RepeatModeler2 for automated genomic discovery of transposable element families

Proceedings of the National Academy of Sciences, Journal Year: 2020, Volume and Issue: 117(17), P. 9451 - 9457

Published: April 16, 2020

The accelerating pace of genome sequencing throughout the tree life is driving need for improved unsupervised annotation components such as transposable elements (TEs). Because types and sequences TEs are highly variable across species, automated TE discovery challenging time-consuming tasks. A critical first step de novo identification accurate compilation sequence models representing all unique families dispersed in genome. Here we introduce RepeatModeler2, a pipeline that greatly facilitates this process. This program brings substantial improvements over original version RepeatModeler, one most widely used tools discovery. In particular, incorporates module structural complete long terminal repeat (LTR) retroelements, which widespread eukaryotic genomes but recalcitrant to because their size complexity. We benchmarked RepeatModeler2 on three model species with diverse landscapes high-quality, manually curated libraries: Drosophila melanogaster (fruit fly), Danio rerio (zebrafish), Oryza sativa (rice). these identified approximately 3 times more consensus matching >95% identity coverage than RepeatModeler. As expected, greatest improvement LTR retroelements. Thus, represents valuable addition toolkit will enhance study sequences. available source code or containerized package under an open license ( https://github.com/Dfam-consortium/RepeatModeler , http://www.repeatmasker.org/RepeatModeler/ ).

Language: Английский

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Benchmarking transposable element annotation methods for creation of a streamlined, comprehensive pipeline

Genome biology, Journal Year: 2019, Volume and Issue: 20(1)

Published: Dec. 16, 2019

Abstract Background Sequencing technology and assembly algorithms have matured to the point that high-quality de novo is possible for large, repetitive genomes. Current assemblies traverse transposable elements (TEs) provide an opportunity comprehensive annotation of TEs. Numerous methods exist each class TEs, but their relative performances not been systematically compared. Moreover, a pipeline needed produce non-redundant library TEs species lacking this resource generate whole-genome TE annotations. Results We benchmark existing programs based on carefully curated rice evaluate performance annotating long terminal repeat (LTR) retrotransposons, inverted (TIR) transposons, short TIR transposons known as miniature (MITEs), Helitrons. Performance metrics include sensitivity, specificity, accuracy, precision, FDR, F 1 . Using most robust programs, we create called Extensive de-novo Annotator (EDTA) produces filtered structurally intact fragmented elements. EDTA also deconvolutes nested insertions frequently found in highly genomic regions. other model with libraries (maize Drosophila), shown be across both plant animal species. Conclusions The benchmarking results developed here will greatly facilitate eukaryotic These annotations promote much more in-depth understanding diversity evolution at intra- inter-species levels. open-source freely available: https://github.com/oushujun/EDTA

Language: Английский

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The transcriptional landscape of polyploid wheat

Science, Journal Year: 2018, Volume and Issue: 361(6403)

Published: Aug. 17, 2018

The coordinated expression of highly related homoeologous genes in polyploid species underlies the phenotypes many world's major crops. Here we combine extensive gene datasets to produce a comprehensive, genome-wide analysis homoeolog patterns hexaploid bread wheat. Bias varies between tissues, with ~30% wheat homoeologs showing nonbalanced expression. We found asymmetries along chromosomes, largest inter-tissue, inter-cultivar, and coding sequence variation, most often located high-recombination distal ends chromosomes. These transcriptionally dynamic potentially represent first steps toward neo- or subfunctionalization homoeologs. Coexpression networks reveal coordination throughout development and, alongside detailed atlas, provide framework target candidate underpinning agronomic traits

Language: Английский

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Gossypium barbadense and Gossypium hirsutum genomes provide insights into the origin and evolution of allotetraploid cotton

Nature Genetics, Journal Year: 2019, Volume and Issue: 51(4), P. 739 - 748

Published: March 18, 2019

Allotetraploid cotton is an economically important natural-fiber-producing crop worldwide. After polyploidization, Gossypium hirsutum L. evolved to produce a higher fiber yield and better survive harsh environments than barbadense, which produces superior-quality fibers. The global genetic molecular bases for these interspecies divergences were unknown. Here we report high-quality de novo–assembled genomes two cultivated allotetraploid species with pronounced improvement in repetitive-DNA-enriched centromeric regions. Whole-genome comparative analyses revealed that species-specific alterations gene expression, structural variations expanded families responsible speciation the evolutionary history of species. These findings help elucidate evolution their domestication history. information generated not only should enable breeders improve quality resilience ever-changing environmental conditions but also can be translated other crops understanding use improvement. High-quality whole-genome provide insights into stress.

