Diverse and mobile:eccDNA‐based identification of carrot low‐copy‐numberLTRretrotransposons active in callus cultures

Abstract

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-copynumber 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.

Long-read sequencing of extrachromosomal circular DNA and genome assembly of aSolanum lycopersicumbreeding line revealed active LTR retrotransposons originating fromS. peruvianumL. introgressions

“…Short read sequencing has been frequently used for eccDNA detection (Esposito et al, 2019; Kwolek et al, 2022; Lanciano et al, 2017). Utilization of long-read WGS and eccDNA sequencing allowed us to accurately determine the structure and full-length sequence of the eccDNAs.…”

Specific suppression of long terminal repeat retrotransposon mobilization in plants

“…DNA transposons), sequence rearrangements, or changes in epigenetic state. Although rice is virtually the only major crop where LTR-TE activation during micropropagation has been extensively described, there are reports of LTR-TE mobilization occurring in tissue culture of other plant species, including tobacco ( Nicotiana tabacum ) ( Hirochika, 1993 ), sweet potato ( Ipomoea batatas ) ( Tahara et al, 2004 ), carrot ( Daucus carota ) ( Kwolek et al, 2022 ), Medicago truncatula (d’ Erfurth et al, 2003 ), bamboo ( Phyllostachys edulis ) ( Zhou et al, 2018 ), and date palm ( Phoenix dactylifera ) ( Mirani et al, 2020 ). Considering that for many crops the genetic resources are still limited, it could be possible that LTR-TE mobilization during plant regeneration has been mostly overlooked.…”

The power of retrotransposons in high-throughput genotyping and sequencing

“…Changes in the copy number of these repeats and internal rearrangements on both homologous chromosomes occur after the induction of recombination processes during prophase of meiosis ( Belyayev et al., 2010 ). TEs create genomic variation in plants, which has been revealed by certain studies ( Kalendar et al., 2000 ; Belyayev et al., 2010 ; Wicker et al., 2018 ; Kwolek et al., 2022 ). According to a comparative study on different plant genomes, most sequences associated with TEs come from modern insertions ( El Baidouri and Panaud, 2013 ).…”