Author
Etienne Paux
Other affiliations: Institut national de la recherche agronomique, Paul Sabatier University, Blaise Pascal University ...read more
Bio: Etienne Paux is an academic researcher from University of Auvergne. The author has contributed to research in topics: Genome & Reference genome. The author has an hindex of 40, co-authored 91 publications receiving 9890 citations. Previous affiliations of Etienne Paux include Institut national de la recherche agronomique & Paul Sabatier University.
Topics: Genome, Reference genome, Chromosome, Genomics, Triticeae
Papers published on a yearly basis
Papers
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TL;DR: This work proposes the first unified hierarchical classification system, designed on the basis of the transposition mechanism, sequence similarities and structural relationships, that can be easily applied by non-experts.
Abstract: Our knowledge of the structure and composition of genomes is rapidly progressing in pace with their sequencing. The emerging data show that a significant portion of eukaryotic genomes is composed of transposable elements (TEs). Given the abundance and diversity of TEs and the speed at which large quantities of sequence data are emerging, identification and annotation of TEs presents a significant challenge. Here we propose the first unified hierarchical classification system, designed on the basis of the transposition mechanism, sequence similarities and structural relationships, that can be easily applied by non-experts. The system and nomenclature is kept up to date at the WikiPoson web site.
2,425 citations
TL;DR: This annotated reference sequence of wheat is a resource that can now drive disruptive innovation in wheat improvement, as this community resource establishes the foundation for accelerating wheat research and application through improved understanding of wheat biology and genomics-assisted breeding.
Abstract: An annotated reference sequence representing the hexaploid bread wheat genome in 21 pseudomolecules has been analyzed to identify the distribution and genomic context of coding and noncoding elements across the A, B, and D subgenomes. With an estimated coverage of 94% of the genome and containing 107,891 high-confidence gene models, this assembly enabled the discovery of tissue- and developmental stage-related coexpression networks by providing a transcriptome atlas representing major stages of wheat development. Dynamics of complex gene families involved in environmental adaptation and end-use quality were revealed at subgenome resolution and contextualized to known agronomic single-gene or quantitative trait loci. This community resource establishes the foundation for accelerating wheat research and application through improved understanding of wheat biology and genomics-assisted breeding.
2,118 citations
Academy of Sciences of the Czech Republic1, University of Saskatchewan2, Bayer3, Kansas State University4, University of California, Riverside5, Blaise Pascal University6, Kyoto University7, University of Dundee8, Punjab Agricultural University9, Indian Agricultural Research Institute10, University of Delhi11, University of Tsukuba12, Yokohama City University13, National Research Council14, Norwegian University of Life Sciences15, Sainsbury Laboratory16, Leibniz Association17, United States Department of Energy18, James Hutton Institute19, Institut national de la recherche agronomique20, University of Zurich21, Sabancı University22, Murdoch University23
TL;DR: Insight into the genome biology of a polyploid crop provide a springboard for faster gene isolation, rapid genetic marker development, and precise breeding to meet the needs of increasing food demand worldwide.
Abstract: An ordered draft sequence of the 17-gigabase hexaploid bread wheat (Triticum aestivum) genome has been produced by sequencing isolated chromosome arms. We have annotated 124,201 gene loci distributed nearly evenly across the homeologous chromosomes and subgenomes. Comparative gene analysis of wheat subgenomes and extant diploid and tetraploid wheat relatives showed that high sequence similarity and structural conservation are retained, with limited gene loss, after polyploidization. However, across the genomes there was evidence of dynamic gene gain, loss, and duplication since the divergence of the wheat lineages. A high degree of transcriptional autonomy and no global dominance was found for the subgenomes. These insights into the genome biology of a polyploid crop provide a springboard for faster gene isolation, rapid genetic marker development, and precise breeding to meet the needs of increasing food demand worldwide.
