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

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.

Exploring ecological specialization in pipefish using genomic, morphometric and ecological evidence

“…We detected SNPs using SAMtools and then filtered them to meet the following criteria: (1) quality score ≥20; (2) coverage depth ≥5 and ≤1,000; (3) SNPs with minor allele frequency (MAF) > 0.01; (4) a missing ratio of samples <50% within each group (Zhang, Ravi, et al, 2020).…”

Genomic Convergence in the Adaptation to Extreme Environments

“…A central question is whether the convergence in phenotype reflects similar underlying molecular events. Most empirical and theoretical work to address this question has focused on unicellular organisms, mammals, model plants, and crops ( Zhang, 2006 ; Li et al., 2010 ; Lin et al., 2012 ; Tenaillon et al., 2012 ; Zhen et al., 2012 ; Lenser and Theißen, 2013 ; Stern, 2013 ; Storz, 2016 ; Woodhouse and Hufford, 2019 ; Wu et al., 2020a , 2020b ; Zhang et al., 2020 ). Recently, the availability of genomic data has enabled the expansion of molecular convergence analyses to non-model organisms.…”

“…Recently, the availability of genomic data has enabled the expansion of molecular convergence analyses to non-model organisms. The detection of convergence at the whole-genome level is emerging as a new frontier in evolutionary biology ( Parker et al., 2013 ; Foote et al., 2015 ; He et al., 2020a ; Zhang et al., 2020 ). However, it is still unknown whether genomic convergence is a common feature of adaptive evolution.…”

Wnt8a is one of the candidate genes that play essential roles in the elongation of the seahorse prehensile tail

“…6 Schematic showing the hypothesized roles of Wnt family members in the seahorse tail extended outgrowth. The development of the specialized seahorse tail is regulated by the combined activity of Wnt5a, Wnt8a, and Wnt11; Wnt5a and Wnt8a strongly promote tail bud extension and Wnt11 promotes tail somite formation and Wilson 2002; Zhang et al 2020). MyoD is a skeletal muscle-specific gene, the expression of which is restricted to the somites (Hopwood et al 1989).…”

“…Seahorses (genus Hippocampus) are known for their unique morphological features, such as an elongated and prehensile tail, and ovoviviparous reproductive strategies (Li et al 2020;Lin et al 2016;Neutens et al 2014;Zhang et al 2020). The seahorse tail is regarded as a remarkable evolutionary innovation, as it is not used for rapid swimming but, instead, as a flexible appendage for grasping (Ashley-Ross 2002;Porter et al 2015).…”