The coelacanth is one of the nearest living relatives of tetrapods. However, a teleost species such as zebrafish or Fugu is typically used as the outgroup in current tetrapod comparative sequence analyses. Such studies are complicated by the fact that teleost genomes have undergone a whole-genome duplication event, as well as individual gene-duplication events. Here, we demonstrate the value of coelacanth genome sequence by complete sequencing and analysis of the protocadherin gene cluster of the Indonesian coelacanth, Latimeria menadoensis. We found that coelacanth has 49 protocadherin cluster genes organized in the same three ordered subclusters, ␣, ␤, and ␥, as the 54 protocadherin cluster genes in human. In contrast, whole-genome and tandem duplications have generated two zebrafish protocadherin clusters comprised of at least 97 genes. Additionally, zebrafish protocadherins are far more prone to homogenizing gene conversion events than coelacanth protocadherins, suggesting that recombination-and duplication-driven plasticity may be a feature of teleost genomes. Our results indicate that coelacanth provides the ideal outgroup sequence against which tetrapod genomes can be measured. We therefore present L. menadoensis as a candidate for whole-genome sequencing.[Supplemental material is available online at www.genome.org and http://www-shgc.stanford.edu/myerslab/. The BAC sequence data from this study have been submitted to GenBank under accession nos. AC150283, AC150284, and AC150308-AC150310.]A primary aim of vertebrate comparative genomics is to reconstruct the evolutionary history of vertebrate genomes. To this end, genome sequence is currently being obtained from organisms at critical positions in the vertebrate phylogeny. Notably absent from the list of planned or completed genomes, however, is a species on a lineage arising between ray-finned fishes and tetrapods, when vertebrates were about to undergo an adaptive transformation. The sarcopterygian fishes, coelacanths and lungfish, are the only extant taxa that occupy this unique phylogenetic position (Gorr et al. 1991;Zardoya andMeyer 1996, 1997). As the nearest living relatives of the tetrapod ancestor, these species provide access to the phenotypic and genomic transitions leading to the emergence of tetrapods.Despite substantial sequence analysis, it is unclear whether coelacanths or lungfish are more closely related to tetrapods (Takezaki et al. 2004). However, lungfish have very large genomes (>100 Gb), making them poor candidates for genomic sequencing. Coelacanths, although abundant in the fossil record, were believed to be extinct before a living specimen was identified in 1938 by Marjorie Latimer and J.L.B. Smith (Smith 1939). The two modern coelacanth species that are known, Latimeria chalumnae and Latimeria menadoensis, are remarkably similar to their fossil relatives, showing little morphological change over 360 million years (Smith 1939;Forey 1998;Holder et al. 1999). In addition, the L. menadoensis genome is smaller than the human or mouse ...

We have generated a BAC library from the Indonesian coelacanth, Latimeria menadoensis. This library was generated using genomic DNA of nuclei isolated from heart tissue, and has an average insert size of 171 kb. There are a total of 288 384-well microtiter dishes in the library (110,592 clones) and its genomic representation is estimated to encompass > or = 7X coverage based on the amount of DNA presumably cloned in the library as well as via hybridization with probes to a small set of single copy genes. This genomic resource has been made available to the public and should prove useful to the scientific community for many applications, including comparative genomics, molecular evolution and conservation genetics.

Hoxc8 early enhancer controls the initiation and establishment phase of Hoxc8 expression in the mouse. Comparative studies indicate the presence of Hoxc8 early enhancer sequences in different vertebrate clades including mammals, birds and fish. Previous studies have shown differences between teleost and mammalian Hoxc8 early enhancers with respect to sequence and organization of protein binding elements. This raises the question of when the Hoxc8 early enhancer arose and how it has become modified in different vertebrate lineages. Here, we describe Hoxc8 early enhancer from the Indonesian coelacanth, Latimeria menadoensis. Coelacanths are the only extant lobefinned fish whose genome is tractable to genome analysis. The Latimeria Hoxc8 early enhancer sequence more closely resembles that of the mouse than that of Fugu or zebrafish. When assayed for enhancer activity by reporter gene analysis in transgenic mouse embryos, Latimeria Hoxc8 early enhancer directs expression to the posterior neural tube and mesoderm similar to that of the mouse enhancer. These observations support a close relationship between coelacanths and tetrapods and place the origin of a common Hoxc8 early enhancer sequence within the sarcopterygian lineage. The divergence of teleost (actinopterygii) Hoxc8 early enhancer may reflect a case of relaxed selection or other forms of instability induced by genome duplication events.