Literature DB >> 10677514

Hox cluster genomics in the horn shark, Heterodontus francisci.

C B Kim1, C Amemiya, W Bailey, K Kawasaki, J Mezey, W Miller, S Minoshima, N Shimizu, G Wagner, F Ruddle.   

Abstract

Reconstructing the evolutionary history of Hox cluster origins will lead to insights into the developmental and evolutionary significance of Hox gene clusters in vertebrate phylogeny and to their role in the origins of various vertebrate body plans. We have isolated two Hox clusters from the horn shark, Heterodontus francisci. These have been sequenced and compared with one another and with other chordate Hox clusters. The results show that one of the horn shark clusters (HoxM) is orthologous to the mammalian HoxA cluster and shows a structural similarity to the amphioxus cluster, whereas the other shark cluster (HoxN) is orthologous to the mammalian HoxD cluster based on cluster organization and a comparison with noncoding and Hox gene-coding sequences. The persistence of an identifiable HoxA cluster over an 800-million-year divergence time demonstrates that the Hox gene clusters are highly integrated and structured genetic entities. The data presented herein identify many noncoding sequence motifs conserved over 800 million years that may function as genetic control motifs essential to the developmental process.

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Year:  2000        PMID: 10677514      PMCID: PMC26491          DOI: 10.1073/pnas.030539697

Source DB:  PubMed          Journal:  Proc Natl Acad Sci U S A        ISSN: 0027-8424            Impact factor:   11.205


  34 in total

1.  Evolution of chordate hox gene clusters.

Authors:  F H Ruddle; C T Amemiya; J L Carr; C B Kim; C Ledje; C S Shashikant; G P Wagner
Journal:  Ann N Y Acad Sci       Date:  1999-05-18       Impact factor: 5.691

2.  Colinear and segmental expression of amphioxus Hox genes.

Authors:  H Wada; J Garcia-Fernàndez; P W Holland
Journal:  Dev Biol       Date:  1999-09-01       Impact factor: 3.582

3.  Exon shuffling by L1 retrotransposition.

Authors:  J V Moran; R J DeBerardinis; H H Kazazian
Journal:  Science       Date:  1999-03-05       Impact factor: 47.728

4.  Organization of an echinoderm Hox gene cluster.

Authors:  P Martinez; J P Rast; C Arenas-Mena; E H Davidson
Journal:  Proc Natl Acad Sci U S A       Date:  1999-02-16       Impact factor: 11.205

5.  Comparative studies on mammalian Hoxc8 early enhancer sequence reveal a baleen whale-specific deletion of a cis-acting element.

Authors:  C S Shashikant; C B Kim; M A Borbély; W C Wang; F H Ruddle
Journal:  Proc Natl Acad Sci U S A       Date:  1998-12-22       Impact factor: 11.205

6.  Expansion of the Hox gene family and the evolution of chordates.

Authors:  J W Pendleton; B K Nagai; M T Murtha; F H Ruddle
Journal:  Proc Natl Acad Sci U S A       Date:  1993-07-01       Impact factor: 11.205

7.  Identification of a Pax paired domain recognition sequence and evidence for DNA-dependent conformational changes.

Authors:  J Epstein; J Cai; T Glaser; L Jepeal; R Maas
Journal:  J Biol Chem       Date:  1994-03-18       Impact factor: 5.157

8.  Retinoic acid-responsive enhancers located 3' of the Hox A and Hox B homeobox gene clusters. Functional analysis.

Authors:  A W Langston; J R Thompson; L J Gudas
Journal:  J Biol Chem       Date:  1997-01-24       Impact factor: 5.157

9.  Functional analysis of the mouse homeobox gene HoxB9 in Drosophila development.

Authors:  J Malicki; L D Bogarad; M M Martin; F H Ruddle; W McGinnis
Journal:  Mech Dev       Date:  1993-08       Impact factor: 1.882

10.  Zebrafish hox clusters and vertebrate genome evolution.

Authors:  A Amores; A Force; Y L Yan; L Joly; C Amemiya; A Fritz; R K Ho; J Langeland; V Prince; Y L Wang; M Westerfield; M Ekker; J H Postlethwait
Journal:  Science       Date:  1998-11-27       Impact factor: 47.728

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  37 in total

Review 1.  The phylogenetic placement of chondrichthyes: inferences from analysis of multiple genes and implications for comparative studies.

Authors:  A Martin
Journal:  Genetica       Date:  2001       Impact factor: 1.082

2.  Evolutionary conservation of regulatory elements in vertebrate Hox gene clusters.

Authors:  Simona Santini; Jeffrey L Boore; Axel Meyer
Journal:  Genome Res       Date:  2003-06       Impact factor: 9.043

3.  Hox cluster duplications and the opportunity for evolutionary novelties.

Authors:  Gunte P Wagner; Chris Amemiya; Frank Ruddle
Journal:  Proc Natl Acad Sci U S A       Date:  2003-11-24       Impact factor: 11.205

4.  Bichir HoxA cluster sequence reveals surprising trends in ray-finned fish genomic evolution.

Authors:  Chi-Hua Chiu; Ken Dewar; Günter P Wagner; Kazuhiko Takahashi; Frank Ruddle; Christina Ledje; Peter Bartsch; Jean-Luc Scemama; Edmund Stellwag; Claudia Fried; Sonja J Prohaska; Peter F Stadler; Chris T Amemiya
Journal:  Genome Res       Date:  2004-01       Impact factor: 9.043

5.  Developmental roles of pufferfish Hox clusters and genome evolution in ray-fin fish.

Authors:  Angel Amores; Tohru Suzuki; Yi-Lin Yan; Jordan Pomeroy; Amy Singer; Chris Amemiya; John H Postlethwait
Journal:  Genome Res       Date:  2004-01       Impact factor: 9.043

Review 6.  The role of gene duplication in the evolution and function of the vertebrate Dlx/distal-less bigene clusters.

Authors:  Kenta Sumiyama; Steven Q Irvine; Frank H Ruddle
Journal:  J Struct Funct Genomics       Date:  2003

7.  Evolution of conserved non-coding sequences within the vertebrate Hox clusters through the two-round whole genome duplications revealed by phylogenetic footprinting analysis.

Authors:  Masatoshi Matsunami; Kenta Sumiyama; Naruya Saitou
Journal:  J Mol Evol       Date:  2010-10-28       Impact factor: 2.395

8.  Molecular evolution of duplicated ray finned fish HoxA clusters: increased synonymous substitution rate and asymmetrical co-divergence of coding and non-coding sequences.

Authors:  Günter P Wagner; Kazuhiko Takahashi; Vincent Lynch; Sonja J Prohaska; Claudia Fried; Peter F Stadler; Chris Amemiya
Journal:  J Mol Evol       Date:  2005-05       Impact factor: 2.395

9.  The Dlx gene complement of the leopard shark, Triakis semifasciata, resembles that of mammals: implications for genomic and morphological evolution of jawed vertebrates.

Authors:  David W Stock
Journal:  Genetics       Date:  2004-10-16       Impact factor: 4.562

Review 10.  The fates of zebrafish Hox gene duplicates.

Authors:  Chris Jozefowicz; James McClintock; Victoria Prince
Journal:  J Struct Funct Genomics       Date:  2003
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