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Using long-read nanopore sequencing to unravel structural genomic variations in plants
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International audience. Transposable elements (TEs) are mobile DNA elements potentially able to move and multiply within genomes. TEs account for 40 % of total size genome in the cultivated rice, Oryza sativa, and 10 % in Arabidopsis thaliana and their insertion polymorphisms are responsible for most of the structural variations between varieties or ecotypes of these two species. Although large genomic datasets are available to study the diversity within these two species, most of these datasets consist in Illumina short reads files and not in fully assembled genomes. To detect TE insertion polymorphisms (TIPs) in these large datasets, we developed a new software, TRACKPOSON and applied it to characterise TIPs for 31 families of retrotransposons in 3,000 cultivated rice varieties. We used DNA Nanopore sequencing to unambiguously validate our in silico results.We further took advantage of cDNA Nanopore sequencing to analyze structural variation within transcripts in rice and Arabidopsis and to improve transcriptome annotation with alternative splicing detection. Moreover, d for the first time we could detect long reads corresponding to entire TE transcripts.
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