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Scooped by Biswapriya Biswavas Misra
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Transcriptome Assembly and Isoform Expression Level Estimation from Biased RNA-Seq Reads

Transcriptome Assembly and Isoform Expression Level Estimation from Biased RNA-Seq Reads | Plant Genomics | Scoop.it

Abstract

Motivation: RNA-Seq uses the high-throughput sequencing technology to identify and quantify transcriptome at an unprecedented high resolution and low cost. However, RNA-Seq reads are usually not uniformly distributed and biases in RNA-Seq data post great challenges in many applications including transcriptome assembly and the expression level estimation of genes or isoforms. Much effort has been made in the literature to calibrate the expression level estimation from biased RNA-Seq data, but the effect of biases on transcriptome assembly remains largely unexplored.

Results: Here, we propose a statistical framework for both transcriptome assembly and isoform expression level estimation from biased RNA-Seq data. Using a quasi-multinomial distribution model, our method is able to capture various types of RNA-Seq biases, including positional, sequencing and mappability biases. Our experimental results on simulated and real RNA-Seq datasets exhibit interesting effects of RNA-Seq biases on both transcriptome assembly and isoform expression level estimation. The advantage of our method is clearly shown in the experimental analysis by its high sensitivity and precision in transcriptome assembly and the high concordance of its estimated expression levels with qRT-PCR data.

Availability: CEM is freely available at http://www.cs.ucr.edu/~liw/cem.html

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De Novo Assembly, Characterization and Functional Annotation of Pineapple Fruit Transcriptome through Massively Parallel Sequencing

De Novo Assembly, Characterization and Functional Annotation of Pineapple Fruit Transcriptome through Massively Parallel Sequencing | Plant Genomics | Scoop.it

Abstract Top

Background

Pineapple (Ananas comosus var. comosus), is an important tropical non-climacteric fruit with high commercial potential. Understanding the mechanism and processes underlying fruit ripening would enable scientists to enhance the improvement of quality traits such as, flavor, texture, appearance and fruit sweetness. Although, the pineapple is an important fruit, there is insufficient transcriptomic or genomic information that is available in public databases. Application of high throughput transcriptome sequencing to profile the pineapple fruit transcripts is therefore needed.

Methodology/Principal Findings

To facilitate this, we have performed transcriptome sequencing of ripe yellow pineapple fruit flesh using Illumina technology. About 4.7 millions Illumina paired-end reads were generated and assembled using the Velvet de novo assembler. The assembly produced 28,728 unique transcripts with a mean length of approximately 200 bp. Sequence similarity search against non-redundant NCBI database identified a total of 16,932 unique transcripts (58.93%) with significant hits. Out of these, 15,507 unique transcripts were assigned to gene ontology terms. Functional annotation against Kyoto Encyclopedia of Genes and Genomes pathway database identified 13,598 unique transcripts (47.33%) which were mapped to 126 pathways. The assembly revealed many transcripts that were previously unknown.

Conclusions

The unique transcripts derived from this work have rapidly increased of the number of the pineapple fruit mRNA transcripts as it is now available in public databases. This information can be further utilized in gene expression, genomics and other functional genomics studies in pineapple.

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Top 10 List Of Crop Killing Fungi

Top 10 List Of Crop Killing Fungi | Plant Genomics | Scoop.it

An enormous international team of experts, almost 500 members strong, has developed a ranking system of the ten most important phytopathogenic fungi on a scientific and economic level. Topping the list is the rice blast fungus Magnaporthe oryzae.

A survey conducted among the researchers resulted in a list of the most important phytopathogenic fungi, with each researcher choosing three that he or she thought most significant. The fungi that received the most votes formed the list.

Published in the journal Molecular Plant Pathology, the fungi on the list were analyzed by an expert in the field. Antonio Di Pietro from the University of Cordoba is one of those experts, describing the fungus Fusarium oxysporum that is number five on the list.

“Most of the pathogens on the list attack cereals like rice, wheat and maize. This is logical considering the huge importance of these crops in world agriculture”, explained Di Pietro.

“Nonetheless, it is important to highlight the presence of the fungi in second and fifth place on the list (Botrytis cinerea and Fusarium oxysporum, respectively). These are generalist, wide-ranging pathogens which can cause damage in more than one hundred different crop species” the researcher added.

The rice blast fungus, at number one on the list, received nearly twice the votes of the number two species. Rice blast devastates rice paddies, which are the food base for more than half the world’s population. Second place belongs to the botrytis bunch rot fungus, Botrytis cinerea, which is a wide-ranging pathogen. Unlike most of the other fungi on the list, boytrytis has positive uses due to its role in some stages of wine production.

The third place species includes the genus Puccinia, which mainly affect wheat crops. Fourth and fifth places are both from the Fusarium genus. Fusarium graminearum damages cereal plantations and Fusarium oxysporum affects tomatoes, cotton and bananas.

