Comparative Genomics Analyses Of Tandem Duplicated Genes In Vertebrates

Gene duplication is a fundamental process in the evolution of species.There are many ways including whole genome duplication(WGD),tandem duplication,segmental duplication and gene transposition to realize gene amplification.Gene duplication may lead to the establishment of lineage specific traits and to the development of novel biological functions.These duplicated genes would have three different fates: neofunctionalization,subfunctionalization,or defunctionalization.Therefore,gene duplication is one of the most important factors that influence the evolution of genome size,the origination of novel gene,the genetic robustness against null mutations and the speciation.Tandem duplication and WGD are the main two of all these duplication models.There are many studies about WGD event occurred in animals and plants while less studies about tandem duplication.Most previous researches on tandem duplication have so far been restricted to single tandem duplicated gene(TDG)or certain family in a few species.The overall understanding of TDGs in vertebrates are still lacking.With the continuous accumulation of genomic data,comparative genomics has become one of the most powerful tools exhibiting significant role in the functional genomics research.Identification of different TDGs in different vertebrates through comparative genomic studies can help us understand the relationship between TDGs and adaptation in vertebrates.Here we performed comprehensive analyses of duplicated genes from 23 vertebrate species: human,gorilla,orangutan,mouse,rat,guineapig,chicken,turkey,zebra finch,anole lizard,tropical clawed frog,coelacanth,spotted gar,platyfish,stickleback,fugu,tetraodon,medaka,nile tilapia,channel catfish,southern catfish,cave fish,zebrafish.We analyzed TDGs distribution,sizes,functions in these species and tissue expression profile of TDGs in tilapia and southern catfish.We also identified shared and species-specific TDGs,compared their distribution among species.The results were as follows:Genome sequences and associated annotation information of 23 species were downloaded from databases,then extracted the longest amino acid sequence of each gene,and removed the genes encoding amino acids less than 25.Through whole-genome BLASTP computing collinear blocks for all possible pairs of chromosomes and scaffolds using MCScan X algorithm,genes within a single genome were classified as singletons,proximal duplicates(in nearby chromosomal region but not adjacent),tandem duplicates(consecutive repeat),segmental/WGD duplicates(i.e.collinear genes in collinear blocks)and dispersed duplicates(other modes than segmental,tandem and proximal)depending on their copy number and genomic distribution.TDGs account for an average of about 10.6% of all genes in these 23 vertebrate genomes,and about 13.5% of all duplications.In mammals,birds and fishes,the percentage of TDGs in all genes or all duplications were 15.3% and 19.9%,7.7% and 10.1%,8.7% and 10.8% respectively.In mammals,the mouse had the largest number 4833 TDGs,and in teleosts the zebrafish had 3955 TDGs.The majority of tandem duplication cluster(55.7-87.1%)has only 2 members.In all 23 species,the proportion of genes that belong to TDGs tends to be higher in large gene families than in small ones.Among these families,TDG sizes of or(olfactory receptor)and pcdh(protocadherin)are greater than 10 in most of vertebrates,and TDG sizes of krt(keratin)and crygm(crystallin gamma)are greater than 10 in tetrapods and teleosts,respectively.However,other families like taar(trace amine associated receptor)and cxcr(chemokine receptor)seem to be unpredictable.These results demonstrated that the number of TDGs display certain taxa similarity and species specificity,which may be related to the adaptability of the taxa or species to the environment.According to sequence similarity,all TDGs from 23 species were divided into 2045 different families.Venn diagrams showed that the more closely related the species are,the more TDGs they share.Gene Ontology(GO)analyses revealed that the tetrapods shared TDGs and the teleosts shared TDGs were involved in different biological processes and molecular functions.The TDGs of teleosts functions respond to stimulation and sensation signals.Based on transcriptome data from 8 tissues of adult tilapia and 12 tissues of southern catfish,most TDGs were found to be expressed in immune and excretory organs,such as gill,spleen,kidney,head kidney.In addition,they showed specific expression patterns in the brain,liver and other tissues.These results suggested that the generation of TDGs were essential for species to adapt their surroundings.On one hand,TDGs help species to enhance basic life activities,on the other,they can improve immunity and ability to respond to external stimulation.We identified some shared and species-specific TDGs.Hox gene clusters and “DMRT1-DMRT3-DMRT2” cluster were conserved in all vertebrates.They play pivotal roles in development and reproduction of vertebrates.Cldn10 and olfm4,which may be important in the fish immune system adapting water environment are TDGs shared in all teleosts.The cldn10 TDGs were occured before the teleost-specific genome duplication(TSGD)while the olfm4 TDGs occured after the TSGD.Species-specific TDGs,fbxw12(F-box and WD repeat domain containing 12),crygm(crystallin gamma)and ZPC(zona pellucida C),were important for reproduction and metabolic regulation of mouse,zebrafish and channel catfish.Together,our results suggested that TDGs provided abundant genetic materials for species to adapt the variable environment.In summary,this work provided a new perspective on the evolution and function of TDGs and novel idea to explore the relationship between gene duplication and adaptive evolution.Identification of TDGs in genome laid the foundation for studying the environmental stress,adaptation and evolution of vertebrates.