Structural Diversity of a Novel LTR Retrotransposon, RTPOSON, in the Genus Oryza

Evolutionary Bioinformatics Online
Yu-Chia HsuYong-Pei Wu

Abstract

Retrotransposons with long terminal repeats (LTRs) are the most abundant transposable elements in plant genomes. A novel LTR retrotransposon named RTPOSON primarily occurs in the genus Oryza and in several species of the Poaceae family. RTPOSON has been identified in the Ty1-copia group of retrotransposons because two of its open reading frames encode an uncharacterized protein and UBN2_2 and zinc knuckle, respectively. More than 700 RTPOSONs were identified in Oryza genomes; 127 RTPOSONs with LTRs and gag-pol elements were classified into three subgroups. The subgroup RTPOSON_sub3 had the smallest DNA size and 97% (32/33) of RTPOSON elements from Oryza punctata are classified in this group. The insertion time of these RTPOSONs varied and their proliferation occurred within the last 8 Mya, with two bursting periods within the last 1.5-5.0 Mya. A total of 37 different orthologous insertions of RTPOSONs, with different nested transposable elements and gene fragments, were identified by comparing the genomes of ssp. japonica cv. Nipponbare and ssp. indica cv. 93-11. A part of intact RTPOSON elements was evolved independently after the divergence of indica and japonica. In addition, intact RTPOSONs and homologous fragments were pre...Continue Reading

References

Nov 1, 1989·Plant Molecular Biology·K Akama, S Tanifuji
Sep 10, 1998·Nature Genetics·P SanMiguelJ L Bennetzen
Feb 26, 2000·Annual Review of Genetics·A Kumar, J L Bennetzen
Dec 29, 2000·Nature·UNKNOWN Arabidopsis Genome Initiative
Oct 10, 2002·Genome Biology·Eugene M McCarthyJohn F McDonald
Mar 23, 2004·Nucleic Acids Research·Robert C Edgar
May 15, 2004·Science·Shozo KobayashiHirohiko Hirochika
Jul 9, 2004·Proceedings of the National Academy of Sciences of the United States of America·Jianxin Ma, Jeffrey L Bennetzen
Oct 1, 2004·Nature·Ning JiangSusan R Wessler
Oct 27, 2004·Molecular Genetics and Genomics : MGG·C VitteO Panaud
Nov 4, 2004·Trends in Genetics : TIG·Lee H Wong, K H Andy Choo
Dec 24, 2004·Molecular Biology and Evolution·Kiyotaka NagakiJiming Jiang
Aug 16, 2005·Nature·UNKNOWN International Rice Genome Sequencing Project
Dec 22, 2006·Molecular Biology and Evolution·Lin-Bin Zhang, Song Ge
May 12, 2007·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Y HoriT Nishio
Sep 4, 2007·The Plant Journal : for Cell and Molecular Biology·Jetty S S AmmirajuRod A Wing
Dec 11, 2007·Genetica·Nicholas KromWusirika Ramakrishna
Dec 20, 2007·The Plant Journal : for Cell and Molecular Biology·Anne RoulinOlivier Panaud
Sep 24, 2008·The Plant Journal : for Cell and Molecular Biology·Keiko Hayashi, Hitoshi Yoshida
Jan 20, 2009·Bioinformatics·Andrew M WaterhouseGeoffrey J Barton
Feb 4, 2009·Nature·Andrew H PatersonDaniel S Rokhsar
Oct 10, 2009·Proceedings of the National Academy of Sciences of the United States of America·Jennifer S HawkinsJonathan F Wendel
Dec 8, 2009·Science·Patrick S SchnableRichard K Wilson
Jan 16, 2010·Nature·Jeremy SchmutzScott A Jackson
Oct 18, 2013·Molecular Biology and Evolution·Koichiro TamuraSudhir Kumar
Jan 8, 2014·Methods in Molecular Biology·Ruslan KalendarAlan H Schulman
Feb 13, 2014·Genome Research·Moaine El BaidouriOlivier Panaud

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Software Mentioned

FastPCR Professional
MEGA
Jalview
tBLASTX
bl2 seq
Vector NTI
BLASTX
BLASTN
RTPOSON
Gramene

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