Main menu

Illuminating the transposon insertion landscape in plants using Cas9-targeted Nanopore sequencing and a novel pipeline


Transposable elements (TEs), which occupy significant portions of most plant genomes, are a major source of genomic novelty, contributing to plant adaptation, speciation and new cultivar production. The often large, complex genomes of plants make identifying TE insertions from short reads challenging, while whole-genome sequencing remains expensive. To expand the toolbox for TE identification in plants, we used the recently developed Cas9-targeted Nanopore sequencing (CANS) approach.

Additionally, as no current bioinformatics tools automatically detect TE insertions after CANS, we developed NanoCasTE, a novel pipeline for target TE insertion discovery. We performed CANS of three copies of EVD retrotransposons in wild-type Arabidopsis thaliana and obtained up to 40× coverage of the targets after only a few hours of sequencing on a MinION sequencer. To estimate the ability to detect new TE insertions, we exploited the A. thaliana ddm1 mutant, which has elevated TE activity.

Using CANS, we detected 84% of these insertions in ddm1 after generating only 4420 Nanopore reads (0.2× genome coverage), and also unambiguously identified their locations, demonstrating the method’s sensitivity. CANS of pooled (∼50 plants) ddm1 plants captured >800 EVD insertions, especially in centromeric regions. CANS also identified insertions of a Ty3/Gypsy retrotransposon in the genomes of two Aegilops tauschii plants, a species with a large genome.

Authors: Ilya Kirov, Pavel Merkulov, Sofya Gvaramiya, Roman Komakhin, Murad Omarov, Maxim Dudnikov, Alina Kocheshkova, Alexander Soloviev, Gennady Karlov, Mikhail Divashuk

入门指南

购买 MinION 启动包 Nanopore 商城 测序服务提供商 全球代理商

联系我们

Intellectual property Cookie policy Corporate reporting Privacy policy Terms & conditions Accessibility

关于 Oxford Nanopore

Contact us 领导团队 媒体资源和联系方式 投资者 在 Oxford Nanopore 工作 BSI 27001 accreditationBSI 90001 accreditationBSI mark of trust
Chinese flag