Sixth and seventh place go to other cereal pathogens, Blumeria graminis and Mycosphaerella graminicola.

Number eight is from the Colletrotrichum genus which attacks fruit and ornamental plants.

In ninth place is the corn smut fungus, Ustilago maydis. This is an edible fungus native to Mexico that made the list for its scientific interest as it has no particularly devastating effects.

Numbers nine and ten, Melampsora lini, both have important uses in the study of molecular bases of plant immunity and infection.

Di Pietro said, “the authors are trying to inform the public about the importance of phytopathogenic fungi as they represent a growing threat to global agriculture.”

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MPP: Xanthomonas campestris pv. campestris (cause of black rot of crucifers) in the genomic era is still a worldwide threat to brassica crops (2012)

MPP: Xanthomonas campestris pv. campestris (cause of black rot of crucifers) in the genomic era is still a worldwide threat to brassica crops (2012) | Plant Genomics | Scoop.it

Background - Xanthomonas campestris pv. campestris (Xcc) (Pammel) Dowson is a Gram-negative bacterium that causes black rot, the most important disease of vegetable brassica crops worldwide. Intensive molecular investigation of Xcc is gaining momentum and several whole genome sequences are available.

 

Race structure, pathogenesis and epidemiology - Collections of Xcc isolates have been differentiated into physiological races based on the response of several brassica species lines. Black rot is a seed-borne disease. The disease is favoured by warm, humid conditions and can spread rapidly from rain dispersal and irrigation water.

 

Genome - The reference genomes of three isolates have been released. The genome consists of a single chromosome of approximately 5 100 000 bp, with a GC content of approximately 65% and an average predicted number of coding DNA sequences (CDS) of 4308.

 

Important genes identified - Three different secretion systems have been identified and studied in Xcc. The gene clusters xps and xcs encode a type II secretion system and xps genes have been linked to pathogenicity. The role of the type IV secretion system in pathogenicity is still uncertain. The hrp gene cluster encodes a type III secretion system that is associated with pathogenicity. An inventory of candidate effector genes has been assembled based on homology with known effectors. A range of other genes have been associated with virulence and pathogenicity, including the rpf, gum and wxc genes involved in the regulation of the synthesis of extracellular degrading enzymes, xanthan gum and lipopolysaccharides.

 

Useful website - http://www.xanthomonas.org

 

Joana G. Vicente, Eric B. Holub


Via Kamoun Lab @ TSL, Nicolas Denancé
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Comparative transcriptome profiling in win... [J Agric Food Chem. 2012] - PubMed - NCBI

Abstract

Wheat (Triticum aestivum L.), one of the three most important cereal crops worldwide, has a dominant position in Europe due to its adaptability and consumer acceptance particularly as organic food commodity. Organic agriculture is developing rapidly, and its authenticity is presently a subject of great concern to food authorities, as incorrect labeling can represent commercial fraud. A comparative transcriptome profiling was conducted on winter wheat flag leaves of several cultivars growing in open fields under different agricultural production systems. Performing a microarray study, ten transcripts differentially expressed in organic and conventional growing conditions were identified in Tommi and Centenaire cultivars. Transcript abundance profiles of selected probe sets were independently confirmed by quantitative reverse-transcription PCR analysis, tested on Tommi, Centenaire, and Cubus cultivars from different growing year and geographical sites. Univariate and multivariate statistical analysis showed that the global wheat transcriptome is influenced by the agricultural system indicating a promising approach for analytical verification of the production system of wheat at the farm level.

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Genome Biology - Epialleles in plant evolution

Abstract

Heritable phenotypic differences caused by epigenetic modifications, rather than DNA sequence mutations, pose a challenge to our understanding of natural variation. Here, we review what is known about plant epialleles and the role of epigenetics in evolution.

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Pyrosequencing-Based Transcriptome Analysis of the Asian Rice Gall Midge Reveals Differential Response during Compatible and Incompatible Interaction

Pyrosequencing-Based Transcriptome Analysis of the Asian Rice Gall Midge Reveals Differential Response during Compatible and Incompatible Interaction | Plant Genomics | Scoop.it

Abstract: The Asian rice gall midge (Orseolia oryzae) is a major pest responsible for immense loss in rice productivity. Currently, very little knowledge exists with regard to this insect at the molecular level. The present study was initiated with the aim of developing molecular resources as well as identifying alterations at the transcriptome level in the gall midge maggots that are in a compatible (SH) or in an incompatible interaction (RH) with their rice host. Roche 454 pyrosequencing strategy was used to develop both transcriptomics and genomics resources that led to the identification of 79,028 and 85,395 EST sequences from gall midge biotype 4 (GMB4) maggots feeding on a susceptible and resistant rice variety, TN1 (SH) and Suraksha (RH), respectively. Comparative transcriptome analysis of the maggots in SH and RH revealed over-representation of transcripts from proteolysis and protein phosphorylation in maggots from RH. In contrast, over-representation of transcripts for translation, regulation of transcription and transcripts involved in electron transport chain were observed in maggots from SH. This investigation, besides unveiling various mechanisms underlying insect-plant interactions, will also lead to a better understanding of strategies adopted by insects in general, and the Asian rice gall midge in particular, to overcome host defense.

