Short transposable elements from the chili pepper genome (Capsicum annuum)

GRABIELE M.; AGUILERA P.M.

Repbase Reports

Genetic Information Research Institute

Lugar: Cupertino, California; Año: 2021 vol. 7 p. 3981 - 3984

The genome of the chili pepper Capsicum annuum GCF_000710875.1 v1.0 was de novo searched for short nonautonomous transposable elements to evaluate their impact on genome and gene structure. In this first approach, four novel elements were identified and further characterized. SINE2-1_Can is a SINE family of the SINE2/tRNA clade of Non-LTR Retrotransposons which holds poly A tail. There exist two major subpopulations (a and b) which consensus share 70.1% sequence similarity. SINE2-1a_Can reference sequence was generated from 130 entire length elements with mean 91.4% identity to consensus and is 91.9% similar to SINE-1_Aip. SINE2-1b_Can reference sequence was generated from 250 entire length elements with mean 90.7% identity to consensus and is 84.5% similar to Lj_SINE-3. hAT-NA1_Can, is a hAT Transposon with typical 14 nt TIRs and 8 nt TSDs. Its reference sequence (189 pb) was generated from 30 entire length elements with mean 89.3% identity to consensus, which is 85% and 82.1% similar to SINE_SO and SINE1_SO, respectively. LTR-1_Can-LTR, is a short (278 bp) LTR Retrotransposon with 82 nt LTRs and 5 nt TSDs. Its reference sequence was generated from 100 entire length elements with mean 82% identity to consensus, which is 61.1% similar to LTR-16_OS-LTR. Sequences with annotated features are deposited at the Repbase Update database (www.girinst.org).