LTR retrotransposon landscape in Medicago truncatula: more rapid removal than in rice

BMC Genomics
Hao Wang, Jin-Song Liu

Abstract

Long terminal repeat retrotransposons (LTR elements) are ubiquitous Eukaryotic TEs that transpose through RNA intermediates. Accounting for significant proportion of many plant genomes, LTR elements have been well established as one of the major forces underlying the evolution of plant genome size, structure and function. The accessibility of more than 40% of genomic sequences of the model legume Medicago truncatula (Mt) has made the comprehensive study of its LTR elements possible. We use a newly developed tool LTR_FINDER to identify LTR retrotransposons in the Mt genome and detect 526 full-length elements as well as a great number of copies related to them. These elements constitute about 9.6% of currently available genomic sequences. They are classified into 85 families of which 64 are reported for the first time. The majority of the LTR retrotransposons belong to either Copia or Gypsy superfamily and the others are categorized as TRIMs or LARDs by their length. We find that the copy-number of Copia-like families is 3 times more than that of Gypsy-like ones but the latter contribute more to the genome. The analysis of PBS and protein-coding domain structure of the LTR families reveals that they tend to use only 4-5 types of ...Continue Reading

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Citations

Mar 27, 2009·Chromosome Research : an International Journal on the Molecular, Supramolecular and Evolutionary Aspects of Chromosome Biology·Beatrice Weber, Thomas Schmidt
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May 1, 2021·International Journal of Molecular Sciences·Ewa Filip, Lidia Skuza

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Software Mentioned

SCAN
FINDER
PLOTCON
HMMER
tRNAscan
SE
CLUSTALW
hmmsearch
PS
LTR

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