Comparative genomics reveal shared genomic changes in syngnathid fishes and signatures of genetic convergence with placental mammals.

Yan-Hong Zhang,He Dai,Hui-Xian Zhang,Geng Qin,Yu-Hong Liu,Feng-Ming Han,Qiang Lin,Jian-Ping Yin,Byrappa Venkatesh,Vydianathan Ravi,Xin Wang,Liang-Min Huang

doi:10.1093/nsr/nwaa002

Abstract

Syngnathids (seahorses, pipefishes and seadragons) exhibit an array of morphological innovations including loss of pelvic fins, a toothless tubular mouth and male pregnancy. They comprise two subfamilies: Syngnathinae and Nerophinae. Genomes of three Syngnathinae members have been analyzed previously. In this study, we have sequenced the genome of a Nerophinae member, the Manado pipefish (Microphis manadensis), which has a semi-enclosed brood pouch. Comparative genomic analysis revealed that the molecular evolutionary rate of the four syngnathids is higher than that of other teleosts. The loss of all but one P/Q-rich SCPP gene in the syngnathids suggests a role for the lost genes in dentin and enameloid formation in teleosts. Genome-wide comparison identified a set of 118 genes with parallel identical amino acid substitutions in syngnathids and placental mammals. Association of some of these genes with placental and embryonic development in mammals suggests a role for them in syngnathid pregnancy.

Highlights

Singapore; 3Southern manadensis), which has a semi-enclosed brood pouch
Libraries with insert sizes ranging from 200 bp to 17 kb were sequenced on the Illumina HiSeq 2500 platform, and 102.02 Gb of sequences filtered for low quality and duplicate reads were generated
The analysis showed that protein as well as nucleotide sequences of all four syngnathid members are evolving at higher rates compared to other teleosts, indicating that the accelerated molecular evolutionary rate is a common feature of the family Syngnathidae

Summary

Introduction

Singapore; 3Southern manadensis), which has a semi-enclosed brood pouch. Comparative genomic analysis revealed that the Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China; 4Biomarker molecular evolutionary rate of the four syngnathids is higher than that of other teleosts. Genome-wide comparison identified a set of 118 genes with parallel identical amino acid substitutions in syngnathids and placental mammals. Association of some of these genes with placental and embryonic development in mammals suggests a role for them in syngnathid pregnancy. Elongated body covered with bony plates, absence of pelvic fins and scales, and a specialized brood pouch. Syngnathids exhibit wide diversity in their morphology and coloration (see Supplementary Fig. S1.1). Besides a set of shared specialized features, syngnathids exhibit a gradient of additional derived morphological features. Recent phylogenetic analyses have revealed two distinct clades within the syngnathids, the tail-brooders and the trunk-brooders representing sub-families Nerophinae (trunk-brooding pipefishes) and Syngnathinae (tail-brooders comprising pipefishes, seadragons, pygmy pipehorses and seahorses), respectively [3,4] (see Supplementary Fig. S1.1)

Methods

Results

Conclusion