Observations on the radiation of lobe-finned fishes, ray-finned fishes, and cartilaginous fishes: phylogeny of the opioid/orphanin gene family and the 2R hypothesis.

At the close of the Devonian Period the rapid decline in the diversity of the lobe-finned fishes was countered by the emergence and diversification of the ray-finned fishes and the cartilaginous fishes that now dominate marine and freshwater ecosystems. All of these jawed vertebrates were derived from the ancestral gnathostomes; a chordate lineage that had experienced two genome duplication events during the evolution of the phylum. This review analyzes trends in the phylogeny of the opioid/orphanin gene family (four prohormone/neuropeptide precursor-coding genes) in the major classes of gnathostomes that survived the extinction events at the close of the Devonian Period and focuses on some features of this gene family that appear to set the cartilaginous fishes (class Chondrichthyes) apart from class Sarcopterygii (lobe-finned fishes and tetrapods) and class Actinopterygii (the ray-finned fishes).

Dores RM ，Majeed Q ，Komorowski L 《-》

From 2R to 3R: evidence for a fish-specific genome duplication (FSGD).

Meyer A ，Van de Peer Y 《BIOESSAYS》

Gnathostome phylogenomics utilizing lungfish EST sequences.

Hallström BM ，Janke A 《-》

Molecular evolution of the opioid/orphanin gene family.

:Gene duplication is a recurring theme in the evolution of vertebrate polypeptide hormones and neuropeptides. These duplication events can lead to the formation of gene families in which divergence of function is the usual outcome. In the case of the opioid/orphanin family of genes, duplication events have proceeded along two paths: (a) an apparent duplication of function as seen in the analgesic activity of Proenkephalin and Prodynorphin end-products; and (b) divergence of function as seen in the nociceptic activity of Proorphanin end-products or the melanocortin (color change and chronic stress regulation) activity of Proopiomelanocortin end-products. Although genes coding for Proopiomelanocortin, Proenkephalin, Prodynorphin, and Proorphanin have been extensively studied in mammals, the distribution and radiation of these genes in nonmammalian vertebrates is less well understood. This review will present the hypothesis that the radiation of the opioid/orphanin gene family is the result of the duplication and divergence of the Proenkephalin gene during the radiation of the chordates. To evaluate the Proenkephalin gene duplication hypothesis, a 3'RACE procedure was used to screen for the presence of Prodynorphin-related, Proenkephalin-related, and Proorphanin-related cDNAs expressed in the brains of nonmammalian vertebrates.

Danielson PB ，Dores RM 《GENERAL AND COMPARATIVE ENDOCRINOLOGY》

Hox clusters of the bichir (Actinopterygii, Polypterus senegalus) highlight unique patterns of sequence evolution in gnathostome phylogeny.

Teleost fishes have extra Hox gene clusters owing to shared or lineage-specific genome duplication events in rayfinned fish (actinopterygian) phylogeny. Hence, extrapolating between genome function of teleosts and human or even between different fish species is difficult. We have sequenced and analyzed Hox gene clusters of the Senegal bichir (Polypterus senegalus), an extant representative of the most basal actinopterygian lineage. Bichir possesses four Hox gene clusters (A, B, C, D); phylogenetic analysis supports their orthology to the four Hox gene clusters of the gnathostome ancestor. We have generated a comprehensive database of conserved Hox noncoding sequences that include cartilaginous, lobe-finned, and ray-finned fishes (bichir and teleosts). Our analysis identified putative and known Hox cis-regulatory sequences with differing depths of conservation in Gnathostoma. We found that although bichir possesses four Hox gene clusters, its pattern of conservation of noncoding sequences is mosaic between outgroups, such as human, coelacanth, and shark, with four Hox gene clusters and teleosts, such as zebrafish and pufferfish, with seven or eight Hox gene clusters. Notably, bichir Hox gene clusters have been invaded by DNA transposons and this trend is further exemplified in teleosts, suggesting an as yet unrecognized mechanism of genome evolution that may explain Hox cluster plasticity in actinopterygians. Taken together, our results suggest that actinopterygian Hox gene clusters experienced a reduction in selective constraints that surprisingly predates the teleost-specific genome duplication.

Raincrow JD ，Dewar K ，Stocsits C ，Prohaska SJ ，Amemiya CT ，Stadler PF ，Chiu CH ... -  《-》