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Precise Genome Editing for Plant Engineering with GeneArt® Precision TALs | Life Technologies

Precise Genome Editing for Plant Engineering with GeneArt® Precision TALs | Life Technologies | Plant Genomics | Scoop.it

Life Technologies recently launched the GeneArt® Precision TALs, generally referred to as TAL effector proteins (TALE), which allow plant researchers the ability to edit genomes and control gene activity with unprecedented precision and reliability.

The TAL effectors have broad utility in plant sciences, from biofuel feed stocks to agricultural crop plant engineering to basic plant biology research.

“We’re very excited about this technology and its implications for plant science research,” said Nathan Wood, vice president of synthetic biology at Life Technologies. “With GeneArt® Precision TAL technology, scientists are provided research use access with a clear licensing path for commercial use through the Two Blades Foundation, making it the first technology of its kind ideal for plant and ag bio researchers.”

TAL effectors can be designed to bind to specific DNA sequences selected by researchers and can deliver a variety of functional elements to activate or repress gene expression or to cut and insert DNA with precision. TAL proteins have an advantage over competing zinc finger technology in that they are simpler to design, bind with greater specificity, displaying fewer “off-target” events.

“People realize now that transgenes should be precisely expressed in plant tissues and at certain times—just as nature does it,” said Neal Stewart, Ph.D., professor of plant sciences at the University of Tennessee, Knoxville. “Synthetic biology offers the prospects of designing promoters to tightly regulate gene expression.”

TALs have the unique capabilities of being targeted, robustly, to promoters in plants—both endogenous promoters and our engineered synthetic promoters—to boost gene expression in a predictable way. The simple TAL effector translation code allows researchers to specifically design TAL binding proteins to bind to a DNA sequence of choice. Researchers specify a sequence they wish to target, and receive a gene encoding the TAL protein that will target it.

“Synthetic biology is just showing up in agricultural and environmental plant research,” said Stewart. “We are making quantum leaps at being able to have an order of precision in gene expression that was unavailable just a few years ago.

“Couple precision with metabolic engineering, and there you have a game-changer in agriculture.”

GeneArt® Precision TALs are supplied as Gateway® compatible entry clones encoding a DNA binding protein for a specific customer-submitted sequence fused to a range of customer selected effector domains. Custom TALs will typically be delivered within two weeks after orders are placed.

Watch the below video to learn more about GeneArt® Precision TALs.

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Pinstripe: a suite of programs for integrating transcriptomic and proteomic datasets identifies novel proteins and improves differentiation of protein-coding and non-coding genes

Pinstripe: a suite of programs for integrating transcriptomic and proteomic datasets identifies novel proteins and improves differentiation of protein-coding and non-coding genes | Plant Genomics | Scoop.it

Abstract

Motivation: Comparing transcriptomic data with proteomic data to identify protein-coding sequences is a long-standing challenge in molecular biology, one exacerbated by the increasing size of high-throughput datasets. To address this challenge, and thereby to improve the quality of genome annotation and understanding of genome biology, we have developed an integrated suite of programs, called Pinstripe. We demonstrate its application, utility and discovery power using transcriptomic and proteomic data from publicly available datasets.

Results: To demonstrate the efficacy of Pinstripe for large-scale analysis, we applied Pinstripe’s reverse peptide mapping pipeline to a transcript library including de novo assembled transcriptomes from the human Illumina Body Atlas (IBA2) and Gencode v10 gene annotations, and the EBI PRIDE peptide database. This analysis identified 736 canonical ORFs supported by three or more PRIDE peptide fragments that are positioned outside any known CDS. Due to the unfiltered nature of the PRIDE database and high probability of false discovery, we further refined this list using independent evidence for translation, including the presence of a Kozak sequence or functional domains, synonymous/non-synonymous substitution ratios, and ORF length. Using this integrative approach, we observed evidence of translation from a previously unknown let7e primary transcript, the archetypical lncRNA H19, and a homolog of RD3. Reciprocally, by exclusion of transcripts with mapped peptides or significant ORFs (>80 codon), we identify 32,187 loci with RNAs longer than 2000 nt that are unlikely to encode proteins.

Availability and Implementation: Pinstripe (pinstripe.matticklab.com) is freely available as source code or a Mono binary. Pinstripe is written in C# and runs under the Mono framework on Linux or Mac OS X, and both under Mono and .Net under Windows.

