Wanda: a database of duplicated fish genes

Comparative genomics has shown that ray-finned fish (Actinopterygii) contain more copies of many genes than other vertebrates. A large number of these additional genes appear to have been produced during a genome duplication event that occurred early during the evolution of Actinopterygii (i.e. before the teleost radiation). In addition to this ancient genome duplication event, many lineages within Actinopterygii have experienced more recent genome duplications. Here we introduce a curated database named Wanda that lists groups of orthologous genes with one copy from man, mouse and chicken, one or two from tetraploid Xenopus and two or more ancient copies (i.e. paralogs) from ray-finned fish. The database also contains the sequence alignments and phylogenetic trees that were necessary for determining the correct orthologous and paralogous relationships among genes. Where available, map positions and functional data are also reported. The Wanda database should be of particular use to evolutionary and developmental biologists who are interested in the evolutionary and functional divergence of genes after duplication. Wanda is available at http://www.evolutionsbiologie.uni-konstanz.de/Wanda/.

[1]  G. Bailey,et al.  Gene duplication in tetraploid fish: model for gene silencing at unlinked duplicated loci. , 1978, Proceedings of the National Academy of Sciences of the United States of America.

[2]  H. Toresson,et al.  Cloning and expression of three members of the zebrafish Bmp family: Bmp2a, Bmp2b and Bmp4. , 1997, Gene.

[3]  Y. Yan,et al.  Zebrafish comparative genomics and the origins of vertebrate chromosomes. , 2000, Genome research.

[4]  Gregory D. Schuler,et al.  Database resources of the National Center for Biotechnology Information , 2021, Nucleic Acids Res..

[5]  David P. Mindell,et al.  Homology evolving , 2001 .

[6]  Gregory D. Schuler,et al.  Database resources of the National Center for Biotechnology Information: update , 2004, Nucleic acids research.

[7]  Martin A. Nowak,et al.  Evolution of genetic redundancy , 1997, Nature.

[8]  G Dingerkus,et al.  Karyotypic analysis and evidence of tetraploidy in the North American paddlefish, Polyodon spathula. , 1976, Science.

[9]  V. Laudet,et al.  Euteleost fish genomes are characterized by expansion of gene families. , 2001, Genome research.

[10]  Byrappa Venkatesh,et al.  Organization of the Fugu rubripes Hox clusters: evidence for continuing evolution of vertebrate Hox complexes , 1997, Nature Genetics.

[11]  R Abagyan,et al.  A genetic linkage map for zebrafish: comparative analysis and localization of genes and expressed sequences. , 1999, Genome research.

[12]  A. Force,et al.  The probability of duplicate gene preservation by subfunctionalization. , 2000, Genetics.

[13]  A. Meyer,et al.  Gene and genome duplications in vertebrates: the one-to-four (-to-eight in fish) rule and the evolution of novel gene functions. , 1999, Current opinion in cell biology.

[14]  A C Sharman,et al.  Some new terms for duplicated genes. , 1999, Seminars in cell & developmental biology.

[15]  M. Westerfield,et al.  Relationships among msx gene structure and function in zebrafish and other vertebrates. , 1997, Molecular biology and evolution.

[16]  Axel Meyer,et al.  Genome Duplications and Accelerated Evolution of Hox Genes and Cluster Architecture in Teleost Fishes1 , 2001 .

[17]  F. Allendorf,et al.  Gene duplication in the family Salmonidae. III. Linkage between two duplicated loci coding for aspartate aminotransferase in the cutthroat trout (Salmo clarki). , 2009, Hereditas.

[18]  Y Van de Peer,et al.  Genome duplication, divergent resolution and speciation. , 2001, Trends in genetics : TIG.

[19]  M. Lynch,et al.  The evolutionary fate and consequences of duplicate genes. , 2000, Science.

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

[21]  M. Kondo,et al.  A detailed linkage map of medaka, Oryzias latipes: comparative genomics and genome evolution. , 2000, Genetics.

[22]  Y L Wang,et al.  Zebrafish hox clusters and vertebrate genome evolution. , 1998, Science.

[23]  Joachim Wittbrodt,et al.  More genes in fish , 1998 .

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

[25]  S. Aparício,et al.  Vertebrate evolution: recent perspectives from fish. , 2000, Trends in genetics : TIG.

[26]  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.

[27]  A. Meyer,et al.  The Ghost of Selection Past: Rates of Evolution and Functional Divergence of Anciently Duplicated Genes , 2001, Journal of Molecular Evolution.

[28]  Evelyn Camon,et al.  The EMBL Nucleotide Sequence Database , 2000, Nucleic Acids Res..

[29]  Marc Robinson-Rechavi,et al.  An ancestral whole-genome duplication may not have been responsible for the abundance of duplicated fish genes , 2001, Current Biology.

[30]  G. S. Whitt,et al.  Loss of duplicate gene expression after polyploidisation , 1977, Nature.

[31]  Y. Yan,et al.  A comparative map of the zebrafish genome. , 2000, Genome research.

[32]  J. Thompson,et al.  The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. , 1997, Nucleic acids research.

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

[34]  Gerald R. Smith,et al.  Tetraploid Origin of the Karyotype of Catostomid Fishes , 1972, Science.

[35]  W. Fitch.  Homology a personal view on some of the problems. , 2000, Trends in genetics : TIG.

[36]  Sarah A. Douglas,et al.  The Zebrafish Information Network (ZFIN): a resource for genetic, genomic and developmental research , 2001, Nucleic Acids Res..

[37]  M. Ekker,et al.  Involvement of the sonic hedgehog, patched 1 and bmp2 genes in patterning of the zebrafish dermal fin rays. , 1998, Development.

[38]  C Kappen,et al.  Analysis of a complete homeobox gene repertoire: implications for the evolution of diversity. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[39]  Dr. Susumu Ohno.  Evolution by Gene Duplication , 1970, Springer Berlin Heidelberg.

[40]  W. Li,et al.  Rate of gene silencing at duplicate loci: a theoretical study and interpretation of data from tetraploid fishes. , 1980, Genetics.