Chris T. Amemiya1*, Jessica Alfoldi2*, Alison P. Lee3, ………Vydianathan Ravi3,…… …..Byrappa Venkatesh3, Federica Di Palma2, Eric Lander2, Axel Meyer4, Kerstin Lindblad-Toh2 (91 authors).
1 - Molecular Genetics Program, Benaroya Research Institute, Seattle, WA, USA.
2 - Broad Institute of MIT and Harvard, Cambridge, MA, USA.
3 - Comparative Genomics Laboratory, Institute of Molecular and Cell Biology, A*STAR, Singapore.
4 - Konstanz Research School of Chemical Biology, University of Konstanz, Konstanz, Germany.
*contributed equally to this work.
Published in Nature on 18 April 2013.
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It was a zoological sensation when a living specimen of the coelacanth was first discovered in 1938, as this lineage of lobe finned fish was thought to have gone extinct 70 million years ago. The modern coelacanth looks remarkably similar to many of its ancient ancestors from the Mesozoic era and its evolutionary proximity to our own fish ancestors provides a glimpse of the fish that first walked on land. Here we report the 2.9 Gb genome sequence of the African coelacanth, Latimeria chalumnae. Through a phylogenomic analysis, including RNA-Seq data from the lungfish, we conclude that the lungfish, and not the coelacanth, is the closest living relative of tetrapods. Coelacanth protein-coding genes are significantly more slowly evolving than those of tetrapods, whereas other genomic features such as the abundance and composition of transposable elements and genomic rearrangements do not show a noticeable reduction in evolutionary rates. Analysis of changes in gene content, and associated regulatory elements, during the vertebrate adaptation to land identify important gene families and functions. These include genes regulating immunity, nitrogen excretion and the development of fins, tail, ear, eye, brain, and smell. Functional assays of enhancers suspected to be involved in the fin-to-limb transition and in the emergence of extra-embryonic placental tissues highlight the value of the coelacanth genome as a blueprint to understand tetrapod evolution.
Figure Legend: Cis-regulatory elements in the HoxD locus of mouse that were predicted as conserved noncoding elements (CNEs). While CNE3 and CNE5 are conserved in all vertebrates, CNE1 is conserved only in coelacanth and tetrapods (terrestrial animals). The latter is specifically expressed in the limb (lower panel). Mouse image: courtesy of Neil Shubin.
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