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ScienceDirect.com - Current Opinion in Biotechnology - Transcriptome analysis using next-generation sequencing

ScienceDirect.com - Current Opinion in Biotechnology - Transcriptome analysis using next-generation sequencing | Plant Genomics | Scoop.it

Up to date research in biology, biotechnology, and medicine requires fast genome and transcriptome analysis technologies for the investigation of cellular state, physiology, and activity. Here, microarray technology and next generation sequencing of transcripts (RNA-Seq) are state of the art. Since microarray technology is limited towards the amount of RNA, the quantification of transcript levels and the sequence information, RNA-Seq provides nearly unlimited possibilities in modern bioanalysis. This chapter presents a detailed description of next-generation sequencing (NGS), describes the impact of this technology on transcriptome analysis and explains its possibilities to explore the modern RNA world.

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Arabidopsis seedling flood-inoculation technique: a rapid and reliable assay for studying plant-bacterial interactions

Arabidopsis seedling flood-inoculation technique: a rapid and reliable assay for studying plant-bacterial interactions | Plant Genomics | Scoop.it

Abstract
Background
The Arabidopsis thaliana-Pseudomonas syringae model pathosystem is one of the most widely used systems to understand the mechanisms of microbial pathogenesis and plant innate immunity. Several inoculation methods have been used to study plant-pathogen interactions in this model system. However, none of the methods reported to date are similar to those occurring in nature and amicable to large-scale mutant screens.

 

Results
In this study, we developed a rapid and reliable seedling flood-inoculation method based on young Arabidopsis seedlings grown on MS medium. This method has several advantages over conventional soil-grown plant inoculation assays, including a shorter growth and incubation period, ease of inoculation and handling, uniform infection and disease development, requires less growth chamber space and is suitable for high-throughput screens. In this study we demonstrated the efficacy of the Arabidopsis seedling assay to study 1) the virulence factors of P. syringae pv. tomato DC3000, including type III protein secretion system (TTSS) and phytotoxin coronatine (COR); 2) the effector-triggered immunity; and 3) Arabidopsis mutants affected in salicylic acid (SA)- and pathogen-associated molecular pattern (PAMPs)-mediated pathways. Furthermore, we applied this technique to study nonhost resistance (NHR) responses in Arabidopsis using nonhost pathogens, such as P. syringae pv. tabaci, pv. glycinea and pv. tomato T1, and confirmed the functional role of FLAGELLIN-SENSING 2 (FLS2) in NHR.

 

Conclusions
The Arabidopsis seedling flood-inoculation assay provides a rapid, efficient and economical method for studying Arabidopsis-Pseudomonas interactions with minimal growth chamber space and time. This assay could also provide an excellent system for investigating the virulence mechanisms of P. syringae. Using this method, we demonstrated that FLS2 plays a critical role in conferring NHR against nonhost pathovars of P. syringae, but not to Xanthomonas campestris pv. vesicatoria. This method is potentially ideal for high-throughput screening of both Arabidopsis and pathogen mutants.


Via Freddy Monteiro
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Long identical multispecies elements in plant and animal genomes

Abstract

Ultraconserved elements (UCEs) are DNA sequences that are 100% identical (no base substitutions, insertions, or deletions) and located in syntenic positions in at least two genomes. Although hundreds of UCEs have been found in animal genomes, little is known about the incidence of ultraconservation in plant genomes. Using an alignment-free information-retrieval approach, we have comprehensively identified all long identical multispecies elements (LIMEs), which include both syntenic and nonsyntenic regions, of at least 100 identical base pairs shared by at least two genomes. Among six animal genomes, we found the previously known syntenic UCEs as well as previously undescribed nonsyntenic elements. In contrast, among six plant genomes, we only found nonsyntenic LIMEs. LIMEs can also be classified as either simple (repetitive) or complex (nonrepetitive), they may occur in multiple copies in a genome, and they are often spread across multiple chromosomes. Although complex LIMEs were found in both animal and plant genomes, they differed significantly in their composition and copy number. Further analyses of plant LIMEs revealed their functional diversity, encompassing elements found near rRNA and enzyme-coding genes, as well as those found in transposons and noncoding DNA. We conclude that despite the common presence of LIMEs in both animal and plant lineages, the evolutionary processes involved in the creation and maintenance of these elements differ in the two groups and are likely attributable to several mechanisms, including transfer of genetic material from organellar to nuclear genomes, de novo sequence manufacturing, and purifying selection.

