Martin Kyle J, Holland Peter W H
Department of Zoology, University of Oxford, Oxford, UK.
Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK.
J Exp Zool B Mol Dev Evol. 2017 Nov;328(7):638-644. doi: 10.1002/jez.b.22726. Epub 2017 Feb 23.
An ancient genome duplication (TGD or 3R) occurred in teleost fish after divergence from the lineage leading to gar. This genome duplication is shared by the three extant teleost lineages: Osteoglossomorpha (bony-tongues), Elopomorpha (eels and tarpons), and Clupeocephala (a large clade including salmon, carp, medaka, zebrafish, cichlids, pufferfish, stickleback, and ∼26,000 other species). After TGD, different clupeocephalan species retained different gene duplicates; this is seen clearly in Hox gene clusters but extends to all genes. Since divergent resolution of TGD paralogs is a potential driving force for speciation, it is possible this contributed to diversification of this clade. The extent to which divergent resolution of TGD paralogs occurred within Osteoglossomorpha has not been investigated in detail, and Hox cluster organization has been reported for just two species: Pantodon buchholzi (Pantodontidae) and Scleropages formosus (Osteoglossidae). We applied survey-scale genome sequencing and de novo assembly to three further osteoglossomorph taxa: Osteoglossum bicirrhosum (Osteoglossidae), Chitala ornata (Notopteridae), and Gnathonemus petersii (Mormyridae). We find that each retained more Hox genes than clupeocephalan taxa (excluding those that underwent additional genome duplication), but fewer than eels. Several Hox genes are missing in all teleosts, including duplicates of two Hox genes present in the slow evolving pre-TGD genome of the spotted gar. We find divergent resolution through individual gene losses, and whole cluster losses have been rampant across osteoglossomorphs, despite their extant species paucity. We suggest that reciprocal gene loss following TGD was probably insufficient to drive the exceptional diversification of teleosts.
硬骨鱼在从与雀鳝分化的谱系中分化出来后发生了一次古老的基因组复制（TGD或3R）。这种基因组复制存在于现存的三个硬骨鱼谱系中：骨舌鱼目（骨舌鱼）、鳗鲡目（鳗鱼和大海鲢）以及全骨鱼类（一个大型类群，包括鲑鱼、鲤鱼、青鳉、斑马鱼、丽鱼、河豚、棘鱼以及约26000个其他物种）。在TGD之后，不同的全骨鱼类物种保留了不同的基因重复；这在Hox基因簇中很明显，但也扩展到了所有基因。由于TGD旁系同源基因的分化解析是物种形成的潜在驱动力，所以有可能这促成了该类群的多样化。骨舌鱼目中TGD旁系同源基因的分化解析程度尚未得到详细研究，并且仅报道了两个物种的Hox簇组织情况：布氏雀鳝（雀鳝科）和美丽硬仆骨舌鱼（骨舌鱼科）。我们对另外三个骨舌鱼分类群应用了调查规模的基因组测序和从头组装：双须骨舌鱼（骨舌鱼科）、长丝鱼芒（长丝鱼芒科）和彼得氏裸臀鱼（裸臀鱼科）。我们发现，每个分类群保留的Hox基因都比全骨鱼类分类群（不包括那些经历了额外基因组复制的分类群）多，但比鳗鱼少。所有硬骨鱼中都缺失了几个Hox基因，包括斑点雀鳝缓慢进化的TGD前基因组中存在的两个Hox基因的重复基因。我们发现通过单个基因丢失实现了分化解析，并且尽管骨舌鱼现存物种较少，但整个簇的丢失在骨舌鱼中很普遍。我们认为，TGD之后的相互基因丢失可能不足以推动硬骨鱼的异常多样化。
