Marie-Christine Carpentier, from the Genome and Plant Development Laboratory in France, presented at London Calling 2019 on “Using long-read nanopore sequencing to unravel structural variations in plants.” We have been trying plant genome sequencing and want to learn more. Carpentier spoke about transposable elements. Mobile elements can move within a genome. Carpentier noted that the bigger the genome, the higher the transposable elements (TEs) percentage. Their question was how do TEs contribute to genomic diversity in rice. In 2014, the 3000 genomes project created an enormous dataset in rice. The 3000 genomes have a mean coverage of 14X and represent a “good representation” of geographical regions. In the reference genome, they know the position of TEs. However, in the 3000 genomes, they don’t. Carpentier developed a pipeline to detect TEs insertion polymorphisms (TIPs). Trackposon was the pipeline they created to identify TEs. In total, they identified 31 TE families and over 53,000 TE insertions. To validate Trackposon, they used nanopore sequencing. Trackposon validation indicated a sensitivity of 81% and a specificity of 94.5%. Carpentier explained that long-read sequencing using Nanopore technology unambiguously detects TEs in rice genomes. The team then used cDNA Nanopore sequencing to identify active TE. They observed differences in TE activity. Their approach is easy to follow and powerful. The biology of transposable elements can now be studied and compared in different genomes.
