Details

Autor(en) / Beteiligte

• Kwolek, Kornelia
• Kędzierska, Patrycja
• Hankiewicz, Magdalena
• Mirouze, Marie
• Panaud, Olivier
• Grzebelus, Dariusz
• Macko-Podgórni, Alicja

Titel

Diverse and mobile - eccDNA-based identification of carrot low-copy LTR retrotransposons active in callus cultures

Ist Teil von

• The Plant journal : for cell and molecular biology, 2022-04

Ort / Verlag

England

Erscheinungsjahr

2022

Quelle

Alma/SFX Local Collection

Beschreibungen/Notizen

• LTR 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, 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 a 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 5,976 carrot LTR-RTs, of which 2,053 and 1,660 were attributed to Copia and Gypsy superfamilies, respectively. They were further classified into lineages, families and subfamilies. More diverse LTR-RT lineages, i.e. those 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 LTR-RT subfamilies, e.g. those belonging to the DcAle lineage, significantly contributed to the carrot genome diversity, as a result of their ongoing 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.