Language: Английский

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Breeding crops to feed 10 billion

Nature Biotechnology, Journal Year: 2019, Volume and Issue: 37(7), P. 744 - 754

Published: June 17, 2019

Language: Английский

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Multiple wheat genomes reveal global variation in modern breeding

Nature, Journal Year: 2020, Volume and Issue: 588(7837), P. 277 - 283

Published: Nov. 25, 2020

Abstract Advances in genomics have expedited the improvement of several agriculturally important crops but similar efforts wheat ( Triticum spp.) been more challenging. This is largely owing to size and complexity genome 1 , lack genome-assembly data for multiple lines 2,3 . Here we generated ten chromosome pseudomolecule five scaffold assemblies hexaploid explore genomic diversity among from global breeding programs. Comparative analysis revealed extensive structural rearrangements, introgressions wild relatives differences gene content resulting complex histories aimed at improving adaptation diverse environments, grain yield quality, resistance stresses 4,5 We provide examples outlining utility these genomes, including a detailed multi-genome-derived nucleotide-binding leucine-rich repeat protein repertoire involved disease characterization Sm1 6 associated with insect resistance. These will basis functional discovery deliver next generation modern cultivars.

Language: Английский

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Durum wheat genome highlights past domestication signatures and future improvement targets

Nature Genetics, Journal Year: 2019, Volume and Issue: 51(5), P. 885 - 895

Published: April 8, 2019

The domestication of wild emmer wheat led to the selection modern durum wheat, grown mainly for pasta production. We describe 10.45 gigabase (Gb) assembly genome cultivar Svevo. enabled genome-wide genetic diversity analyses revealing changes imposed by thousands years empirical and breeding. Regions exhibiting strong signatures divergence associated with breeding were widespread in several major losses pericentromeric regions. A locus on chromosome 5B carries a gene encoding metal transporter (TdHMA3-B1) non-functional variant causing high accumulation cadmium grain. high-cadmium allele, among cultivars but undetected accessions, increased frequency from domesticated wheat. rapid cloning TdHMA3-B1 rescues beneficial allele demonstrates practical use Svevo improvement. Genome enables highlighting modifications

Language: Английский

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Horizontal gene transfer of Fhb7 from fungus underlies Fusarium head blight resistance in wheat

Science, Journal Year: 2020, Volume and Issue: 368(6493)

Published: April 9, 2020

Fungal disease meets its match Fusarium head blight (FHB), caused by a fungus, reduces wheat crop yield and introduces toxins into the harvest. From assembly of genome Thinopyrum elongatum , wild relative used in breeding programs to improve cultivated wheat, Wang et al. cloned gene that can address both problems (see Perspective Wulff Jones). The encoded glutathione S -transferase detoxifies trichothecene toxin and, when expressed confers resistance FHB. Science this issue p. eaba5435 ; see also 822

Language: Английский

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Ensembl Genomes 2020—enabling non-vertebrate genomic research

Nucleic Acids Research, Journal Year: 2019, Volume and Issue: 48(D1), P. D689 - D695

Published: Oct. 2, 2019

Ensembl Genomes (http://www.ensemblgenomes.org) is an integrating resource for genome-scale data from non-vertebrate species, complementing the resources vertebrate genomics developed in context of project (http://www.ensembl.org). Together, two provide a consistent set interfaces to genomic across tree life, including reference genome sequence, gene models, transcriptional data, genetic variation and comparative analysis. Data may be accessed via our website, online tools platform programmatic interfaces, with updates made four times per year (in synchrony Ensembl). Here, we overview Genomes, focus on recent developments. These include continued growth, more robust reproducible sets orthologues paralogues, enriched views expression function plants. Finally, report deeper integration project, which forms key part future strategy dealing increasing quantity available life.

Language: Английский

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Worldwide Research Trends on Wheat and Barley: A Bibliometric Comparative Analysis

Agronomy, Journal Year: 2019, Volume and Issue: 9(7), P. 352 - 352

Published: July 3, 2019

Grain cereals such as wheat, barley, rice, and maize are the nutritional basis of humans animals worldwide. Thus, these crop plants essential in terms global food security. We conducted a bibliometric assessment scientific documents patents related to wheat barley through Scopus database. The number published per year, their affiliation corresponding areas, publishing journals, document types languages were metricized. main keywords included research publications concerning crops also analysed globally clustered thematic groups. In case agronomy or genetics molecular biology, we considered dated up 1999, from 2000 2018, separately. Comparison results obtained for revealed some remarkable different trends, which underlying reasons further discussed.

Language: Английский

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