Analysis Based On Gene Copy Number And Sequence Provides Insights Into The Adaptive Evolution Of Vertebrates

The importance of gene duplication in providing genetic basis to the evolutionary innovations and phenotypic diversity of organisms has been extensively discussed.Genes derived from gene duplication are often called paralogs,which form gene families.Previous studies have revealed that many gene families sharing sequence and functional homology between different species have different numbers of genes,which is the result of the process of differential gene gain and loss among species.Changes in gene family size have been recognized to be related to speciation or adaptation.However,the pattern of gene family size evolution in vertebrates is still not well understood.In recent years,with the advancement of sequencing technology,more than 100 vertebrates have been sequenced at the whole-genome scale,which provides good data resources for the present study.In this paper,64 species that represent almost all the vertebrate groups(agnatha,fish,amphibian,reptilia,birds,mammalian)and spanning an evolutionary period of about 600 million years were selected.It is expected to reveal the evolution of vertebrate gene family size and the patterns of gene gain and loss span a large evolutionary time scale,and then to explore its connection with the adaptive evolution of vertebrates.Furthermore,transcriptome data and functional annotation data were integrated to describe the characteristics and biological significances of species-and lineage-specific genes and single-copy genes that are conserved across species.Among the 66 species,a total of 35592 gene families were clustered and their size distribution in different species was analyzed.The results show that more than 50% genes in each vertebrate genome are singletons(specifically,ranges from 51.65% in Nile tilapia to80.05% in Alpaca),with the exception of zebrafish.Meanwhile,the proportions of single-copy and multi-copy genes in the vertebrate genomes have greater inter-species variation than that of two-copy genes.For the 6857 gene families present in the most recent common ancestor of the vertebrates,likelihood analysis was used to infer the evolution of the size of these families.The results suggest that:(1)6712 of the 6857 gene families have either expanded or contracted along at least one lineage.(2)Vertebrate gene families were contracted in most lineages,which implies frequent gene loss.(3)The rate of gene gains and losses in vertebrates estimated by likelihood analysis is about 0.0006 per gene per million years.(4)A total of 148 gene families have been identified as rapidly evolving gene families;functional annotation show that these gene families are involved in various biological processes,including metabolic processes,developmental processes,circadian rhythm,and stimuli responses.High dynamics of the evolution of gene family size in vertebrates motivate us to identify any genomic signal with regard to the distinct gene family size that may have shaped the evolution of particular clades.We observed that a high proportion of gene families were proliferated in the recent ancestor leading to extant teleosts and then contracted in the decedents due to the extensive gene fractionation after whole-genome duplication.Species-and lineage-specific gene families(or genes)often have low expression and high tissue-specificity and may contribute to the phenotypic differences between vertebrates.Indeed,many bonefish-specific orphan genes have been found to be more prone to specifically expressed in pharyngeal gill and are involved in the development of fin,tail,and kidney,which suggests that these genes may be closely related to the adaptive evolution of fish in the aquatic environment.Bird-specific genes are enriched with feather keratin genes that associated with the birds-specific phenotype,that is feathers.Finally,to further investigate the characteristics of genes that always remain a single copy state during the evolution of vertebrates,their sequences,expression patterns and functions were analyzed.Analysis on sequence level reveals that these genes are highly conserved and are subjected to strong selection pressure.Analysis of expression patterns shows that such genes have higher expression levels and lower tissue specificity than non-single copy genes.Functional annotations indicate that such genes usually function as housekeeping genes.In summary,this study provides insight into the evolution of the vertebrate gene family size and supplies several lines of evidence for elucidating the genome evolution and phenotypic diversity of vertebrates.