Harbinger-1_Car, a family of Harbinger transposons from the Coffea arabica genome

AGUILERA P.M.; GRABIELE M.

Repbase Reports

Genetic Information Research Institute

Lugar: Cupertino, California; Año: 2021 vol. 10 p. 5416 - 5417

The genome of coffee (Coffea arabica) GCA_003713225.1 v1.0 was de novo searched for short nonautonomous transposable elements to evaluate their impact on genome and gene structure. This approach identified and further characterized a novel family of Harbinger transposons. Consensus sequences were built from total genomic TIR to TIR (Terminal Inverted Repeats) length copies with mean pairwise identity to consensus >90%. The Harbinger-1_Car family characterized by 16 nt TIRs, two pairs of subterminal inverted repeats, 12 and 14 nt in length respectively, and 3 nt TSDs (Target Site Duplications), mainly TTA/TAA sequences. Two major subpopulations occurr in coffee, a) 517 copies of 802 bp in length which carry a full length Dorothy SINE with poly A tail and both TSDs (GAATATACTA/GAACATACTA) at position 489 to 578 of the consensus, and b) 12 copies (701 bp) deprived of the mentioned SINE. Sequences with annotated features are deposited at the Repbase Update database (www.girinst.org).