Retroposons from the yerba mate genome (Ilex paraguariensis)

AGUILERA P.M.; GRABIELE M.

Repbase Reports

Genetic Information Research Institute

Lugar: Cupertino, California; Año: 2021 vol. 8 p. 4627 - 4636

The genome of yerba mate (Ilex paraguariensis) GCA_905181385.1 was de novo searched for repetitive elements followed to classification, consensus sequence determination from total genomic full length copies and further characterization to support reference sequence based annotation. This approach identified novel transposable elements, eight LTR Retrotransposons with 5 nt TSDs and two SINE families of the SINE2/tRNA clade of Non-LTR Retrotransposons: LTR-1_Ipa-LTR (LTR portion; 1206 bp; 100 seqs PI 83.6%), LTR-2a_Ipa-LTR (LTR portion; 2279 bp; 100 seqs PI 86.4%), LTR-2b_Ipa-LTR (LTR portion; 2269 bp; 45 seqs PI 90.9%), LTR-2c_Ipa-LTR (LTR portion; 2175 bp; 50 seqs PI 86.7%), LTR-3_Ipa (nonautonomous; 1795 bp; 194 nt LTRs; 25 seqs PI 91.2%), LTR-4a_Ipa (nonautonomous; 481 bp; 178 nt LTRs; 120 seqs PI 90.4%) arranged single or in tandem structures up to 15 repetitions, LTR-4b_Ipa (nonautonomous; 539 bp; 205 nt LTRs; 25 seqs PI 99.9%) arranged single or in tandem structures up to 20 repetitions, LTR-5_Ipa (nonautonomous; 248 bp; 72 nt LTRs; 300 seqs PI 82.7%), SINE2-2_Ipa (nonautonomous; 179 bp; poly A tail; 6, 8, 13 or 14 nt TSDs; consensus of total genomic 13 seqs, 6 full length, 7 insertional events, PI 89.7%) and SINE2-3_Ipa (nonautonomous; 250 bp; poly A tail; 100 seqs PI 87.8%). Sequences with annotated features are deposited at the Repbase Update database (www.girinst.org).