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Jessica A. Schlueter

Other affiliations: Texas A&M University, Purdue University, University of Georgia  ...read more
Bio: Jessica A. Schlueter is an academic researcher from University of North Carolina at Charlotte. The author has contributed to research in topics: Genome & Genome evolution. The author has an hindex of 23, co-authored 43 publications receiving 6535 citations. Previous affiliations of Jessica A. Schlueter include Texas A&M University & Purdue University.
Topics: Genome, Genome evolution, Gene, Population, Synteny

Papers
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Journal ArticleDOI
14 Jan 2010-Nature
TL;DR: An accurate soybean genome sequence will facilitate the identification of the genetic basis of many soybean traits, and accelerate the creation of improved soybean varieties.
Abstract: Soybean (Glycine max) is one of the most important crop plants for seed protein and oil content, and for its capacity to fix atmospheric nitrogen through symbioses with soil-borne microorganisms. We sequenced the 1.1-gigabase genome by a whole-genome shotgun approach and integrated it with physical and high-density genetic maps to create a chromosome-scale draft sequence assembly. We predict 46,430 protein-coding genes, 70% more than Arabidopsis and similar to the poplar genome which, like soybean, is an ancient polyploid (palaeopolyploid). About 78% of the predicted genes occur in chromosome ends, which comprise less than one-half of the genome but account for nearly all of the genetic recombination. Genome duplications occurred at approximately 59 and 13 million years ago, resulting in a highly duplicated genome with nearly 75% of the genes present in multiple copies. The two duplication events were followed by gene diversification and loss, and numerous chromosome rearrangements. An accurate soybean genome sequence will facilitate the identification of the genetic basis of many soybean traits, and accelerate the creation of improved soybean varieties.

3,743 citations

Journal ArticleDOI
TL;DR: This reference genome sequence will facilitate the identification of the genetic basis of agronomically important traits, and accelerate the development of improved pigeonpea varieties that could improve food security in many developing countries.
Abstract: Pigeonpea is an important legume food crop grown primarily by smallholder farmers in many semi-arid tropical regions of the world. We used the Illumina next-generation sequencing platform to generate 237.2 Gb of sequence, which along with Sanger-based bacterial artificial chromosome end sequences and a genetic map, we assembled into scaffolds representing 72.7% (605.78 Mb) of the 833.07 Mb pigeonpea genome. Genome analysis predicted 48,680 genes for pigeonpea and also showed the potential role that certain gene families, for example, drought tolerance-related genes, have played throughout the domestication of pigeonpea and the evolution of its ancestors. Although we found a few segmental duplication events, we did not observe the recent genome-wide duplication events observed in soybean. This reference genome sequence will facilitate the identification of the genetic basis of agronomically important traits, and accelerate the development of improved pigeonpea varieties that could improve food security in many developing countries.

741 citations

Journal ArticleDOI
01 Oct 2004-Genome
TL;DR: Pearson's correlation coefficients were calculated to provide a measure of how gene expression patterns have changed between duplicate pairs, and showed that some duplicates seemed to retain expression patterns between pairs, whereas others showed uncorrelated expression.
Abstract: Using plant EST collections, we obtained 1392 potential gene duplicates across 8 plant species: Zea mays, Oryza sativa, Sorghum bicolor, Hordeum vulgare, Solanum tuberosum, Lycopersicon esculentum,...

332 citations

Journal ArticleDOI
TL;DR: This volume presents a brief synopsis of NGS technologies and the development of exemplary applications of such methods in the fields of molecular marker development, hybridization and introgression, transcriptome investigations, phylogenetic and ecological studies, polyploid genetics, and applications for large genebank collections.
Abstract: The last several years have seen revolutionary advances in DNA sequencing technologies with the advent of next-generation sequencing (NGS) techniques. NGS methods now allow millions of bases to be sequenced in one round, at a fraction of the cost relative to traditional Sanger sequencing. As costs and capabilities of these technologies continue to improve, we are only beginning to see the possibilities of NGS platforms, which are developing in parallel with online availability of a wide range of biological data sets and scientific publications and allowing us to address a variety of questions not possible before. As techniques and data sets continue to improve and grow, we are rapidly moving to the point where every organism, not just select "model organisms", is open to the power of NGS. This volume presents a brief synopsis of NGS technologies and the development of exemplary applications of such methods in the fields of molecular marker development, hybridization and introgression, transcriptome investigations, phylogenetic and ecological studies, polyploid genetics, and applications for large genebank collections.

