encoded by genes in the scrABY cluster. A UW551 scrA mutant was significantly reduced in virulence on resistant and susceptible tomato as well as on potato and the epidemiologically important weed host Solanum dulcamara. Functional scrA contributed to pathogen competitive fitness during colonization of tomato xylem, which contained ~300 µM sucrose. scrA expression was induced by sucrose, but to a much greater degree by growth in planta. Unexpectedly, 45% of the genes directly regulated by HrpB, the transcriptional activator of the type 3 secretion system (T3SS), were upregulated in planta at high cell densities. This result modifies a regulatory model based on bacterial behavior in culture, where this key virulence factor is repressed at high cell densities. The active transcription of these genes in wilting plants suggests that T3SS has a biological role throughout the disease cycle.

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A Whole-Cell Computational Model Predicts Phenotype from Genotype

Understanding how complex phenotypes arise from individual molecules and their interactions is a primary challenge in biology that computational approaches are poised to tackle. We report a whole-cell computational model of the life cycle of the human pathogen Mycoplasma genitalium that includes all of its molecular components and their interactions. An integrative approach to modeling that combines diverse mathematics enabled the simultaneous inclusion of fundamentally different cellular processes and experimental measurements. Our whole-cell model accounts for all annotated gene functions and was validated against a broad range of data. The model provides insights into many previously unobserved cellular behaviors, including in vivo rates of protein-DNA association and an inverse relationship between the durations of DNA replication initiation and replication. In addition, experimental analysis directed by model predictions identified previously undetected kinetic parameters and biological functions. We conclude that comprehensive whole-cell models can be used to facilitate biological discovery.

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Trends in Biotechnology - Genomes for jeans: cotton genomics for engineering superior fiber

Twenty years ago, scientists predicted that better understanding of fiber development would lead to novel ways to engineer superior cotton fiber. Advances in genetic resources, DNA markers, DNA sequence information, and gene expression data have indeed provided new insights into fiber initiation, elongation and maturation. Many exciting applications of this knowledge offer the potential to select better cotton genotypes more effectively in mainstream breeding programs or engineer genotypes with improved agronomic and/or quality traits. Here, we discuss recent progress in understanding genes involved in fiber development, and their regulation and manipulation to engineer improved fibers. Better understanding of quantitative trait loci/gene interactions that influence fiber quality and yield may help to tailor superior cotton genotypes to diverse environments.

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Effector identification in the lettuce downy mildew Bremia lactucae by massively parallel transcriptome sequencing - STASSEN - 2012 - Molecular Plant Pathology - Wiley Online Library

Effector identification in the lettuce downy mildew Bremia lactucae by massively parallel transcriptome sequencing - STASSEN - 2012 - Molecular Plant Pathology - Wiley Online Library | Plant Genomics | Scoop.it

Lettuce downy mildew (Bremia lactucae) is a rapidly adapting oomycete pathogen affecting commercial lettuce cultivation. Oomycetes are known to use a diverse arsenal of secreted proteins (effectors) to manipulate their hosts. Two classes of effector are known to be translocated by the host: the RXLRs and Crinklers. To gain insight into the repertoire of effectors used by B. lactucae to manipulate its host, we performed massively parallel sequencing of cDNA derived from B. lactucae spores and infected lettuce (Lactuca sativa) seedlings. From over 2.3 million 454 GS FLX reads, 59 618 contigs were assembled representing both plant and pathogen transcripts. Of these, 19 663 contigs were determined to be of B. lactucae origin as they matched pathogen genome sequences (SOLiD) that were obtained from >270 million reads of spore-derived genomic DNA. After correction of cDNA sequencing errors with SOLiD data, translation into protein models and filtering, 16 372 protein models remained, 1023 of which were predicted to be secreted. This secretome included elicitins, necrosis and ethylene-inducing peptide 1-like proteins, glucanase inhibitors and lectins, and was enriched in cysteine-rich proteins. Candidate host-translocated effectors included 78 protein models with RXLR effector features. In addition, we found indications for an unknown number of Crinkler-like sequences. Similarity clustering of secreted proteins revealed additional effector candidates. We provide a first look at the transcriptome of B. lactucae and its encoded effector arsenal.

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