Completa caracterização do grupo HOX do celacanto fornece mais evidência de evolução lenta de seu genoma

Complete HOX cluster characterization of the coelacanth provides further evidence for slow evolution of its genome

Chris T. Amemiya a,b,1, Thomas P. Powers a, Sonja J. Prohaska c, Jane Grimwood d,2, Jeremy Schmutz d,2, Mark Dickson e, Tsutomu Miyake a,3,  Michael A. Schoenborn a, Richard M. Myers d,2, Francis H. Ruddle f,1, and Peter F. Stadler c,g,h,i,1

-Author Affiliations

aBenaroya Research Institute at Virginia Mason, Seattle, WA 98101;

bDepartment of Biology, University of Washington, Seattle, WA 98195;

cDepartment of Computer Science, University of Leipzig, Haertelstrasse 16-18, D-04107 Leipzig, Germany;

dThe Stanford Human Genome Center and the Department of Genetics, Stanford University School of Medicine, Palo Alto, CA 94304;

eCardiodx, Palo Alto, CA 94303;

fDepartment of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520;

gMax Planck Institute for Mathematics in Science and Fraunhofer Institut für Zelltherapie und Immunologie, D-04103 Leipzig, Germany;

hDepartment of Theoretical Chemistry, University of Vienna, A-1090 Vienna, Austria; and

iSanta Fe Institute, Santa Fe, NM 87501


↵2Present address: HudsonAlpha Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL 35806.


↵3Present address: Department of Anatomy, Jikei University School of Medicine, 3-25-8 NishiShinbashi, Minatoku, Tokyo 105-8461, Japan.


Contributed by Francis H. Ruddle, December 18, 2009 (sent for review November 27, 2009)

Abstract

The living coelacanth is a lobe-finned fish that represents an early evolutionary departure from the lineage that led to land vertebrates, and is of extreme interest scientifically. It has changed very little in appearance from fossilized coelacanths of the Cretaceous (150 to 65 million years ago), and is often referred to as a “living fossil.” An important general question is whether long-term stasis in morphological evolution is associated with stasis in genome evolution. To this end we have used targeted genome sequencing for acquiring 1,612,752 bp of high quality finished sequence encompassing the four HOX clusters of the Indonesian coelacanth Latimeria menadoensis. Detailed analyses were carried out on genomic structure, gene and repeat contents, conserved noncoding regions, and relative rates of sequence evolution in both coding and noncoding tracts. Our results demonstrate conclusively that the coelacanth HOX clusters are evolving comparatively slowly and that this taxon should serve as a viable outgroup for interpretation of the genomes of tetrapod species.

genomics    Latimeria menadoensis    BAC clone    

Footnotes

1To whom correspondence may be addressed: 

E-mail:camemiya@benaroyaresearch.org,frank.ruddle@yale.edu, orstudla@bioinf.uni-leipzig.de.

Author contributions: C.T.A., T.P.P., R.M.M., and F.H.R. designed research; C.T.A., T.P.P., S.J.P., J.G., J.S., M.D., T.M., M.A.S., and P.F.S. performed research; C.T.A., T.P.P., S.J.P., J.G., J.S., M.D., M.A.S., R.M.M., and P.F.S. contributed new reagents/analytic tools; C.T.A., T.P.P., S.J.P., T.M., R.M.M., F.H.R., and P.F.S. analyzed data; and C.T.A., T.P.P., S.J.P., F.H.R., and P.F.S. wrote the paper.

The authors declare no conflict of interest.

Data deposition: The sequences reported in this paper have been deposited in the GenBank database (accession nos. FJ497005, FJ497006, FJ497007, andFJ497008).

This article contains supporting information online at www.pnas.org/cgi/content/full/0914312107/DCSupplemental.

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