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Search Results: 1 - 10 of 222082 matches for " C Robin Buell "
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Gene Coexpression Network Analysis as a Source of Functional Annotation for Rice Genes
Kevin L. Childs,Rebecca M. Davidson,C. Robin Buell
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0022196
Abstract: With the existence of large publicly available plant gene expression data sets, many groups have undertaken data analyses to construct gene coexpression networks and functionally annotate genes. Often, a large compendium of unrelated or condition-independent expression data is used to construct gene networks. Condition-dependent expression experiments consisting of well-defined conditions/treatments have also been used to create coexpression networks to help examine particular biological processes. Gene networks derived from either condition-dependent or condition-independent data can be difficult to interpret if a large number of genes and connections are present. However, algorithms exist to identify modules of highly connected and biologically relevant genes within coexpression networks. In this study, we have used publicly available rice (Oryza sativa) gene expression data to create gene coexpression networks using both condition-dependent and condition-independent data and have identified gene modules within these networks using the Weighted Gene Coexpression Network Analysis method. We compared the number of genes assigned to modules and the biological interpretability of gene coexpression modules to assess the utility of condition-dependent and condition-independent gene coexpression networks. For the purpose of providing functional annotation to rice genes, we found that gene modules identified by coexpression analysis of condition-dependent gene expression experiments to be more useful than gene modules identified by analysis of a condition-independent data set. We have incorporated our results into the MSU Rice Genome Annotation Project database as additional expression-based annotation for 13,537 genes, 2,980 of which lack a functional annotation description. These results provide two new types of functional annotation for our database. Genes in modules are now associated with groups of genes that constitute a collective functional annotation of those modules. Additionally, the expression patterns of genes across the treatments/conditions of an expression experiment comprise a second form of useful annotation.
Identification and characterization of pseudogenes in the rice gene complement
Fran?oise Thibaud-Nissen, Shu Ouyang, C Robin Buell
BMC Genomics , 2009, DOI: 10.1186/1471-2164-10-317
Abstract: A total of 1,439 pseudogenes, identified among genes with pseudogene features, were characterized by similarity to fully-supported gene models and the presence of frameshifts or premature translational stop codons. Significant difference in the length of duplicated genes within segmentally-duplicated regions was the optimal indicator of pseudogenization. Among the 816 pseudogenes for which a probable origin could be determined, 75% originated from gene duplication events while 25% were the result of retrotransposition events. A total of 12% of the pseudogenes were expressed. Finally, F-box proteins, BTB/POZ proteins, terpene synthases, chalcone synthases and cytochrome P450 protein families were found to harbor large numbers of pseudogenes.These pseudogenes still have a detectable open reading frame and are thus distinct from pseudogenes detected within intergenic regions which typically lack definable open reading frames. Families containing the highest number of pseudogenes are fast-evolving families involved in ubiquitination and secondary metabolism.Pseudogenes are defined as genes that have lost their ability to produce a functional protein. Although such relics have been identified in all genomes, the number and persistence of pseudogenes varies greatly among species: in human, the estimated number of pseudogenes ranges from 10,000 to 20,000 [1,2], while in Drosophila, only 110 pseudogenes (or 1 pseudogene per 130 genes) were identified [3]. Pseudogenes are hypothesized to arise by gene duplication, including retrotransposition during which a retrotransposase mediates the integration a transcript into the genome [4] (see Additional file 1). Since they are redundant with the genes from which the transcript originated (hereafter termed parent gene) and are integrated without a promoter into random locations in the genome, the products of retrotransposition events are likely to be nonfunctional and to accumulate disabling mutations faster than functional genes. I
Intron gain and loss in segmentally duplicated genes in rice
Haining Lin, Wei Zhu, Joana C Silva, Xun Gu, C Robin Buell
Genome Biology , 2006, DOI: 10.1186/gb-2006-7-5-r41
