Genome-wide analysis of transposable elements and tandem repeats in the compact placozoan genome

The placozoan Trichoplax adhaerens has a compact genome with many primitive eumetazoan characteristics. In order to gain a better understanding of its genome architecture, we conducted a detailed analysis of repeat content in this genome. The transposable element (TE) content is lower than that of other metazoans, and the few TEs present in the genome appear to be inactive. A new phylogenetic clade of the gypsy-like LTR retrotransposons was identified, which includes the majority of gypsy-like elements in Trichoplax. A particular microsatellite motif (ACAGT) exhibits unexpectedly high abundance, and also has strong association with its nearby genes.ReviewersThis article was reviewed by Dr. Jerzy Jurka and Dr. I. King Jordan.

[1]  H. Ellegren.  Microsatellites: simple sequences with complex evolution , 2004, Nature Reviews Genetics.

[2]  J. V. Moran,et al.  Initial sequencing and analysis of the human genome. , 2001, Nature.

[3]  John P. Huelsenbeck,et al.  MRBAYES: Bayesian inference of phylogenetic trees , 2001, Bioinform..

[4]  J. Jurka,et al.  Repetitive sequences in complex genomes: structure and evolution. , 2007, Annual review of genomics and human genetics.

[5]  J. Weissenbach,et al.  An active non-LTR retrotransposon with tandem structure in the compact genome of the pufferfish Tetraodon nigroviridis. , 2003, Genome research.

[6]  Shi Wang,et al.  Initial analysis of tandemly repetitive sequences in the genome of Zhikong scallop (Chlamys farreri Jones et Preston) , 2008, DNA sequence : the journal of DNA sequencing and mapping.

[7]  C. Mungall,et al.  The Release 5.1 Annotation of Drosophila melanogaster Heterochromatin , 2007, Science.

[8]  J. Berg.  Genome sequence of the nematode C. elegans: a platform for investigating biology. , 1998, Science.

[9]  L. Buss,et al.  Molecular signatures for sex in the Placozoa , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[10]  David Q. Matus,et al.  Broad phylogenomic sampling improves resolution of the animal tree of life , 2008, Nature.

[11]  Zhao Xu,et al.  LTR_FINDER: an efficient tool for the prediction of full-length LTR retrotransposons , 2007, Nucleic Acids Res..

[12]  E. Nevo,et al.  Microsatellites: genomic distribution, putative functions and mutational mechanisms: a review , 2002, Molecular ecology.

[13]  Alan M. Lambowitz,et al.  Mobile DNA III , 2002 .

[14]  L. Caporale.  The implicit genome , 2006 .

[15]  J. Thompson,et al.  CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. , 1994, Nucleic acids research.

[16]  Stephen M. Mount,et al.  The genome sequence of Drosophila melanogaster. , 2000, Science.

[17]  S. Whelan,et al.  A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach. , 2001, Molecular biology and evolution.

[18]  石柠.  My favorite animal , 2006 .

[19]  M. Rhyu,et al.  CsRn1, a novel active retrotransposon in a parasitic trematode, Clonorchis sinensis, discloses a new phylogenetic clade of Ty3/gypsy-like LTR retrotransposons. , 2001, Molecular biology and evolution.

[20]  International Human Genome Sequencing Consortium.  Initial sequencing and analysis of the human genome , 2001, Nature.

[21]  S. Wessler.  Eukaryotic Transposable Elements : Teaching Old Genomes New Tricks , 2006 .

[22]  F. Zhou,et al.  MUST: a system for identification of miniature inverted-repeat transposable elements and applications to Anabaena variabilis and Haloquadratum walsbyi. , 2009, Gene.

[23]  B. Schierwater.  My favorite animal, Trichoplax adhaerens. , 2005, BioEssays : news and reviews in molecular, cellular and developmental biology.

[24]  Andrew Smith.  Genome sequence of the nematode C-elegans: A platform for investigating biology , 1998 .

[25]  Robert Kofler,et al.  SciRoKo: a new tool for whole genome microsatellite search and investigation , 2007, Bioinform..

[26]  H. Kazazian.  Mobile Elements: Drivers of Genome Evolution , 2004, Science.

[27]  C. Fizames,et al.  Characterization and repeat analysis of the compact genome of the freshwater pufferfish Tetraodon nigroviridis. , 2000, Genome research.

[28]  B. Schierwater,et al.  Concatenated Analysis Sheds Light on Early Metazoan Evolution and Fuels a Modern “Urmetazoon” Hypothesis , 2009, PLoS biology.

[29]  Cédric Feschotte,et al.  Miniature Inverted-Repeat Transposable Elements and Their Relationship to Established DNA Transposons , 2002 .

[30]  E. Myers,et al.  Basic local alignment search tool. , 1990, Journal of molecular biology.

[31]  G. Benson,et al.  Tandem repeats finder: a program to analyze DNA sequences. , 1999, Nucleic acids research.

[32]  M. V. Katti,et al.  Differential distribution of simple sequence repeats in eukaryotic genome sequences. , 2001, Molecular biology and evolution.

[33]  Günter Kahl,et al.  Mining microsatellites in eukaryotic genomes. , 2007, Trends in biotechnology.

[34]  J. Jurka,et al.  Repbase Update, a database of eukaryotic repetitive elements , 2005, Cytogenetic and Genome Research.

[35]  Charles E. Chapple,et al.  Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype , 2004, Nature.

[36]  T. Eickbush,et al.  Modular Evolution of the Integrase Domain in the Ty3/Gypsy Class of LTR Retrotransposons , 1999, Journal of Virology.

[37]  J. Jurka,et al.  Microsatellites in different eukaryotic genomes: survey and analysis. , 2000, Genome research.

[38]  Nicholas H. Putnam,et al.  The Trichoplax genome and the nature of placozoans , 2008, Nature.