 

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Reshaping of the maize transcriptome by domestication

Reshaping of the maize transcriptome by domestication | Plant Genomics | Scoop.it

Through domestication, humans have substantially altered the morphology of Zea mays ssp. parviglumis (teosinte) into the currently recognizable maize. This system serves as a model for studying adaptation, genome evolution, and the genetics and evolution of complex traits. To examine how domestication has reshaped the transcriptome of maize seedlings, we used expression profiling of 18,242 genes for 38 diverse maize genotypes and 24 teosinte genotypes. We detected evidence for more than 600 genes having significantly different expression levels in maize compared with teosinte. Moreover, more than 1,100 genes showed significantly altered coexpression profiles, reflective of substantial rewiring of the transcriptome since domestication. The genes with altered expression show a significant enrichment for genes previously identified through population genetic analyses as likely targets of selection during maize domestication and improvement; 46 genes previously identified as putative targets of selection also exhibit altered expression levels and coexpression relationships. We also identified 45 genes with altered, primarily higher, expression in inbred relative to outcrossed teosinte. These genes are enriched for functions related to biotic stress and may reflect responses to the effects of inbreeding. This study not only documents alterations in the maize transcriptome following domestication, identifying several genes that may have contributed to the evolution of maize, but highlights the complementary information that can be gained by combining gene expression with population genetic analyses.


Via Dorian Q Fuller, Eve Emshwiller
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Transcriptome Analysis Reveals Putative Genes Involved in Iridoid Biosynthesis in Rehmannia glutinosa

Transcriptome Analysis Reveals Putative Genes Involved in Iridoid Biosynthesis in Rehmannia glutinosa | Plant Genomics | Scoop.it

Abstract: Rehmannia glutinosa, one of the most widely used herbal medicines in the Orient, is rich in biologically active iridoids. Despite their medicinal importance, no molecular information about the iridoid biosynthesis in this plant is presently available. To explore the transcriptome of R. glutinosa and investigate genes involved in iridoid biosynthesis, we used massively parallel pyrosequencing on the 454 GS FLX Titanium platform to generate a substantial EST dataset. Based on sequence similarity searches against the public sequence databases, the sequences were first annotated and then subjected to Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) based analysis. Bioinformatic analysis indicated that the 454 assembly contained a set of genes putatively involved in iridoid biosynthesis. Significantly, homologues of the secoiridoid pathway genes that were only identified in terpenoid indole alkaloid producing plants were also identified, whose presence implied that route II iridoids and route I iridoids share common enzyme steps in the early stage of biosynthesis. The gene expression patterns of four prenyltransferase transcripts were analyzed using qRT-PCR, which shed light on their putative functions in tissues of R. glutinosa. The data explored in this study will provide valuable information for further studies concerning iridoid biosynthesis.

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Tricking the Guard: Exploiting Plant Defense for Disease Susceptibility

Abstract

Typically, pathogens deploy virulence effectors to disable defense. Plants defeat effectors with resistance proteins that guard effector targets. Here, we show that a pathogen exploits a resistance protein by activating it to confer susceptibility. Interactions of victorin, an effector produced by the necrotrophic fungus Cochliobolus victoriae, TRX-h5, a defense-associated thioredoxin, and LOV1, an Arabidopsis susceptibility protein, recapitulate the guard mechanism of plant defense. In LOV1's absence, victorin inhibits TRX-h5 resulting in compromised defense but not disease by C. victoriae. In LOV1's presence, victorin binding to TRX-h5 activates LOV1 and elicits a resistance-like response that confers disease susceptibility. We propose that victorin is or mimics a conventional pathogen virulence effector that was defeated by LOV1 and confers virulence to C. victoriae solely because it incites defense.

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Genomic Characterization for Parasitic Weeds of the Genus Striga by Sample Sequence Analysis

Genomic Characterization for Parasitic Weeds of the Genus Striga by Sample Sequence Analysis | Plant Genomics | Scoop.it

Genomic Characterization for Parasitic Weeds of the Genus Striga by Sample Sequence Analysis

 

Generation of ∼2200 Sanger sequence reads or ∼10,000 454 reads for seven Striga Lour. DNA samples (five species) allowed identification of the highly repetitive DNA content in these genomes. The 14 most abundant repeats in these Striga species were identified and partially assembled. Annotation indicated that they represent nine long terminal repeat (LTR) retrotransposon families, three tandem satellite repeats, one long interspersed element (LINE) retroelement, and one DNA transposon. All of these repeats are most closely related to repetitive elements in other closely related plants and are not products of horizontal transfer from their host species. These repeats were differentially abundant in each species, with the LTR retrotransposons and satellite repeats most responsible for variation in genome size. Each species had some repetitive elements that were more abundant and some less abundant than the other Striga species examined, indicating that no single element or any unilateral growth or decrease trend in genome behavior was responsible for variation in genome size and composition. Genome sizes were determined by flow sorting, and the values of 615 Mb [S. asiatica (L.) Kuntze], 1330 Mb [S. gesnerioides (Willd.) Vatke], 1425 Mb [S. hermonthica (Delile) Benth.] and 2460 Mb (S. forbesii Benth.) suggest a ploidy series, a prediction supported by repetitive DNA sequence analysis. Phylogenetic analysis using six chloroplast loci indicated the ancestral relationships of the five most agriculturally important Striga species, with the unexpected result that the one parasite of dicotyledonous plants (S. gesnerioides) was found to be more closely related to some of the grass parasites than many of the grass parasites are to each other.


