Linking the International Wheat Genome Sequencing Consortium bread wheat reference genome sequence to wheat genetic and phenomic data

Alaux, Michaël; Rogers, Jane; Letellier, Thomas; Flores, Raphaël; Alfama, Françoise; Pommier, Cyril; Mohellibi, Nacer; Durand, Sophie; Kimmel, Erik; Michotey, Célia; Guerche, Claire; Loaec, Mikaël; Lainé, Mathilde; Steinbach, Delphine; Choulet, Frédéric; Rimbert, Hélène; Leroy, Philippe; Guilhot, Nicolas; Salse, Jérôme; Feuillet, Catherine; Paux, Etienne; Eversole, Kellye; Adam-Blondon, Anne-Françoise; Quesneville, Hadi

doi:10.1186/s13059-018-1491-4

Cited by 214 publications

(165 citation statements)

References 34 publications

(36 reference statements)

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“…For instance, each DNA TEs (TIRs, MITEs and Helitrons) covered almost the same percentage of the genome with 0.51, 0.72 and 0.72 %, respectively. These coverage patterns are in accordance with most plant genomes that had TEs identification projects(Du et al, 2010;Andorf et al, 2015;Badouin et al, 2017;Alaux et al, 2018).…”

supporting

confidence: 82%

“…However, in the past years, TEs discovery and annotation for the main crops have been emerging with diverse results of coverage, complexity and accuracy. For instance, by using the CLARITE software on the IWGSC RefSeq v1.0 genome assembly, Alaux et al (2018) found over 5 million elements from all types of TEs in wheat. On the other hand, maize repeat elements were annotated with the Ensembl Genomes repeat feature pipeline which comprised the discovery of low complexity regions (Dust) (Morgulis et al, 2006), tandem repeat (TRF) (Benson et al, 1999) and complex repeats (RepeatMasker) (Smit et al, 1996) but lacking on TEs classes and types categorization (Andorf et al, 2015).…”

Section: Resultsmentioning

confidence: 99%

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Genomic re-assessment of the transposable element landscape of the potato genome

Zavallo

Crescente

Gantuz

et al. 2019

Preprint

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Transposable elements (TEs) are DNA sequences with the ability to auto-replicate and move throughout the host genome. TEs are major drivers in stress response and genome evolution. Given their significance, the development of clear and efficient TE annotation pipelines has become essential for many species. The latest de novo TE discovery tools, along with available TEs from Repbase and sRNA-seq data, allowed us to perform a reliable potato TEs detection, classification and annotation through an open-source and freely available pipeline (https://github.com/DiegoZavallo/TE_Discovery). Using a variety of tools, approaches and rules, our pipeline revealed that ca. 16% of the potato genome can be clearly annotated as TEs. Additionally, we described the distribution of the different types of TEs across the genome, where LTRs and MITEs present a clear clustering pattern in pericentromeric and subtelomeric/telomeric regions respectively. Finally, we analyzed the insertion age and distribution of LTR retrotransposon families which display a distinct pattern between the two major superfamilies. While older Gypsy elements concentrated around heterochromatic regions, younger Copia elements located predominantly on euchromatic regions. Overall, we delivered not only a reliable, ready-to-use potato TE annotation files, but also all the necessary steps to perform de novo detection for other species.Key MessageWe provide a comprehensive and reliable potato TE landscape, based on a wide variety of identification tools and integrative approaches, producing clear and ready-to-use outputs for the scientific community.

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supporting

confidence: 82%

Section: Resultsmentioning

confidence: 99%

Genomic re-assessment of the transposable element landscape of the potato genome

Zavallo

Crescente

Gantuz

et al. 2019

Preprint

View full text Add to dashboard Cite

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“…This led to 68 958 SNP markers available for subsequent analyses. Markers were physically mapped on the wheat genome refSeq v1.0 (IWGSC et al ., ) accessible at https://urgi.versailles.inra.fr/jbrowseiwgsc/gmod_jbrowse (Alaux et al ., ).…”

Section: Methodsmentioning

confidence: 97%

Functional mapping of N deficiency‐induced response in wheat yield‐component traits by implementing high‐throughput phenotyping

Jiang

Sun

et al. 2019

The Plant Journal

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As overfertilization leads to environmental concerns and the cost of N fertilizer increases, the issue of how to select crop cultivars that can produce high yields on N‐deficient soils has become crucially important. However, little information is known about the genetic mechanisms by which crops respond to environmental changes induced by N signaling. Here, we dissected the genetic architecture of N‐induced phenotypic plasticity in bread wheat (Triticum aestivum L.) by integrating functional mapping and semiautomatic high‐throughput phenotyping data of yield‐related canopy architecture. We identified a set of quantitative trait loci (QTLs) that determined the pattern and magnitude of how wheat cultivars responded to low N stress from normal N supply throughout the wheat life cycle. This analysis highlighted the phenological landscape of genetic effects exerted by individual QTLs, as well as their interactions with N‐induced signals and with canopy measurement angles. This information may shed light on our mechanistic understanding of plant adaptation and provide valuable information for the breeding of N‐deficiency tolerant wheat varieties.

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“…Although the genomes of grassland plant species are large and will require a large amount of sequencing capacity, some reference genomes are already available for such species (e.g., red clover [114,115], perennial ryegrass [116]), and Italian ryegrass [117], which can help in assembling additional genomes with low coverage data. Furthermore, pangenomic information is becoming available for crop species with similarly large genomes, such as wheat, thanks to the joint efforts of international consortia (e.g., the International Wheat Genome Sequencing Consortium, [118]).…”

Section: Whole Genome Re-sequencingmentioning

confidence: 99%

DNA-Based Assessment of Genetic Diversity in Grassland Plant Species: Challenges, Approaches, and Applications

2019

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Grasslands are wide-spread, multi-species ecosystems that provide many valuable services. Plant genetic diversity (i.e., the diversity within species) is closely linked to ecosystem functioning in grasslands and constitutes an important reservoir of genetic resources that can be used to breed improved cultivars of forage grass and legume species. Assessing genetic diversity in grassland plant species is demanding due to the large number of different species and the level of resolution needed. However, recent methodological advances could help in tackling this challenge at a larger scale. In this review, we outline the methods that can be used to measure genetic diversity in plants, highlighting their strengths and limitations for genetic diversity assessments of grassland plant species, with a special focus on forage plants. Such methods can be categorized into DNA fragment, hybridization array, and high-throughput sequencing (HTS) methods, and they differ in terms of resolution, throughput, and multiplexing potential. Special attention is given to HTS approaches (i.e., plastid genome skimming, whole genome re-sequencing, reduced representation libraries, sequence capture, and amplicon sequencing), because they enable unprecedented large-scale assessments of genetic diversity in non-model organisms with complex genomes, such as forage grasses and legumes. As no single method may be suited for all kinds of purposes, we also provide practical perspectives for genetic diversity analyses in forage breeding and genetic resource conservation efforts.

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Linking the International Wheat Genome Sequencing Consortium bread wheat reference genome sequence to wheat genetic and phenomic data

Cited by 214 publications

References 34 publications

Genomic re-assessment of the transposable element landscape of the potato genome

Genomic re-assessment of the transposable element landscape of the potato genome

Functional mapping of N deficiency‐induced response in wheat yield‐component traits by implementing high‐throughput phenotyping

DNA-Based Assessment of Genetic Diversity in Grassland Plant Species: Challenges, Approaches, and Applications

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