Abstract: Analysis of segmental duplication in rice revealed that 159 Mb of the 371 Mb genome and 21,570 of the 43,719 non-transposable element-related genes were contained within a duplicated region. In these duplicated regions, 3,101 collinear paired genes were present. Using this set of segmentally duplicated genes, we investigated intron evolution from full-length cDNA-supported non-transposable element-related gene models of rice. Using gene pairs that have an ortholog in the dicotyledonous model species Arabidopsis thaliana, we identified more intron loss (49 introns within 35 gene pairs) than intron gain (5 introns within 5 gene pairs) following segmental duplication. We were unable to demonstrate preferential intron loss at the 3' end of genes as previously reported in mammalian genomes. However, we did find that the four nucleotides of exons that flank lost introns had less frequently used 4-mers.We observed that intron evolution within rice following segmental duplication is largely dominated by intron loss. In two of the five cases of intron gain within segmentally duplicated genes, the gained sequences were similar to transposable elements.Introns are under less selection pressure than exons, and consequently, their sequences diverge faster than exons. However, the position of the intron with respect to the protein sequence is relatively conserved and conservation of intron position has been observed between distinct eukaryotic lineages throughout about 1.5 billion years of evolution such as between animal and fungal genes [1] and between the malaria parasite Plasmodium falciparum and other eukaryotes [2]. With respect to intron position within genes, introns within intron-sparse species as well as single intron genes are preferentially located near the 5' end of the gene [3,4], suggesting a biased pattern of intron distribution. Indeed, recent studies on 684 eukaryotic orthologous genes from eight eukaryotic species of animals, plants, fungi, and protists showed
The Transcriptome of the Reference Potato Genome Solanum tuberosum Group Phureja Clone DM1-3 516R44
Alicia N. Massa, Kevin L. Childs, Haining Lin, Glenn J. Bryan, Giovanni Giuliano, C. Robin Buell
PLOS ONE , 2011, DOI: 10.1371/journal.pone.0026801
Abstract: Advances in molecular breeding in potato have been limited by its complex biological system, which includes vegetative propagation, autotetraploidy, and extreme heterozygosity. The availability of the potato genome and accompanying gene complement with corresponding gene structure, location, and functional annotation are powerful resources for understanding this complex plant and advancing molecular breeding efforts. Here, we report a reference for the potato transcriptome using 32 tissues and growth conditions from the doubled monoploid Solanum tuberosum Group Phureja clone DM1-3 516R44 for which a genome sequence is available. Analysis of greater than 550 million RNA-Seq reads permitted the detection and quantification of expression levels of over 22,000 genes. Hierarchical clustering and principal component analyses captured the biological variability that accounts for gene expression differences among tissues suggesting tissue-specific gene expression, and genes with tissue or condition restricted expression. Using gene co-expression network analysis, we identified 18 gene modules that represent tissue-specific transcriptional networks of major potato organs and developmental stages. This information provides a powerful resource for potato research as well as studies on other members of the Solanaceae family.
mRNA-Seq Analysis of the Pseudoperonospora cubensis Transcriptome During Cucumber (Cucumis sativus L.) Infection
Elizabeth A. Savory, Bishwo N. Adhikari, John P. Hamilton, Brieanne Vaillancourt, C. Robin Buell, Brad Day
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0035796
Abstract: Pseudoperonospora cubensis, an oomycete, is the causal agent of cucurbit downy mildew, and is responsible for significant losses on cucurbit crops worldwide. While other oomycete plant pathogens have been extensively studied at the molecular level, Ps. cubensis and the molecular basis of its interaction with cucurbit hosts has not been well examined. Here, we present the first large-scale global gene expression analysis of Ps. cubensis infection of a susceptible Cucumis sativus cultivar, ‘Vlaspik’, and identification of genes with putative roles in infection, growth, and pathogenicity. Using high throughput whole transcriptome sequencing, we captured differential expression of 2383 Ps. cubensis genes in sporangia and at 1, 2, 3, 4, 6, and 8 days post-inoculation (dpi). Additionally, comparison of Ps. cubensis expression profiles with expression profiles from an infection time course of the oomycete pathogen Phytophthora infestans on Solanum tuberosum revealed similarities in expression patterns of 1,576–6,806 orthologous genes suggesting a substantial degree of overlap in molecular events in virulence between the biotrophic Ps. cubensis and the hemi-biotrophic P. infestans. Co-expression analyses identified distinct modules of Ps. cubensis genes that were representative of early, intermediate, and late infection stages. Collectively, these expression data have advanced our understanding of key molecular and genetic events in the virulence of Ps. cubensis and thus, provides a foundation for identifying mechanism(s) by which to engineer or effect resistance in the host.