Via Strigagenome
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Comparison of transcriptome technologies in the pathogenic fungus Aspergillus fumigatus reveals novel insights into the genome and MpkA dependent gene expression

Abstract (provisional)

Background

The filamentous fungus Aspergillus fumigatus has become the most important airborne fungal pathogen causing life-threatening infections in immuno-compromised patients. Recently developed high-throughput transcriptome and proteome technologies, such as microarrays, RNA deep-sequencing, and LC-MS/MS of peptide mixtures, are of enormous value for systematically investigating pathogenic organisms. In the field of infection biology, one of the priorities is to collect and standardise data, in order to generate datasets that can be used to investigate and compare pathways and gene responses involved in pathogenicity. The "omics" era provides a multitude of inputs that need to be integrated and assessed. We therefore evaluated the potential of paired-end mRNA-Seq for investigating the regulatory role of the central mitogen activated protein kinase (MpkA). This kinase is involved in the cell wall integrity signalling pathway of A. fumigatus and essential for maintaining an intact cell wall in response to stress.

Results

The comparison of the transcriptome and proteome of an A. fumigatus wild-type strain with an mpkA null mutant strain revealed that 70.4% of the genome was found to be expressed and that MpkA plays a significant role in the regulation of many genes involved in cell wall remodelling, oxidative stress and iron starvation response, and secondary metabolite biosynthesis. Moreover, absence of the mpkA gene also strongly affects the expression of genes involved in primary metabolism. The data were further processed to evaluate the potential of the mRNA-Seq technique. We comprehensively matched up our data to published transcriptome studies and were able to show an improved data comparability of mRNA-Seq experiments independently of the technique used. Analysis of transcriptome and proteome data revealed only a weak correlation between mRNA and protein abundance.

Conclusions

High-throughput analysis of MpkA-dependent gene expression confirmed many previous findings that this kinase is important for regulating many genes involved in metabolic pathways. Our analysis showed more than 2000 differentially regulated genes. RNA deep-sequencing is less error-prone than established microarray-based technologies. It also provides additional information in A. fumigatus studies and as a result is more suitable for the creation of extensive datasets.

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BMC Genetics- Molecular mapping of QTLs for plant type and earliness traits in pigeonpea (Cajanus cajan L. Millsp.)

Abstract (provisional)

Background

Pigeonpea is an important grain legume of the semi-arid tropics and sub-tropical regions where it plays a crucial role in the food and nutritional security of the people. The average productivity of pigeonpea has remained very low and stagnant for over five decades due to lack of genomic information and intensive breeding efforts. Previous SSR-based linkage maps of pigeonpea used inter-specific crosses due to low inter-varietal polymorphism. Here our aim was to construct a high density intra-specific linkage map using genic-SNP markers for mapping of major quantitative trait loci (QTLs) for key agronomic traits, including plant height, number of primary and secondary branches, number of pods, days to flowering and days to maturity in pigeonpea.

Results

A population of 186 F2:3 lines derived from an intra-specific cross between inbred lines 'Pusa Dwarf' and 'HDM04-1' was used to construct a dense molecular linkage map of 296 genic SNP and SSR markers covering a total adjusted map length of 1520.22 cM for the 11 chromosomes of the pigeonpea genome. This is the first dense intra-specific linkage map of pigeonpea with the highest genome length coverage. Phenotypic data from the F2:3 families were used to identify thirteen QTLs for the six agronomic traits. The proportion of phenotypic variance explained by the individual QTLs ranged from 3.18% to 51.4%. Ten of these QTLs were clustered in just two genomic regions, indicating pleiotropic effects or close genetic linkage. In addition to the main effects, significant epistatic interaction effects were detected between the QTLs for number of pods per plant.

Conclusions

A large amount of information on transcript sequences, SSR markers and draft genome sequence is now available for pigeonpea. However, there is need to develop high density linkage maps and identify genes/QTLs for important agronomic traits for practical breeding applications. This is the first report on identification of QTLs for plant type and maturity traits in pigeonpea. The QTLs identified in this study provide a strong foundation for further validation and fine mapping for utilization in the pigeonpea improvement.

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Why size really matters when sequencing plant genomes

Why size really matters when sequencing plant genomes | Plant Genomics | Scoop.it

Abstract

Genome sequencing has been restricted to species with a small genome size. With the advent of second- and third-generation sequencing technologies, the potential to sequence genomes of all sizes is becoming a reality. As the field of whole genome sequencing has developed, there has been a growing appreciation of the need to better represent the major lineages of the plant tree of life, rather than just those that contain economically important taxa. We argue that as well as accounting for phylogenetic diversity when selecting species to analyse, in order to gain a comprehensive understanding of genome evolution, large-scale sequencing projects also need to reflect the diversity of genome sizes in plants. In this article we briefly outline evidence from the literature to support this view.

