Pattern of New Gene Origination in a Special Fish Lineage, the Flatfishes

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.

Evolutionary New Genes in a Growing Paradigm

“…It is now clear that some of the patterns of the origination of new genes have been consistent across the tree of life. For example, Li et al [ 4 ] used comparative genomics to identify new genes in the starry flounder and found, consistently with previous observations, that DNA-mediated duplications are 10 times more abundant than either RNA-mediated duplications or the genes categorized as potentially de novo genes. Interestingly, in this work, they observed that some of the newly evolved genes were differentially expressed between the left and the right side of the starry flounder body, and their contribution to the asymmetric body plan of flatfishes needs to be explored from this new angle in the evolution of this developmental trait.…”

Chromosome-level genome of butterflyfish unveils genomic features of unique colour patterns and morphological traits

“…Physiological and morphological phenotypic diversity in the past was driven by genomic innovations, including gene gain and lost. 15–17 Genes underwent duplication through various mechanisms, such as tandem duplication, segmental duplication and whole-genome duplication. 18 , 19 The expansion of gene numbers likely facilitated morphological innovation.…”

Evolutionarily new genes in humans with disease phenotypes reveal functional enrichment patterns shaped by adaptive innovation and sexual selection.

“…New genes have also been found with roles in early larval development of Drosophila (Kasinathan et al 2020). In nematodes, insects, and fish, some lineage-specific genes are thought to be involved in the functions of morphological development, a process which was long believed to be governed by deeply conserved genetic mechanisms (Ragsdale et al 2013; Klomp et al 2015; Li et al 2021). These studies from model species reveal various important biological functions of new genes.…”