1,421 citations
Norwich Research Park1, Bayer2, University of Toronto3, Agriculture and Agri-Food Canada4, University of Saskatchewan5, Paris Diderot University6, Institut national de la recherche agronomique7, National Research Council8, Technische Universität München9, University of Melbourne10, University of Maryland, College Park11
TL;DR: This study leverages 850 wheat RNA-sequencing samples, alongside the annotated genome, to determine the similarities and differences between homoeolog expression across a range of tissues, developmental stages, and cultivars and suggests that the transposable elements in promoters relate more closely to the variation in the relative expression of homoeologicals across tissues than to a ubiquitous effect across all tissues.
Abstract: The coordinated expression of highly related homoeologous genes in polyploid species underlies the phenotypes of many of the world's major crops. Here we combine extensive gene expression datasets to produce a comprehensive, genome-wide analysis of homoeolog expression patterns in hexaploid bread wheat. Bias in homoeolog expression varies between tissues, with ~30% of wheat homoeologs showing nonbalanced expression. We found expression asymmetries along wheat chromosomes, with homoeologs showing the largest inter-tissue, inter-cultivar, and coding sequence variation, most often located in high-recombination distal ends of chromosomes. These transcriptionally dynamic genes potentially represent the first steps toward neo- or subfunctionalization of wheat homoeologs. Coexpression networks reveal extensive coordination of homoeologs throughout development and, alongside a detailed expression atlas, provide a framework to target candidate genes underpinning agronomic traits in wheat.
609 citations
TL;DR: The distribution of structural and functional features along the chromosome revealed partitioning correlated with meiotic recombination and high wheat-specific inter- and intrachromosomal gene duplication activities that are potential sources of variability for adaption.
Abstract: We produced a reference sequence of the 1-gigabase chromosome 3B of hexaploid bread wheat. By sequencing 8452 bacterial artificial chromosomes in pools, we assembled a sequence of 774 megabases carrying 5326 protein-coding genes, 1938 pseudogenes, and 85% of transposable elements. The distribution of structural and functional features along the chromosome revealed partitioning correlated with meiotic recombination. Comparative analyses indicated high wheat-specific inter- and intrachromosomal gene duplication activities that are potential sources of variability for adaption. In addition to providing a better understanding of the organization, function, and evolution of a large and polyploid genome, the availability of a high-quality sequence anchored to genetic maps will accelerate the identification of genes underlying important agronomic traits.
522 citations
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TL;DR: A high-quality genome sequence of domesticated tomato is presented, a draft sequence of its closest wild relative, Solanum pimpinellifolium, is compared, and the two tomato genomes are compared to each other and to the potato genome.
Abstract: Tomato (Solanum lycopersicum) is a major crop plant and a model system for fruit development. Solanum is one of the largest angiosperm genera1 and includes annual and perennial plants from diverse habitats. Here we present a high-quality genome sequence of domesticated tomato, a draft sequence of its closest wild relative, Solanum pimpinellifolium2, and compare them to each other and to the potato genome (Solanum tuberosum). The two tomato genomes show only 0.6% nucleotide divergence and signs of recent admixture, but show more than 8% divergence from potato, with nine large and several smaller inversions. In contrast to Arabidopsis, but similar to soybean, tomato and potato small RNAs map predominantly to gene-rich chromosomal regions, including gene promoters. The Solanum lineage has experienced two consecutive genome triplications: one that is ancient and shared with rosids, and a more recent one. These triplications set the stage for the neofunctionalization of genes controlling fruit characteristics, such as colour and fleshiness.
2,687 citations
TL;DR: This annotated reference sequence of wheat is a resource that can now drive disruptive innovation in wheat improvement, as this community resource establishes the foundation for accelerating wheat research and application through improved understanding of wheat biology and genomics-assisted breeding.
