Sequencing and analysis of 10967 full-length cDNA clones from Xenopus laevis and Xenopus tropicalis

Sequencing of full-insert clones from full-length cDNA libraries from both Xenopus laevis and Xenopus tropicalis has been ongoing as part of the Xenopus Gene Collection initiative. Here we present an analysis of 10967 clones (8049 from X. laevis and 2918 from X. tropicalis). The clone set contains 2013 orthologs between X. laevis and X. tropicalis as well as 1795 paralog pairs within X. laevis. 1199 are in-paralogs, believed to have resulted from an allotetraploidization event approximately 30 million years ago, and the remaining 546 are likely out-paralogs that have resulted from more ancient gene duplications, prior to the divergence between the two species. We do not detect any evidence for positive selection by the Yang and Nielsen maximum likelihood method of approximating d{sub N}/d{sub S}. However, d{sub N}/d{sub S} for X. laevis in-paralogs is elevated relative to X. tropicalis orthologs. This difference is highly significant, and indicates an overall relaxation of selective pressures on duplicated gene pairs. Within both groups of paralogs, we found evidence of subfunctionalization, manifested as differential expression of paralogous genes among tissues, as measured by EST information from public resources. We have observed, as expected, a higher instance of subfunctionalization in out-paralogs relative to in-paralogs.

[1]  Jonathan F Wendel,et al.  Polyploidy and Genome Evolution in Plants This Review Comes from a Themed Issue on Genome Studies and Molecular Genetics Edited , 2022 .

[2]  High-throughput sequencing: a failure mode analysis , 2005, BMC Genomics.

[3]  D. Kelley,et al.  A mitochondrial DNA phylogeny of African clawed frogs: phylogeography and implications for polyploid evolution. , 2004, Molecular phylogenetics and evolution.

[4]  Nick Goldman,et al.  Accuracy and Power of Statistical Methods for Detecting Adaptive Evolution in Protein Coding Sequences and for Identifying Positively Selected Sites , 2004, Genetics.

[5]  Nancy Papalopulu,et al.  Defining a large set of full-length clones from a Xenopus tropicalis EST project. , 2004, Developmental biology.

[6]  A. Fuglsang,et al.  The 'effective number of codons' revisited. , 2004, Biochemical and biophysical research communications.

[7]  Ryan D. Morin,et al.  The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). , 2004, Genome research.

[8]  Damian Smedley,et al.  Ensembl 2004 , 2004, Nucleic Acids Res..

[9]  Anders Gorm Pedersen,et al.  RevTrans: multiple alignment of coding DNA from aligned amino acid sequences , 2003, Nucleic Acids Res..

[10]  L. Wagner,et al.  21. UniGene: A Unified View of the Transcriptome , 2003 .

[11]  G. Rubin,et al.  Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[12]  L. Zimmerman,et al.  Xenopus, the next generation: X. Tropicalis genetics and genomics , 2002, Developmental dynamics : an official publication of the American Association of Anatomists.

[13]  Brandon S Gaut,et al.  Patterns of nucleotide substitution among simultaneously duplicated gene pairs in Arabidopsis thaliana. , 2002, Molecular biology and evolution.

[14]  M. Krzywinski,et al.  An efficient strategy for large-scale high-throughput transposon-mediated sequencing of cDNA clones. , 2002, Nucleic acids research.

[15]  Kevin R. Thornton,et al.  Rapid divergence of gene duplicates on the Drosophila melanogaster X chromosome. , 2002, Molecular biology and evolution.

[16]  Z. Gu,et al.  Extent of gene duplication in the genomes of Drosophila, nematode, and yeast. , 2002, Molecular biology and evolution.

[17]  Christian E. V. Storm,et al.  Automatic clustering of orthologs and in-paralogs from pairwise species comparisons. , 2001, Journal of molecular biology.

[18]  Y Van de Peer,et al.  Comparative genomics provides evidence for an ancient genome duplication event in fish. , 2001, Philosophical transactions of the Royal Society of London. Series B, Biological sciences.

[19]  P. Blackshear,et al.  The NIEHS Xenopus maternal EST project: interim analysis of the first 13,879 ESTs from unfertilized eggs. , 2001, Gene.

[20]  Alex Bateman,et al.  The InterPro database, an integrated documentation resource for protein families, domains and functional sites , 2001, Nucleic Acids Res..

[21]  M. Ashburner,et al.  Gene Ontology: tool for the unification of biology , 2000, Nature Genetics.

[22]  A. Force,et al.  Preservation of duplicate genes by complementary, degenerative mutations. , 1999, Genetics.

[23]  B. Rost.  Twilight zone of protein sequence alignments. , 1999, Protein engineering.

[24]  P Green,et al.  Base-calling of automated sequencer traces using phred. II. Error probabilities. , 1998, Genome research.

[25]  T J Gibson,et al.  Genetic redundancy in vertebrates: polyploidy and persistence of genes encoding multidomain proteins. , 1998, Trends in genetics : TIG.

[26]  J. Claverie,et al.  The significance of digital gene expression profiles. , 1997, Genome research.

[27]  Thomas L. Madden,et al.  Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. , 1997, Nucleic acids research.

[28]  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.

[29]  A. Hughes,et al.  Evolution of duplicate genes in a tetraploid animal, Xenopus laevis. , 1993, Molecular biology and evolution.

[30]  H. Kobel,et al.  Genetics of Xenopus laevis. , 1991, Methods in cell biology.

[31]  D. Hillis,et al.  Phylogenetic relationships of the pipid frogs Xenopus and Silurana: an integration of ribosomal DNA and morphology. , 1990, Molecular biology and evolution.