Your browser doesn't support javascript.
loading
Epigenetic Stress and Long-Read cDNA Sequencing of Sunflower (Helianthus annuus L.) Revealed the Origin of the Plant Retrotranscriptome.
Kirov, Ilya; Merkulov, Pavel; Polkhovskaya, Ekaterina; Konstantinov, Zakhar; Kazancev, Mikhail; Saenko, Ksenia; Polkhovskiy, Alexander; Dudnikov, Maxim; Garibyan, Tsovinar; Demurin, Yakov; Soloviev, Alexander.
Afiliación
  • Kirov I; All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya Str. 42, 127550 Moscow, Russia.
  • Merkulov P; Moscow Institute of Physics and Technology, 141701 Dolgoprudny, Russia.
  • Polkhovskaya E; All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya Str. 42, 127550 Moscow, Russia.
  • Konstantinov Z; Moscow Institute of Physics and Technology, 141701 Dolgoprudny, Russia.
  • Kazancev M; All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya Str. 42, 127550 Moscow, Russia.
  • Saenko K; All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya Str. 42, 127550 Moscow, Russia.
  • Polkhovskiy A; All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya Str. 42, 127550 Moscow, Russia.
  • Dudnikov M; Moscow Institute of Physics and Technology, 141701 Dolgoprudny, Russia.
  • Garibyan T; All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya Str. 42, 127550 Moscow, Russia.
  • Demurin Y; Federal Research Center of Biological Plant Protection, 350039 Krasnodar, Russia.
  • Soloviev A; All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya Str. 42, 127550 Moscow, Russia.
Plants (Basel) ; 11(24)2022 Dec 19.
Article en En | MEDLINE | ID: mdl-36559691
Transposable elements (TEs) contribute not only to genome diversity but also to transcriptome diversity in plants. To unravel the sources of LTR retrotransposon (RTE) transcripts in sunflower, we exploited a recently developed transposon activation method ('TEgenesis') along with long-read cDNA Nanopore sequencing. This approach allows for the identification of 56 RTE transcripts from different genomic loci including full-length and non-autonomous RTEs. Using the mobilome analysis, we provided a new set of expressed and transpositional active sunflower RTEs for future studies. Among them, a Ty3/Gypsy RTE called SUNTY3 exhibited ongoing transposition activity, as detected by eccDNA analysis. We showed that the sunflower genome contains a diverse set of non-autonomous RTEs encoding a single RTE protein, including the previously described TR-GAG (terminal repeat with the GAG domain) as well as new categories, TR-RT-RH, TR-RH, and TR-INT-RT. Our results demonstrate that 40% of the loci for RTE-related transcripts (nonLTR-RTEs) lack their LTR sequences and resemble conventional eucaryotic genes encoding RTE-related proteins with unknown functions. It was evident based on phylogenetic analysis that three nonLTR-RTEs encode GAG (HadGAG1-3) fused to a host protein. These HadGAG proteins have homologs found in other plant species, potentially indicating GAG domestication. Ultimately, we found that the sunflower retrotranscriptome originated from the transcription of active RTEs, non-autonomous RTEs, and gene-like RTE transcripts, including those encoding domesticated proteins.
Palabras clave
Texto completo
Añadir a Mi BVS
Imprimir
XML
PubMed Links
Buscar en Google

Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Idioma: En Revista: Plants (Basel) Año: 2022 Tipo del documento: Article País de afiliación: Rusia Pais de publicación: Suiza
Texto completo
Añadir a Mi BVS
Imprimir
XML
PubMed Links
Buscar en Google

Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Idioma: En Revista: Plants (Basel) Año: 2022 Tipo del documento: Article País de afiliación: Rusia Pais de publicación: Suiza