Comprehensive analysis of alternative splicing in rice and comparative analyses with Arabidopsis
Matthew A Campbell, Brian J Haas, John P Hamilton, Stephen M Mount, C Robin Buell
BMC Genomics , 2006, DOI: 10.1186/1471-2164-7-327
Abstract: A comprehensive analysis of alternative splicing was performed in rice that started with >1.1 million publicly available spliced ESTs and over 30,000 full length cDNAs in conjunction with the newly enhanced PASA software. A parallel analysis was performed with Arabidopsis to compare and ascertain potential differences between monocots and dicots. Alternative splicing is a widespread phenomenon (observed in greater than 30% of the loci with transcript support) and we have described nine alternative splicing variations. While alternative splicing has the potential to create many RNA isoforms from a single locus, the majority of loci generate only two or three isoforms and transcript support indicates that these isoforms are generally not rare events. For the alternate donor (AD) and acceptor (AA) classes, the distance between the splice sites for the majority of events was found to be less than 50 basepairs (bp). In both species, the most frequent distance between AA is 3 bp, consistent with reports in mammalian systems. Conversely, the most frequent distance between AD is 4 bp in both plant species, as previously observed in mouse. Most alternative splicing variations are localized to the protein coding sequence and are predicted to significantly alter the coding sequence.Alternative splicing is widespread in both rice and Arabidopsis and these species share many common features. Interestingly, alternative splicing may play a role beyond creating novel combinations of transcripts that expand the proteome. Many isoforms will presumably have negative consequences for protein structure and function, suggesting that their biological role involves post-transcriptional regulation of gene expression.Cultivated rice (Oryza sativa) is considered a model for species within the Poaceae family and, in particular, for agronomically important cereals such as maize (Zea mays), wheat (Triticum aestivum), and barley (Hordeum vulgare). Recently, map-based sequencing of a japonica subs
Analysis of 90 Mb of the potato genome reveals conservation of gene structures and order with tomato but divergence in repetitive sequence composition
Wei Zhu, Shu Ouyang, Marina Iovene, Kimberly O'Brien, Hue Vuong, Jiming Jiang, C Robin Buell
BMC Genomics , 2008, DOI: 10.1186/1471-2164-9-286
Abstract: In this study, we report on analysis 89.9 Mb of potato genomic sequence representing 10.2% of the genome generated through end sequencing of a potato bacterial artificial chromosome (BAC) clone library (87 Mb) and sequencing of 22 potato BAC clones (2.9 Mb). The GC content of potato is very similar to Solanum lycopersicon (tomato) and other dicotyledonous species yet distinct from the monocotyledonous grass species, Oryza sativa. Parallel analyses of repetitive sequences in potato and tomato revealed substantial differences in their abundance, 34.2% in potato versus 46.3% in tomato, which is consistent with the increased genome size per haploid genome of these two Solanum species. Specific classes and types of repetitive sequences were also differentially represented between these two species including a telomeric-related repetitive sequence, ribosomal DNA, and a number of unclassified repetitive sequences. Comparative analyses between tomato and potato at the gene level revealed a high level of conservation of gene content, genic feature, and gene order although discordances in synteny were observed.Genomic level analyses of potato and tomato confirm that gene sequence and gene order are conserved between these solanaceous species and that this conservation can be leveraged in genomic applications including cross-species annotation and genome sequencing initiatives. While tomato and potato share genic features, they differ in their repetitive sequence content and composition suggesting that repetitive sequences may have a more significant role in shaping speciation than previously reported.The potato (Solanum tuberosum) tuber is a specialized underground storage organ that develops from modified stems termed stolons. Although the tuber is primarily composed of starch, it also contains high levels of proteins and due to its importance as a food source, a prime focus in potato research has been tuber quality [1-6]. Another key focus in potato research is disease resi
Comparative analyses of six solanaceous transcriptomes reveal a high degree of sequence conservation and species-specific transcripts
Willem Rensink, Yuandan Lee, Jia Liu, Stacy Iobst, Shu Ouyang, C Robin Buell
BMC Genomics , 2005, DOI: 10.1186/1471-2164-6-124
