Retrotranspositional landscape of Asian rice revealed by 3000 genomes

Carpentier, Marie-Christine; Manfroi, Ernandes; Wei, Fu‐Jin; Wu, Huimin; Lasserre, Éric; Llauro, Christel; Debladis, Emilie; Akakpo, Roland; Hsing, Yue‐Ie C.; Panaud, Olivier

doi:10.1038/s41467-018-07974-5

Cited by 121 publications

(143 citation statements)

References 53 publications

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“…Despite a relatively narrow genetic diversity, the 25,000 cultivars grown around the world today exhibit an extraordinary phenotypic diversity and the underlying allelic variants are being progressively identified thanks to the advent of high-throughput genome sequencing. In this context, we show that TIPs, which to date have been ignored from population genomic studies in tomato, are an important diversifying force to consider, as has been proposed for other plant species 27,33,34,[52][53][54][55][56][57] . In particular, most TE insertions are low frequency variants, they are typically not tagged by SNPs, representing a previously uncharacterized source of phenotypic variation.…”

Section: Discussionmentioning

confidence: 78%

The impact of transposable elements on tomato diversity

Domínguez

Dugas

Benchouaia

et al. 2020

Preprint

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Tomatoes come in a multitude of shapes and flavors despite a narrow genetic pool. Here, we leveraged whole-genome resequencing data available for 602 cultivated and wild accessions to determine the contribution of transposable elements (TEs) to tomato diversity. We identified 6,906 TE insertions polymorphisms (TIPs), which result from the mobilization of 337 distinct TE families. Most TIPs are low frequency variants and disproportionately located within or adjacent to genes involved in environmental response. In addition, we show that genic TE insertions tend to have strong transcriptional effects and can notably lead to the generation of multiple transcript isoforms. We also uncovered through genome-wide association studies (GWAS) ~180 TIPs associated with extreme variations in major agronomic traits or secondary metabolites. Importantly, these TIPs tend to affect loci that are distinct from those tagged by SNPs. Collectively, our findings suggest a unique and important role for TE mobilization in tomato diversification, with important implications for future breeding.

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Section: Discussionmentioning

confidence: 78%

The impact of transposable elements on tomato diversity

Domínguez

Dugas

Benchouaia

et al. 2020

Preprint

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“…Carpentier et al . () developed a new software package, Trackposon , that was used to identify retrotransposon TIPs among the 3000 rice genomes (Rice genome project, ). This method is a two‐step procedure consisting of first mapping the Illumina reads onto a consensus TE sequence and then mapping the un‐mapped paired reads onto the reference rice genome.…”

Section: Te Activity In Cultivated Ricementioning

confidence: 99%

“…The efficiency of GWAS is such that it is usually able to detect associations between traits and alleles with a minimum allele frequency (MAF) of at least 5% (Willard, 2013). However, the majority of TIPs in rice are found at a much lower frequency (Carpentier et al, 2019). Consequently, we had to adapt our method to this peculiarity of TE insertions.…”

Section: Te-gwasa New Strategy To Unravel the Functional Impact Ofmentioning

confidence: 99%

The impact of transposable elements on the structure, evolution and function of the rice genome

et al. 2020

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Summary Transposable elements (TEs) are ubiquitous in plants and are the primary genomic component of the majority of taxa. Knowledge of their impact on the structure, function and evolution of plant genomes is therefore a priority in the field of genomics. Rice, as one of the most prevalent crops for food security worldwide, has been subjected to intense research efforts over recent decades. Consequently, a considerable amount of genomic resources has been generated and made freely available to the scientific community. These can be exploited both to improve our understanding of some basic aspects of genome biology of this species and to develop new concepts for crop improvement. In this review, we describe the current knowledge on how TEs have shaped rice chromosomes and propose a new strategy based on a genome‐wide association study (GWAS) to address the important question of their functional impact on this crop.

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“…Detailed analyses suggested that there were also examples of gene fragments that had been captured and moved by Helitron transposons (Lai et al ., ; Du et al ., ; Morgante et al ., ). Studies of TE variability in plants on a genome‐wide scale have largely focused on using short‐read resequencing data to map new insertions (Quadrana et al ., ; Carpentier et al ., ; Tian et al ., ; Lai et al ., ; Stuart et al ., ); however, this approach can be complicated by non‐alignable sequences and the repetitive nature of TEs.…”

Section: Introductionmentioning

confidence: 99%

Transposable elements contribute to dynamic genome content in maize

et al. 2019

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Transposable elements (TEs) are ubiquitous components of eukaryotic genomes and can create variation in genome organization and content. Most maize genomes are composed of TEs. We developed an approach to define shared and variable TE insertions across genome assemblies and applied this method to four maize genomes (B73, W22, Mo17 and PH207) with uniform structural annotations of TEs. Among these genomes we identified approximately 400 000 TEs that are polymorphic, encompassing 1.6 Gb of variable TE sequence. These polymorphic TEs include a combination of recent transposition events as well as deletions of older TEs. There are examples of polymorphic TEs within each of the superfamilies of TEs and they are found distributed across the genome, including in regions of recent shared ancestry among individuals. There are many examples of polymorphic TEs within or near maize genes. In addition, there are 2380 gene annotations in the B73 genome that are located within variable TEs, providing evidence for the role of TEs in contributing to the substantial differences in annotated gene content among these genotypes. TEs are highly variable in our survey of four temperate maize genomes, highlighting the major contribution of TEs in driving variation in genome organization and gene content.

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Retrotranspositional landscape of Asian rice revealed by 3000 genomes

Cited by 121 publications

References 53 publications

The impact of transposable elements on tomato diversity

The impact of transposable elements on tomato diversity

The impact of transposable elements on the structure, evolution and function of the rice genome

Transposable elements contribute to dynamic genome content in maize

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