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

BMC Genomics
Hao Wang, Jin-Song Liu


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


Jan 29, 1986·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·R B Flavell
Nov 1, 1996·Science·P SanMiguelJ L Bennetzen
May 29, 2000·Trends in Genetics : TIG·P RiceA Bleasby
Feb 14, 2003·Bioinformatics·Eugene M McCarthy, John F McDonald
Mar 20, 2003·Plant Physiology·Peter H Graham, Carroll P Vance
Jul 30, 2003·Molecular Biology and Evolution·Eric W GankoJohn F McDonald
Mar 9, 2004·Genome Biology·Eugene M McCarthy, John F McDonald
Jul 9, 2004·Proceedings of the National Academy of Sciences of the United States of America·Jianxin Ma, Jeffrey L Bennetzen
Jan 26, 2005·Molecular Genetics and Genomics : MGG·Pavel NeumannJirí Macas
Aug 12, 2005·Cytogenetic and Genome Research·C Vitte, O Panaud
Dec 31, 2005·Nucleic Acids Research·Robert D FinnAlex Bateman
Aug 18, 2006·BMC Evolutionary Biology·Chunguang DuJoachim Messing
Sep 28, 2006·Proceedings of the National Academy of Sciences of the United States of America·Steven B CannonNevin D Young
Nov 15, 2006·Proceedings of the National Academy of Sciences of the United States of America·Clémentine Vitte, Jeffrey L Bennetzen
Dec 5, 2006·Nucleic Acids Research·UNKNOWN UniProt Consortium
May 10, 2007·Molecular Biology and Evolution·Koichiro TamuraSudhir Kumar
Sep 27, 2007·Nucleic Acids Research·C LlorénsA Moya
Nov 7, 2007·Nature Reviews. Genetics·Thomas WickerAlan H Schulman

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