Cas9‐targeted Nanopore sequencing rapidly elucidates the transposition preferences and DNA methylation profiles of mobile elements in plants

Author:

Merkulov Pavel12ORCID,Gvaramiya Sofya1ORCID,Dudnikov Maxim12ORCID,Komakhin Roman1ORCID,Omarov Murad1,Kocheshkova Alina1ORCID,Konstantinov Zakhar1ORCID,Soloviev Alexander134ORCID,Karlov Gennady1ORCID,Divashuk Mikhail1ORCID,Kirov Ilya12ORCID

Affiliation:

1. All‐Russia Research Institute of Agricultural Biotechnology Moscow 127550 Russia

2. Moscow Institute of Physics and Technology Dolgoprudny 141701 Russia

3. All‐Russia Center for Plant Quarantine Ramenski 140150 Russia

4. N.V. Tsitsin Main Botanical Garden of the Russian Academy of Sciences Moscow 127276 Russia

Abstract

ABSTRACTTransposable element insertions (TEIs) are an important source of genomic innovation by contributing to plant adaptation, speciation, and the production of new varieties. The often large, complex plant genomes make identifying TEIs from short reads difficult and expensive. Moreover, rare somatic insertions that reflect mobilome dynamics are difficult to track using short reads. To address these challenges, we combined Cas9‐targeted Nanopore sequencing (CANS) with the novel pipeline NanoCasTE to trace both genetically inherited and somatic TEIs in plants. We performed CANS of the EVADÉ (EVD) retrotransposon in wild‐type Arabidopsis thaliana and rapidly obtained up to 40× sequence coverage. Analysis of hemizygous T‐DNA insertion sites and genetically inherited insertions of the EVD transposon in the ddm1 (decrease in DNA methylation 1) genome uncovered the crucial role of DNA methylation in shaping EVD insertion preference. We also investigated somatic transposition events of the ONSEN transposon family, finding that genes that are downregulated during heat stress are preferentially targeted by ONSENs. Finally, we detected hypomethylation of novel somatic insertions for two ONSENs. CANS and NanoCasTE are effective tools for detecting TEIs and exploring mobilome organization in plants in response to stress and in different genetic backgrounds, as well as screening T‐DNA insertion mutants and transgenic plants.

Funder

Ministry of Science and Higher Education of the Russian Federation

Russian Science Foundation

Publisher

Wiley

Subject

Plant Science,General Biochemistry, Genetics and Molecular Biology,Biochemistry

Cited by 1 articles. 订阅此论文施引文献 订阅此论文施引文献,注册后可以免费订阅5篇论文的施引文献,订阅后可以查看论文全部施引文献

1. Toward Transgene-Free Transposon-Mediated Biological Mutagenesis for Plant Breeding;International Journal of Molecular Sciences;2023-12-02

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