284 citations

Journal ArticleDOI
TL;DR: It is found that transcription factors and ribosomal protein genes were differentially expressed in many tissues, suggesting that the main consequence of polyploidy in soybean may be at the regulatory level.
Abstract: SUMMARYPolyploidy is generally not tolerated in animals, but is widespread in plant genomes and may result inextensive genetic redundancy. The fate of duplicated genes is poorly understood, both functionally andevolutionarily. Soybean (Glycine max L.) has undergone two separate polyploidy events (13 and 59 millionyears ago) that have resulted in 75% of its genes being present in multiple copies. It therefore constitutesa good model to study the impact of whole-genome duplication on gene expression. Using RNA-seq, wetested the functional fate of a set of approximately 18 000 duplicated genes. Across seven tissues tested,approximately 50% of paralogs were differentially expressed and thus had undergone expression sub-functionalization. Based on gene ontology and expression data, our analysis also revealed that only asmall proportion of the duplicated genes have been neo-functionalized or non-functionalized. In addition,duplicated genes were often found in collinear blocks, and several blocks of duplicated genes wereco-regulated, suggesting some type of epigenetic or positional regulation. We also found thattranscription factors and ribosomal protein genes were differentially expressed in many tissues, suggest-ing that the main consequence of polyploidy in soybean may be at the regulatory level.Keywords: polyploidy, duplicated gene expression, sub-functionalization, Glycine max, RNA-seq, genomeevolution.INTRODUCTIONAngiosperms represent the largest group of plants, with350 000 known taxa (Van de Peer et al., 2009). They under-went diversification in the mid-Cretaceous period (i.e. 100million years ago, MYA), and, in contrast to pteridophytesand gymnosperms, maintained a high radiation rate over along period of time (Lidgard and Crane, 1988; Crane andLidgard, 1989; Crepet and Niklas, 2009). Defined by Darwinas an ‘abominable mystery’, this prominence of floweringplants on earth has been extensively studied. Recent theo-ries suggest that carpel evolution, double fertilization andflower development, as well as additional innovations suchas reduced cost of seed production and short generationtime, contributed to the explosive success of angiosperms(Stuessy, 2004; Lord and Westoby, 2011). Because manygenes involved in reproduction and flower developmentwere duplicated before the monocot/dicot radiation (Jiaoet al., 2011), whole-genome duplications (WGDs) arebelieved to be at the origin of angiosperm radiation(De Bodt et al., 2005). Polyploidy, or WGD, is a process thatrecurrently shaped eukaryotic genomes. Although, in ani-mals, this process is mainly restricted to amphibians andfish (Otto and Whitton, 2000), polyploidy has played amajor evolutionary role in plants. Complete genomeanalyses strongly support the conclusion that, in additionto lineage-specific WGDs, a triplication (c) and two WGD(q and r), respectively, occurred in eudicots and monocots(Vision, 2000; Jaillon et al., 2007; Lyons et al., 2008; Tanget al., 2010). Recent work also demonstrated that two

251 citations


Cited by
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Journal ArticleDOI
14 Jan 2010-Nature
TL;DR: An accurate soybean genome sequence will facilitate the identification of the genetic basis of many soybean traits, and accelerate the creation of improved soybean varieties.
Abstract: Soybean (Glycine max) is one of the most important crop plants for seed protein and oil content, and for its capacity to fix atmospheric nitrogen through symbioses with soil-borne microorganisms. We sequenced the 1.1-gigabase genome by a whole-genome shotgun approach and integrated it with physical and high-density genetic maps to create a chromosome-scale draft sequence assembly. We predict 46,430 protein-coding genes, 70% more than Arabidopsis and similar to the poplar genome which, like soybean, is an ancient polyploid (palaeopolyploid). About 78% of the predicted genes occur in chromosome ends, which comprise less than one-half of the genome but account for nearly all of the genetic recombination. Genome duplications occurred at approximately 59 and 13 million years ago, resulting in a highly duplicated genome with nearly 75% of the genes present in multiple copies. The two duplication events were followed by gene diversification and loss, and numerous chromosome rearrangements. An accurate soybean genome sequence will facilitate the identification of the genetic basis of many soybean traits, and accelerate the creation of improved soybean varieties.

3,743 citations

Journal ArticleDOI
TL;DR: Phytozome provides a view of the evolutionary history of every plant gene at the level of sequence, gene structure, gene family and genome organization, while at the same time providing access to the sequences and functional annotations of a growing number of complete plant genomes.
Abstract: The number of sequenced plant genomes and associated genomic resources is growing rapidly with the advent of both an increased focus on plant genomics from funding agencies, and the application of inexpensive next generation sequencing. To interact with this increasing body of data, we have developed Phytozome (http://www.phytozome.net), a comparative hub for plant genome and gene family data and analysis. Phytozome provides a view of the evolutionary history of every plant gene at the level of sequence, gene structure, gene family and genome organization, while at the same time providing access to the sequences and functional annotations of a growing number (currently 25) of complete plant genomes, including all the land plants and selected algae sequenced at the Joint Genome Institute, as well as selected species sequenced elsewhere. Through a comprehensive plant genome database and web portal, these data and analyses are available to the broader plant science research community, providing powerful comparative genomics tools that help to link model systems with other plants of economic and ecological importance.

3,728 citations

Journal ArticleDOI
TL;DR: The MCScanX toolkit implements an adjusted MCScan algorithm for detection of synteny and collinearity that extends the original software by incorporating 14 utility programs for visualization of results and additional downstream analyses.
Abstract: MCScan is an algorithm able to scan multiple genomes or subgenomes in order to identify putative homologous chromosomal regions, and align these regions using genes as anchors. The MCScanX toolkit implements an adjusted MCScan algorithm for detection of synteny and collinearity that extends the original software by incorporating 14 utility programs for visualization of results and additional downstream analyses. Applications of MCScanX to several sequenced plant genomes and gene families are shown as examples. MCScanX can be used to effectively analyze chromosome structural changes, and reveal the history of gene family expansions that might contribute to the adaptation of lineages and taxa. An integrated view of various modes of gene duplication can supplement the traditional gene tree analysis in specific families. The source code and documentation of MCScanX are freely available at http://chibba.pgml.uga.edu/mcscan2/.

3,388 citations

Journal ArticleDOI
TL;DR: It is becoming clear that a single WRKY transcription factor might be involved in regulating several seemingly disparate processes, and that members of the family play roles in both the repression and de-repression of important plant processes.

1,967 citations