期刊
PLANT JOURNAL
卷 110, 期 6, 页码 1811-1828出版社
WILEY
DOI: 10.1111/tpj.15773
关键词
Daucus carota; extrachromosomal circular DNA; active retrotransposons; long terminal repeats; LTR-RTs; transposition
资金
- Polish Ministry of Education and Science (MEiN)
- French Ministry of 'Enseignement Superieur et de la Recherche' (Polish-French bilateral program POLONIUM)
- Polish National Science Center (NCN) [MINIATURA1 2017/01/X/NZ9/00930, OPUS17 2019/33/B/NZ9/00757]
- University of Agriculture in Krakow
- (MEiN) [ANR-10-LABX-41]
- 'Ecole Universitaire de Recherche (EUR)' TULIP-GS [ANR-18-EURE-0019]
- French National Agency for Research [ANR-21-CE20-0047]
- Agence Nationale de la Recherche (ANR) [ANR-21-CE20-0047] Funding Source: Agence Nationale de la Recherche (ANR)
Long terminal repeat retrotransposons (LTR-RTs) make up a significant portion of repetitive DNA in plant genomes, including the carrot genome. Certain LTR-RT lineages have been active in carrots and have contributed to genome diversity. Low-copy-number LTR-RT subfamilies, such as those belonging to the DcAle lineage, have played a significant role in this diversity.
Long terminal repeat retrotransposons (LTR-RTs) are mobilized via an RNA intermediate using a 'copy and paste' mechanism, and account for the majority of repetitive DNA in plant genomes. As a side effect of mobilization, the formation of LTR-RT-derived extrachromosomal circular DNAs (eccDNAs) occurs. Thus, high-throughput sequencing of eccDNA can be used to identify active LTR-RTs in plant genomes. Despite the release of a reference genome assembly, carrot LTR-RTs have not yet been thoroughly characterized. LTR-RTs are abundant and diverse in the carrot genome. We identified 5976 carrot LTR-RTs, 2053 and 1660 of which were attributed to Copia and Gypsy superfamilies, respectively. They were further classified into lineages, families and subfamilies. More diverse LTR-RT lineages, i.e. lineages comprising many low-copy-number subfamilies, were more frequently associated with genic regions. Certain LTR-RT lineages have been recently active in Daucus carota. In particular, low-copy-number LTR-RT subfamilies, e.g. those belonging to the DcAle lineage, have significantly contributed to carrot genome diversity as a result of continuing activity. We utilized eccDNA sequencing to identify and characterize two DcAle subfamilies, Alex1 and Alex3, active in carrot callus. We documented 14 and 32 de novo insertions of Alex1 and Alex3, respectively, which were positioned in non-repetitive regions.
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