Cargando…

An Independent Genome Duplication Inferred from Hox Paralogs in the American Paddlefish—A Representative Basal Ray-Finned Fish and Important Comparative Reference

Vertebrates have experienced two rounds of whole-genome duplication (WGD) in the stem lineages of deep nodes within the group and a subsequent duplication event in the stem lineage of the teleosts—a highly diverse group of ray-finned fishes. Here, we present the first full Hox gene sequences for any...

Descripción completa

Detalles Bibliográficos
Autores principales: Crow, Karen D., Smith, Christopher D., Cheng, Jan-Fang, Wagner, Günter P., Amemiya, Chris T.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2012
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3509897/
https://www.ncbi.nlm.nih.gov/pubmed/22851613
http://dx.doi.org/10.1093/gbe/evs067
_version_ 1782251395185901568
author Crow, Karen D.
Smith, Christopher D.
Cheng, Jan-Fang
Wagner, Günter P.
Amemiya, Chris T.
author_facet Crow, Karen D.
Smith, Christopher D.
Cheng, Jan-Fang
Wagner, Günter P.
Amemiya, Chris T.
author_sort Crow, Karen D.
collection PubMed
description Vertebrates have experienced two rounds of whole-genome duplication (WGD) in the stem lineages of deep nodes within the group and a subsequent duplication event in the stem lineage of the teleosts—a highly diverse group of ray-finned fishes. Here, we present the first full Hox gene sequences for any member of the Acipenseriformes, the American paddlefish, and confirm that an independent WGD occurred in the paddlefish lineage, approximately 42 Ma based on sequences spanning the entire HoxA cluster and eight genes on the HoxD gene cluster. These clusters comprise different HOX loci and maintain conserved synteny relative to bichir, zebrafish, stickleback, and pufferfish, as well as human, mouse, and chick. We also provide a gene genealogy for the duplicated fzd8 gene in paddlefish and present evidence for the first Hox14 gene in any ray-finned fish. Taken together, these data demonstrate that the American paddlefish has an independently duplicated genome. Substitution patterns of the “alpha” paralogs on both the HoxA and HoxD gene clusters suggest transcriptional inactivation consistent with functional diploidization. Further, there are similarities in the pattern of sequence divergence among duplicated Hox genes in paddlefish and teleost lineages, even though they occurred independently approximately 200 Myr apart. We highlight implications on comparative analyses in the study of the “fin-limb transition” as well as gene and genome duplication in bony fishes, which includes all ray-finned fishes as well as the lobe-finned fishes and tetrapod vertebrates.
format Online
Article
Text
id pubmed-3509897
institution National Center for Biotechnology Information
language English
publishDate 2012
publisher Oxford University Press
record_format MEDLINE/PubMed
spelling pubmed-35098972012-11-29 An Independent Genome Duplication Inferred from Hox Paralogs in the American Paddlefish—A Representative Basal Ray-Finned Fish and Important Comparative Reference Crow, Karen D. Smith, Christopher D. Cheng, Jan-Fang Wagner, Günter P. Amemiya, Chris T. Genome Biol Evol Research Articles Vertebrates have experienced two rounds of whole-genome duplication (WGD) in the stem lineages of deep nodes within the group and a subsequent duplication event in the stem lineage of the teleosts—a highly diverse group of ray-finned fishes. Here, we present the first full Hox gene sequences for any member of the Acipenseriformes, the American paddlefish, and confirm that an independent WGD occurred in the paddlefish lineage, approximately 42 Ma based on sequences spanning the entire HoxA cluster and eight genes on the HoxD gene cluster. These clusters comprise different HOX loci and maintain conserved synteny relative to bichir, zebrafish, stickleback, and pufferfish, as well as human, mouse, and chick. We also provide a gene genealogy for the duplicated fzd8 gene in paddlefish and present evidence for the first Hox14 gene in any ray-finned fish. Taken