Abstract: All available ESTs and Expressed Transcripts (ETs), 449,224 sequences for six Solanaceae species (potato, tomato, pepper, petunia, tobacco and Nicotiana benthamiana), were clustered and assembled into gene indices. Examination of gene ontologies revealed that the transcripts within the gene indices encode a similar suite of biological processes. Although the ESTs and ETs were derived from a variety of tissues, 55–81% of the sequences had significant similarity at the nucleotide level with sequences among the six species. Putative orthologs could be identified for 28–58% of the sequences. This high degree of sequence conservation was supported by expression profiling using heterologous hybridizations to potato cDNA arrays that showed similar expression patterns in mature leaves for all six solanaceous species. 16–19% of the transcripts within the six Solanaceae gene indices did not have matches among Solanaceae, Arabidopsis, rice or 21 other plant gene indices.Results from this genome scale analysis confirmed a high level of sequence conservation at the nucleotide level of the coding sequence among Solanaceae. Additionally, the results indicated that part of the Solanaceae transcriptome is likely to be unique for each species.The Solanaceae family encompasses a number of species of agronomic and ornamental importance. With regards to cultivation for food consumption, in 2003, potato was the world's fifth largest crop in world-wide production acreage and the solanaceous vegetables tomato, eggplant, and pepper ranked 11th, 19th, and 22nd, respectively [1]. Species grown for ornamental purposes include petunia and Nicotiana species. While not consumed for food, these horticultural species are a substantial component of the US agronomic economy. For example, petunia represents greater than $148M output per year in the US [2]. Tobacco represents another crop of significant economical importance with $1.6B in crop value in 2003 [3]. A close relative of tobacco, Nicotiana b
Comparative Genomics Reveals Insight into Virulence Strategies of Plant Pathogenic Oomycetes
Bishwo N. Adhikari, John P. Hamilton, Marcelo M. Zerillo, Ned Tisserat, C. André Lévesque, C. Robin Buell
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0075072
Abstract: The kingdom Stramenopile includes diatoms, brown algae, and oomycetes. Plant pathogenic oomycetes, including Phytophthora, Pythium and downy mildew species, cause devastating diseases on a wide range of host species and have a significant impact on agriculture. Here, we report comparative analyses on the genomes of thirteen straminipilous species, including eleven plant pathogenic oomycetes, to explore common features linked to their pathogenic lifestyle. We report the sequencing, assembly, and annotation of six Pythium genomes and comparison with other stramenopiles including photosynthetic diatoms, and other plant pathogenic oomycetes such as Phytophthora species, Hyaloperonospora arabidopsidis, and Pythium ultimum var. ultimum. Novel features of the oomycete genomes include an expansion of genes encoding secreted effectors and plant cell wall degrading enzymes in Phytophthora species and an over-representation of genes involved in proteolytic degradation and signal transduction in Pythium species. A complete lack of classical RxLR effectors was observed in the seven surveyed Pythium genomes along with an overall reduction of pathogenesis-related gene families in H. arabidopsidis. Comparative analyses revealed fewer genes encoding enzymes involved in carbohydrate metabolism in Pythium species and H. arabidopsidis as compared to Phytophthora species, suggesting variation in virulence mechanisms within plant pathogenic oomycete species. Shared features between the oomycetes and diatoms revealed common mechanisms of intracellular signaling and transportation. Our analyses demonstrate the value of comparative genome analyses for exploring the evolution of pathogenesis and survival mechanisms in the oomycetes. The comparative analyses of seven Pythium species with the closely related oomycetes, Phytophthora species and H. arabidopsidis, and distantly related diatoms provide insight into genes that underlie virulence.
Carbohydrate-Active Enzymes in Pythium and Their Role in Plant Cell Wall and Storage Polysaccharide Degradation
Marcelo M. Zerillo, Bishwo N. Adhikari, John P. Hamilton, C. Robin Buell, C. André Lévesque, Ned Tisserat
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0072572
Abstract: Carbohydrate-active enzymes (CAZymes) are involved in the metabolism of glycoconjugates, oligosaccharides, and polysaccharides and, in the case of plant pathogens, in the degradation of the host cell wall and storage compounds. We performed an in silico analysis of CAZymes predicted from the genomes of seven Pythium species (Py. aphanidermatum, Py. arrhenomanes, Py. irregulare, Py. iwayamai, Py. ultimum var. ultimum, Py. ultimum var. sporangiiferum and Py. vexans) using the “CAZymes Analysis Toolkit” and “Database for Automated Carbohydrate-active Enzyme Annotation” and compared them to previously published oomycete genomes. Growth of Pythium spp. was assessed in a minimal medium containing selected carbon sources that are usually present in plants. The in silico analyses, coupled with our in vitro growth assays, suggest that most of the predicted CAZymes are involved in the metabolism of the oomycete cell wall with starch and sucrose serving as the main carbohydrate sources for growth of these plant pathogens. The genomes of Pythium spp. also encode pectinases and cellulases that facilitate degradation of the plant cell wall and are important in hyphal penetration; however, the species examined in this study lack the requisite genes for the complete saccharification of these carbohydrates for use as a carbon source. Genes encoding for xylan, xyloglucan, (galacto)(gluco)mannan and cutin degradation were absent or infrequent in Pythium spp.. Comparative analyses of predicted CAZymes in oomycetes indicated distinct evolutionary histories. Furthermore, CAZyme gene families among Pythium spp. were not uniformly distributed in the genomes, suggesting independent gene loss events, reflective of the polyphyletic relationships among some of the species.
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