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Genome resequencing reveals multiscale geographic structure and extensive linkage disequilibrium in the forest tree Populus trichocarpa - Slavov - 2012 - New Phytologist - Wiley Online Library

Genome resequencing reveals multiscale geographic structure and extensive linkage disequilibrium in the forest tree Populus trichocarpa - Slavov - 2012 - New Phytologist - Wiley Online Library | Plant Genomics | Scoop.it

Plant population genomics informs evolutionary biology, breeding, conservation and bioenergy feedstock development. For example, the detection of reliable phenotype–genotype associations and molecular signatures of selection requires a detailed knowledge about genome-wide patterns of allele frequency variation, linkage disequilibrium and recombination.

We resequenced 16 genomes of the model tree Populus trichocarpa and genotyped 120 trees from 10 subpopulations using 29 213 single-nucleotide polymorphisms.

Significant geographic differentiation was present at multiple spatial scales, and range-wide latitudinal allele frequency gradients were strikingly common across the genome. The decay of linkage disequilibrium with physical distance was slower than expected from previous studies in Populus, with r2 dropping below 0.2 within 3–6 kb. Consistent with this, estimates of recent effective population size from linkage disequilibrium (Ne ≈ 4000–6000) were remarkably low relative to the large census sizes of P. trichocarpa stands. Fine-scale rates of recombination varied widely across the genome, but were largely predictable on the basis of DNA sequence and methylation features.

Our results suggest that genetic drift has played a significant role in the recent evolutionary history of P. trichocarpa. Most importantly, the extensive linkage disequilibrium detected suggests that genome-wide association studies and genomic selection in undomesticated populations may be more feasible in Populus than previously assumed.


Via Andres Zurita
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Biotechnology for Biofuels | Abstract | Transcriptome profiling of Zymomonas mobilis under ethanol stress

Abstract (provisional)

Background

High tolerance to ethanol is a desirable characteristics for ethanologenic strains used in industrial ethanol fermentation. A deeper understanding of the molecular mechanisms underlying ethanologenic strains tolerance of ethanol stress may guide the design of rational strategies to increase process performance in industrial alcoholic production. Many extensive studies have been performed in Saccharomyces cerevisiae and Escherichia coli. However, the physiological basis and genetic mechanisms involved in ethanol tolerance for Zymomonas mobilis are poorly understood on genomic level. To identify the genes required for tolerance to ethanol, microarray technology was used to investigate the transcriptome profiling of the ethanologenic Z. mobilis in response to ethanol stress.

Results

We successfully identified 127 genes which were differentially expressed in response to ethanol. Ethanol up- or down-regulated genes related to cell wall/membrane biogenesis, metabolism, and transcription. These genes were classified as being involved in a wide range of cellular processes including carbohydrate metabolism, cell wall/membrane biogenesis, respiratory chain, terpenoid biosynthesis, DNA replication, DNA recombination, DNA repair, transport, transcriptional regulation, some universal stress response, etc.

Conclusion

In this study, genome-wide transcriptional responses to ethanol were investigated for the first time in Z. mobilis using microarray analysis.Our results revealed that ethanol had effects on multiple aspects of cellular metabolism at the transcriptional level and that membrane might play important roles in response to ethanol. Although the molecular mechanism involved in tolerance and adaptation of ethanologenic strains to ethanol is still unclear, this research has provided insights into molecular response to ethanol in Z. mobilis. These data will also be helpful to construct more ethanol resistant strains for cellulosic ethanol production in the future.

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In-depth proteome mining of cultured Catharanthus roseus cells identifies candidate proteins involved in the synthesis and transport of secondary metabolites - Champagne - PROTEOMICS - Wiley Online...

In-depth proteome mining of cultured Catharanthus roseus cells identifies candidate proteins involved in the synthesis and transport of secondary metabolites - Champagne - PROTEOMICS - Wiley Online... | Plant Genomics | Scoop.it

Alkaloids;Catharanthus roseus;MALDI-MS/MS;terpenoid indole alkaloids;MudPIT;terpenes

Madagascar periwinkle (Catharanthus roseus) is the major source of terpenoid indole alkaloids, such as vinblastine or vincristine, used as natural drugs against various cancers. In this study, we have extensively analyzed the proteome of cultured C. roseus cells. Comparison of the proteomes of two independent cell lines with different terpenoid indole alkaloid metabolism by 2D-DiGE revealed 358 proteins that differed quantitatively by at least a two-fold average ratio. Of these, 172 were identified by mass spectrometry; most corresponded to house-keeping proteins. Less abundant proteins were identified by LC separation of tryptic peptides of proteins from one of the lines. We identified 1,663 proteins, most of which are housekeeping proteins or involved in primary metabolism. However, 63 enzymes potentially involved in secondary metabolism were also identified, of which 22 are involved in terpenoid indole alkaloid biosynthesis and sixteen are predicted transporters putatively involved in secondary metabolite transport. About 30% of the proteins identified have an unclear or unknown function, indicating important gaps in knowledge of plant metabolism. This study is an important step towards elucidating the proteome of C. roseus, which is critical for a better understanding of how this plant synthesizes terpenoid indole alkaloids.

