SINE retroposons from the Coffea arabica genome

GRABIELE M.; AGUILERA P.M.

Repbase Reports

Genetic Information Research Institute

Lugar: Cupertino, California; Año: 2021 vol. 7 p. 3985 - 3991

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. In this first approach, seven novel SINE families of the SINE2/tRNA clade of Non-LTR Retrotransposons were identified and further characterized, all of them with poly A tail. SINE2-1_Car (304 bp) reference sequence was generated from 80 entire length elements with mean 89.2% identity to consensus. SINE2-2_Car (260 bp) reference sequence was generated from 40 entire length elements with mean 85.1% identity to consensus. SINE2-3_Car (213 bp) reference sequence was generated from 60 entire length elements with mean 78.7% identity to consensus. SINE2-4_Car (212 bp) reference sequence was generated from 40 entire length elements with mean 79.2% identity to consensus. SINE2-5_Car (192 bp) reference sequence was generated from 120 entire length elements with mean 90.5% identity to consensus. Giuseppina (117 bp) reference sequence was generated from 80 entire length elements with mean 77.1% identity to consensus. Dorothy, with 91 bp and complete lack of the tRNA-unrelated region is one of the smallest and unusual plant SINEs. Its reference sequence was generated from 1000 entire length elements with mean 83.4% identity to consensus. There exist 622 copies of Dorothy in coffee flanked by 10 nt TSDs (GAATATACTA/GAACATACTA) within a Harbinger-like element (817 nt; 54 nt TIRs) which TIRs and next 100 nt are 70% similar to corresponding regions of Harbinger-N1_NS and DNA3-6_Stu. Sequences with annotated features are deposited at the Repbase Update database (www.girinst.org).