together, these data demonstrate that the American paddlefish has an independently duplicated genome. Substitution patterns of the “alpha” paralogs on both the HoxA and HoxD gene clusters suggest transcriptional inactivation consistent with functional diploidization. Further, there are similarities in the pattern of sequence divergence among duplicated Hox genes in paddlefish and teleost lineages, even though they occurred independently approximately 200 Myr apart. We highlight implications on comparative analyses in the study of the “fin-limb transition” as well as gene and genome duplication in bony fishes, which includes all ray-finned fishes as well as the lobe-finned fishes and tetrapod vertebrates. Oxford University Press 2012 2012-07-31 /pmc/articles/PMC3509897/ /pubmed/22851613 http://dx.doi.org/10.1093/gbe/evs067 Text en © The Author(s) 2012. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. http://creativecommons.org/licenses/by-nc/3.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Research Articles
Crow, Karen D.
Smith, Christopher D.
Cheng, Jan-Fang
Wagner, Günter P.
Amemiya, Chris T.
An Independent Genome Duplication Inferred from Hox Paralogs in the American Paddlefish—A Representative Basal Ray-Finned Fish and Important Comparative Reference
title An Independent Genome Duplication Inferred from Hox Paralogs in the American Paddlefish—A Representative Basal Ray-Finned Fish and Important Comparative Reference
title_full An Independent Genome Duplication Inferred from Hox Paralogs in the American Paddlefish—A Representative Basal Ray-Finned Fish and Important Comparative Reference
title_fullStr An Independent Genome Duplication Inferred from Hox Paralogs in the American Paddlefish—A Representative Basal Ray-Finned Fish and Important Comparative Reference
title_full_unstemmed An Independent Genome Duplication Inferred from Hox Paralogs in the American Paddlefish—A Representative Basal Ray-Finned Fish and Important Comparative Reference
title_short An Independent Genome Duplication Inferred from Hox Paralogs in the American Paddlefish—A Representative Basal Ray-Finned Fish and Important Comparative Reference
title_sort independent genome duplication inferred from hox paralogs in the american paddlefish—a representative basal ray-finned fish and important comparative reference
topic Research Articles
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3509897/
https://www.ncbi.nlm.nih.gov/pubmed/22851613
http://dx.doi.org/10.1093/gbe/evs067
work_keys_str_mv AT crowkarend anindependentgenomeduplicationinferredfromhoxparalogsintheamericanpaddlefisharepresentativebasalrayfinnedfishandimportantcomparativereference
AT smithchristopherd anindependentgenomeduplicationinferredfromhoxparalogsintheamericanpaddlefisharepresentativebasalrayfinnedfishandimportantcomparativereference
AT chengjanfang anindependentgenomeduplicationinferredfromhoxparalogsintheamericanpaddlefisharepresentativebasalrayfinnedfishandimportantcomparativereference
AT wagnergunterp anindependentgenomeduplicationinferredfromhoxparalogsintheamericanpaddlefisharepresentativebasalrayfinnedfishandimportantcomparativereference
AT amemiyachrist anindependentgenomeduplicationinferredfromhoxparalogsintheamericanpaddlefisharepresentativebasalrayfinnedfishandimportantcomparativereference
AT crowkarend independentgenomeduplicationinferredfromhoxparalogsintheamericanpaddlefisharepresentativebasalrayfinnedfishandimportantcomparativereference
AT smithchristopherd independentgenomeduplicationinferredfromhoxparalogsintheamericanpaddlefisharepresentativebasalrayfinnedfishandimportantcomparativereference
AT chengjanfang independentgenomeduplicationinferredfromhoxparalogsintheamericanpaddlefisharepresentativebasalrayfinnedfishandimportantcomparativereference
AT wagnergunterp independentgenomeduplicationinferredfromhoxparalogsintheamericanpaddlefisharepresentativebasalrayfinnedfishandimportantcomparativereference
AT amemiyachrist independentgenomeduplicationinferredfromhoxparalogsintheamericanpaddlefisharepresentativebasalrayfinnedfishandimportantcomparativereference