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QconCAT Standard for Calibration of Ion Mobility-Mass Spectrometry Systems - Journal of Proteome Research (ACS Publications)

QconCAT Standard for Calibration of Ion Mobility-Mass Spectrometry Systems - Journal of Proteome Research (ACS Publications) | Plant Genomics | Scoop.it

Ion mobility-mass spectrometry (IM-MS) is a useful technique for determining information about analyte ion conformation in addition to mass/charge ratio. The physical principles that govern the mobility of an ion through a gas in the presence of a uniform electric field are well understood, enabling rotationally averaged collision cross sections (Ω) to be directly calculated from measured drift times under well-defined experimental conditions. However, such “first principle” calculations are not straightforward for Traveling Wave (T-Wave) mobility separations due to the range of factors that influence ion motion through the mobility cell. If collision cross section information is required from T-Wave mobility separations, then calibration of the instruments using known standards is essential for each set of experimental conditions. To facilitate such calibration, we have designed and generated an artificial protein based on the QconCAT technology, QCAL-IM, which upon proteolysis can be used as a universal ion mobility calibration standard. This single unique standard enables empirical calculation of peptide ion collision cross sections from the drift time on a T-Wave mobility instrument.

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Genome sequence of the button mushroom Agaricus bisporus reveals mechanisms governing adaptation to a humic-rich ecological niche

Abstract

Agaricus bisporus is the model fungus for the adaptation, persistence, and growth in the humic-rich leaf-litter environment. Aside from its ecological role, A. bisporus has been an important component of the human diet for over 200 y and worldwide cultivation of the “button mushroom” forms a multibillion dollar industry. We present two A. bisporus genomes, their gene repertoires and transcript profiles on compost and during mushroom formation. The genomes encode a full repertoire of polysaccharide-degrading enzymes similar to that of wood-decayers. Comparative transcriptomics of mycelium grown on defined medium, casing-soil, and compost revealed genes encoding enzymes involved in xylan, cellulose, pectin, and protein degradation are more highly expressed in compost. The striking expansion of heme-thiolate peroxidases and β-etherases is distinctive from Agaricomycotina wood-decayers and suggests a broad attack on decaying lignin and related metabolites found in humic acid-rich environment. Similarly, up-regulation of these genes together with a lignolytic manganese peroxidase, multiple copper radical oxidases, and cytochrome P450s is consistent with challenges posed by complex humic-rich substrates. The gene repertoire and expression of hydrolytic enzymes in A. bisporus is substantially different from the taxonomically related ectomycorrhizal symbiont Laccaria bicolor. A common promoter motif was also identified in genes very highly expressed in humic-rich substrates. These observations reveal genetic and enzymatic mechanisms governing adaptation to the humic-rich ecological niche formed during plant degradation, further defining the critical role such fungi contribute to soil structure and carbon sequestration in terrestrial ecosystems. Genome sequence will expedite mushroom breeding for improved agronomic characteristics.

 

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Transcriptome Analysis of Quantitative Resistance-Specific Response upon Ralstonia solanacearum Infection in Tomato

Transcriptome Analysis of Quantitative Resistance-Specific Response upon Ralstonia solanacearum Infection in Tomato | Plant Genomics | Scoop.it

Abstract Top

Bacterial wilt, caused by the soil-borne bacterium Ralstonia solanacearum, is a lethal disease of tomato, but the molecular mechanisms of the host resistance responses to R. solanacearum remain unclear. In this study, we report the first work describing the transcriptome of cultivar resistance and susceptible tomato cultivar after inoculation with R. solanacearum. To elucidate the characteristics of resistance early in the interaction, we analyzed microarrays for resistant cultivar LS-89 and susceptible cultivar Ponderosa 1 day after stem inoculation. No change in gene expression was detected for Ponderosa, but expression levels of over 140 genes, including pathogenesis-related, hormone signaling and lignin biosynthesis genes, increased in LS-89. Expression of β-1,3-glucanase genes increased substantially. In an immunohistochemical study, glucanase in LS-89 accumulated in the xylem and pith tissues surrounding xylem vessels filled with R. solanacearum. The expression of these genes also increased in four other resistant cultivars, but changed little in four susceptible cultivars in response to R. solanacearum, suggesting that similar reactions occur in other cultivars. These gene expression profiles will serve as fundamental information to elucidate the molecular mechanisms in the resistance response to R. solanacearum in tomato.

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