@article{fdi:010085079,
  title = {{D}iverse and mobile : ecc{DNA}-based identification of carrot low-copy-number {LTR} retrotransposons active in callus cultures},
  author = {{K}wolek, {K}. and {K}edzierska, {P}. and {H}ankiewicz, {M}. and {M}irouze, {M}arie and {P}anaud, {O}. and {G}rzebelus, {D}. and {M}acko-{P}odgorni, {A}.},
  editor = {},
  language = {{ENG}},
  abstract = {{L}ong terminal repeat retrotransposons ({LTR}-{RT}s) are mobilized via an {RNA} intermediate using a 'copy and paste' mechanism, and account for the majority of repetitive {DNA} in plant genomes. {A}s a side effect of mobilization, the formation of {LTR}-{RT}-derived extrachromosomal circular {DNA}s (ecc{DNA}s) occurs. {T}hus, high-throughput sequencing of ecc{DNA} can be used to identify active {LTR}-{RT}s in plant genomes. {D}espite the release of a reference genome assembly, carrot {LTR}-{RT}s have not yet been thoroughly characterized. {LTR}-{RT}s are abundant and diverse in the carrot genome. {W}e identified 5976 carrot {LTR}-{RT}s, 2053 and 1660 of which were attributed to {C}opia and {G}ypsy superfamilies, respectively. {T}hey were further classified into lineages, families and subfamilies. {M}ore diverse {LTR}-{RT} lineages, i.e. lineages comprising many low-copy-number subfamilies, were more frequently associated with genic regions. {C}ertain {LTR}-{RT} lineages have been recently active in {D}aucus carota. {I}n particular, low-copy-number {LTR}-{RT} subfamilies, e.g. those belonging to the {D}c{A}le lineage, have significantly contributed to carrot genome diversity as a result of continuing activity. {W}e utilized ecc{DNA} sequencing to identify and characterize two {D}c{A}le subfamilies, {A}lex1 and {A}lex3, active in carrot callus. {W}e documented 14 and 32 de novo insertions of {A}lex1 and {A}lex3, respectively, which were positioned in non-repetitive regions.},
  keywords = {{D}aucus carota ; extrachromosomal circular {DNA} ; active retrotransposons ; long terminal repeats ; {LTR}-{RT}s ; transposition},
  booktitle = {},
  journal = {{P}lant {J}ournal},
  volume = {[{E}arly access]},
  numero = {},
  pages = {[14 p.]},
  ISSN = {0960-7412},
  year = {2022},
  DOI = {10.1111/tpj.15773},
  URL = {https://www.documentation.ird.fr/hor/fdi:010085079},
}