Abstract: An annotated reference sequence representing the hexaploid bread wheat genome in 21 pseudomolecules has been analyzed to identify the distribution and genomic context of coding and noncoding elements across the A, B, and D subgenomes. With an estimated coverage of 94% of the genome and containing 107,891 high-confidence gene models, this assembly enabled the discovery of tissue- and developmental stage-related coexpression networks by providing a transcriptome atlas representing major stages of wheat development. Dynamics of complex gene families involved in environmental adaptation and end-use quality were revealed at subgenome resolution and contextualized to known agronomic single-gene or quantitative trait loci. This community resource establishes the foundation for accelerating wheat research and application through improved understanding of wheat biology and genomics-assisted breeding.
2,118 citations
TL;DR: Recent updates of RU are introduced, focusing on technical issues concerning the submission and updating of Repbase entries and will give short examples of using RU data.
Abstract: Repbase Update (RU) is a database of representative repeat sequences in eukaryotic genomes. Since its first development as a database of human repetitive sequences in 1992, RU has been serving as a well-curated reference database fundamental for almost all eukaryotic genome sequence analyses. Here, we introduce recent updates of RU, focusing on technical issues concerning the submission and updating of Repbase entries and will give short examples of using RU data. RU sincerely invites a broader submission of repeat sequences from the research community.
1,997 citations
University of Évry Val d'Essonne1, Crops Research Institute2, Agriculture and Agri-Food Canada3, Fujian Agriculture and Forestry University4, J. Craig Venter Institute5, Plant Genome Mapping Laboratory6, University of Giessen7, French Alternative Energies and Atomic Energy Commission8, Institut national de la recherche agronomique9, National Research Council10, Australian Centre for Plant Functional Genomics11, University of Cologne12, Purdue University13, University of California, Berkeley14, University of British Columbia15, Fondation Jean Dausset Centre d'Etude du Polymorphisme Humain16, Huazhong Agricultural University17, Hunan Agricultural University18, Chungnam National University19, University of Arizona20, University of York21, University of Missouri22, Southern Cross University23, University of Western Australia24, Centre national de la recherche scientifique25
TL;DR: The polyploid genome of Brassica napus, which originated from a recent combination of two distinct genomes approximately 7500 years ago and gave rise to the crops of rape oilseed, is sequenced.
Abstract: Oilseed rape (Brassica napus L.) was formed ~7500 years ago by hybridization between B. rapa and B. oleracea, followed by chromosome doubling, a process known as allopolyploidy. Together with more ancient polyploidizations, this conferred an aggregate 72× genome multiplication since the origin of angiosperms and high gene content. We examined the B. napus genome and the consequences of its recent duplication. The constituent An and Cn subgenomes are engaged in subtle structural, functional, and epigenetic cross-talk, with abundant homeologous exchanges. Incipient gene loss and expression divergence have begun. Selection in B. napus oilseed types has accelerated the loss of glucosinolate genes, while preserving expansion of oil biosynthesis genes. These processes provide insights into allopolyploid evolution and its relationship with crop domestication and improvement.
1,743 citations
TL;DR: It is shown that a relatively recent (>50 million years ago) genome-wide duplication has resulted in the transition from nine ancestral chromosomes to 17 chromosomes in the Pyreae, which partly support the monophyly of the ancestral paleohexaploidy of eudicots.
Abstract: We report a high-quality draft genome sequence of the domesticated apple (Malus × domestica). We show that a relatively recent (>50 million years ago) genome-wide duplication (GWD) has resulted in the transition from nine ancestral chromosomes to 17 chromosomes in the Pyreae. Traces of older GWDs partly support the monophyly of the ancestral paleohexaploidy of eudicots. Phylogenetic reconstruction of Pyreae and the genus Malus, relative to major Rosaceae taxa, identified the progenitor of the cultivated apple as M. sieversii. Expansion of gene families reported to be involved in fruit development may explain formation of the pome, a Pyreae-specific false fruit that develops by proliferation of the basal part of the sepals, the receptacle. In apple, a subclade of MADS-box genes, normally involved in flower and fruit development, is expanded to include 15 members, as are other gene families involved in Rosaceae-specific metabolism, such as transport and assimilation of sorbitol.
1,718 citations