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Detection of transcriptomic structural variations in wild rice using Nanopore direct RNA sequencing.
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International audience. Oryza australiensis is a wild rice species native to Australia, known for adaptation to harsh environments. Despite its ecological importance, particularly its tolerance to heat stress, O.australiensis remains relatively understudied compared to other rice species. Genomic studies have highlighted its evolutionary genetic history, as well as a large number of insertions of transposable elements compared to cultivated rice leading to a doubling of genome size [1] .Transposable elements (TE) are mobile genetic elements abundant in plant genomes. Knowledge of their impact on the structure, function and evolution of genome, these mobile entities can provide a more precise picture of rice genome dynamics.Nanopore sequencing enables whole RNA molecules to be sequenced directly in real time, using nanopores and electrical potential. It produces long reads with a median size of around 20kb. This technology is revolutionizing genomics.Thanks to Nanopore novelties, this technology allows direct sequencing of native RNA strands (DRS), offering advantages in capturing full-length transcripts and identifying various SVs such as insertions, deletions, inversions, and translocations.It is a tool dedicated to the detection of structural variation in genomes linked to TE.We sequenced the transcriptome of 2 O.australiensis plants (one under stress-free condition and the other under heat-stress condition). We then detected alternative isoforms due to TE insertions. The biological question is whether we have more chimerictranscripts in stress conditions, and in which gene type/function.Nanopore direct RNA sequencing offers a comprehensive view of transcriptomes enabling the discovery of novel RNA isoforms and elucidation of complex gene expression patterns. This approach will improve our understanding of gene regulation and the functional impact of transposable element in genomes.References[1] - Piegu B et al. Doubling genome size without polyploidization: dynamics of retrotransposition-driven genomic expansions in Oryza australiensis, a wild relative of rice. Genome Res. 2006 Oct;16(10):1262-9
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