Genome wide annotation and characterization of young, intact long terminal repeat retrotransposons (In-LTR-RTs) of seven
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ORIGINAL PAPER
Genome wide annotation and characterization of young, intact long terminal repeat retrotransposons (In‑LTR‑RTs) of seven legume species Pawan Kumar Jayaswal1,2 · Asheesh Shanker2,3 · Nagendra Kumar Singh1 Received: 29 May 2019 / Accepted: 2 September 2020 © Springer Nature Switzerland AG 2020
Abstract Availability of genome sequence of different legume species has provided an opportunity to characterize the abundance, distribution, and divergence of canonical intact long terminal retrotransposons (In-LTR-RT) superfamilies. Among seven legume species, Arachis ipaensis (Aip) showed the highest number of full-length canonical In-LTR-RTs (3325), followed by Glycine max (Gma, 2328), Vigna angularis (Van, 1625), Arachis durensis (Adu, 1348), Lotus japonicus (Lja, 1294), Medicago truncatula (Mtr, 788), and Circer arietinum (Car, 124). Divergence time analysis demonstrated that the amplification timeframe of LTR-RTs dramatically varied in different families. The average insertion time of Copia element varied from 0.51 (Van) to 1.37 million years ago (Mya) (Adu, and Aip), whereas that of Gypsy was between 0.22 (Mtr) and 1.82 Mya (Adu). Bayesian phylogenetic tree analysis suggested that the 1397 and 1917 reverse transcriptase (RT) domains of Copia and Gypsy families of the seven legume species were clustered into 7 and 14 major groups, respectively. The highest proportion (approximately 94.79–100%) of transposable element (TE)-associated genes assigned to pathways was mapped to metabolism-related pathways in all species. The results enabled the structural understanding of full-length In-LTR-RTs and will be valuable resource for the further study of the impact of TEs on gene structure and expression in legume species. Keywords Copia · Gypsy · Intact LTR · Long terminal repeat · Transposable element
Introduction TEs are important components of the genome that influence and drive the evolution of the genome structure (Feschotte and Pritham 2007; Wicker et al. 2018). TEs are classified into two main categories: class I retrotransposons transpose through the reverse transcription process and class II DNA transposons contain only DNA and transpose directly through the cut-and-paste mechanism (Piegu et al. 2015). A typical full-length intact LTR-RT (In-LTR-RT) element is composed Electronic supplementary material The online version of this article (https://doi.org/10.1007/s10709-020-00103-5) contains supplementary material, which is available to authorized users. * Nagendra Kumar Singh [email protected] 1
National Institute for Plant Biotechnology, New Delhi 110012, India
2
Banasthali Vidyapith, Banasthali, Rajasthan 228371, India
3
Department of Bioinformatics, Central University of South Bihar, Gaya 824236, India
of two identical or similar LTRs, a 4–6-bp short direct target site duplication (TSD) at the 5′ and 3′ regions, a primerbinding site (PBS), a polypurine tract (PPT), and two functional genes, namely gag and pol. pol includes genes encoding aspartic protease (AP), integrase (IN), RNA
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