Abstract
Origination of new genes are of inherent interest of evolutionary geneticists for decades, but few studies have addressed the general pattern in a fish lineage. Using our recent released whole genome data of flatfishes, which evolved one of the most specialized body plans in vertebrates, we identified 1541 (6.9% of the starry flounder genes) flatfish-lineage-specific genes. The origination pattern of these flatfish new genes is largely similar to those observed in other vertebrates, as shown by the proportion of DNA-mediated duplication (1317; 85.5%), RNA-mediated duplication (retrogenes; 96; 6.2%), and de novo–origination (128; 8.3%). The emergence rate of species-specific genes is 32.1 per Mya and the whole average level rate for the flatfish-lineage-specific genes is 20.9 per Mya. A large proportion (31.4%) of these new genes have been subjected to selection, in contrast to the 4.0% in primates, while the old genes remain quite similar (66.4% vs. 65.0%). In addition, most of these new genes (70.8%) are found to be expressed, indicating their functionality. This study not only presents one example of systematic new gene identification in a teleost taxon based on comprehensive phylogenomic data, but also shows that new genes may play roles in body planning.
Highlights
New genes may play significant roles in evolution of organisms [1,2]
The results show that the flatfish-specific new genes have similar evolutionary pattern to those identified in primates, and perhaps due to longer divergence time (73.7 million year ago (Mya)) higher proportion of new genes of flatfishes were under functional constraint
The divergence time between the reference species (P. stellatus) and its closest species is around 41.8 million year ago (Mya), and in the flatfishes with outgroups is 73.7 Mya
Summary
The term “new gene” refers to a novel genetic unit that originated in a specific lineage [2] As they only exist in certain species or evolutionary lineages, new genes are called species or lineage-specific genes [3]. The synteny-based pipeline (SBP) method [7] is suited for recently duplicated genes’ identification, whereas the protein-family-based methods are useful for ancient new genes [8,9]. The establishment of these method provides us an opportunity to understand the pattern of origin of new genes in a lineage
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