Identification of high-copy number long terminal repeat retrotransposons and their expansion in Phalaenopsis orchids.

BMC Genomics
Chia-Chi HsuHong-Hwa Chen

Abstract

Transposable elements (TEs) are fragments of DNA that can insert into new chromosomal locations. They represent a great proportion of eukaryotic genomes. The identification and characterization of TEs facilitates understanding the transpositional activity of TEs with their effects on the orchid genome structure. We combined the draft whole-genome sequences of Phalaenopsis equestris with BAC end sequences, Roche 454, and Illumina/Solexa, and identified long terminal repeat (LTR) retrotransposons in these genome sequences by using LTRfinder and classified by using Gepard software. Among the 10 families Gypsy-like retrotransposons, three families Gypsy1, Gypsy2, and Gypsy3, contained the most copies among these predicted elements. In addition, six high-copy retrotransposons were identified according to their reads in the sequenced raw data. The 12-kb Orchid-rt1 contains 18,000 copies representing 220 Mbp of the P. equestris genome. Southern blot and slot blot assays showed that these four retrotransposons Gypsy1, Gypsy2, Gypsy3, and Orchid-rt1 contained high copies in the large-genome-size/large-chromosome species P. violacea and P. bellina. Both Orchid-rt1 and Gypsy1 displayed various ratios of copy number for the LTR sequences v...Continue Reading

References

Apr 1, 1989·Trends in Genetics : TIG·D J Finnegan
Nov 1, 1996·Science·P SanMiguelJ L Bennetzen
Feb 26, 2000·Annual Review of Genetics·A Kumar, J L Bennetzen
Mar 10, 2001·Nature·E S LanderUNKNOWN International Human Genome Sequencing Consortium
May 14, 2003·Proceedings of the National Academy of Sciences of the United States of America·Vladimir V Kapitonov, Jerzy Jurka
Jan 17, 2004·The Journal of Biological Chemistry·Vicente SancenónLola Peñarrubia
Oct 1, 2004·Nature·Ning JiangSusan R Wessler
Aug 12, 2005·Cytogenetic and Genome Research·C Vitte, O Panaud
Oct 13, 2005·Current Opinion in Genetics & Development·Jeffrey L Bennetzen
Feb 21, 2007·Bioinformatics·Jan KrumsiekThomas Rattei
Oct 10, 2009·Proceedings of the National Academy of Sciences of the United States of America·Jennifer S HawkinsJonathan F Wendel
Jan 7, 2011·BMC Plant Biology·Chia-Chi HsuHong-Hwa Chen
Jan 7, 2011·Genome Research·Szymon M KiełbasaMartin C Frith
Jan 4, 2012·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Kai WangTianzhen Zhang
Feb 22, 2013·Genome Biology and Evolution·Moaine El Baidouri, Olivier Panaud
Jun 19, 2014·Genetics and Molecular Research : GMR·A M Oliveira-SilvaN R Sousa
Nov 25, 2014·Nature Genetics·Jing CaiZhong-Jian Liu
May 13, 2015·BMC Genomics·Ingrid GarbusViviana Echenique
Sep 21, 2015·Chromosome Research : an International Journal on the Molecular, Supramolecular and Evolutionary Aspects of Chromosome Biology·Fabíola Carvalho SantosAndré Luís Laforga Vanzela
Jan 20, 2018·The New Phytologist·Marta SenovillaManuel González-Guerrero

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Methods Mentioned

BETA
RNAseq
RNA-seq
PCR

Software Mentioned

BLASTX
BLAST2
BLASTN
RepeatMasker
Adobe Photoshop
LTRfinder
Dot
BLAST
Gepard
LTRharvest

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