Comparative Genomics Analysis Of Origin And Evolution Of Ruminant Headgear

Ruminants are the only extant mammalian group possessing bony(osseous)headgear.The headgear is a key innovative organ of rumiants during evolution.Each family within the Pecorans exhibits a unique headgear morphology.Such as the pronghorns of Antilocapridae and the horns of Bovidae possess a keratinous sheath,and the antlers of Cervidae are wholly deciduous,regenerating annually.The evolutionary origin of headgear,notably whether headgear evolved only once or multiple times,has been a matter of considerable scientific discussion.In addition,antlers grow extremely fast and the cell proliferation surpassing even cancerous tissue growth.The precisely regulated cell growth regulators are required to controll antler regeneration may confer protection in the development of cancers.However,there is no comparative genomic analysis to reveal the genetic basis of these complex biological issues.We de novo assembled a high qualiy genome of Hydropotinae and two contig levels genomes of Moshidae,and collected one genome of Traguloidea,one genome of Antilocaprinae,two genomes of Giraffoidea,eight genomes of Cervidae,and 38 genomes of Bovidae.The 54 rumiants'genomes covered all families of extant rumiants.In addition,we obtained 270 transcriptomes data,including 20 transcriptomes of sika deer,20transcriptomes of roe deer,68 transcriptomes of goat and 162 transcriptomes of sheep.The results of our genome and transcriptome analysis were described as below:1,We provide a high quality reference genome from a antlerless species,the Chinese water deer(Hydropotes inermis,Conttig N50:47.9 Kb,Scaffold N50:5.7Mb)of the cervid subfamily Hydropotinae,and two contig-level genomes of Moschidae species(Moschus chrysogaster and M.leucogaster).We investigated pseudogenization in the shape of premature stop codons and frameshifts in both of these lineages.Of 289 pseudogenes identified in these two distant lineages,RXFP2 could be the functional mechanism behind the convergent secondary loss of headgear in the Moschidae and Hydropotinae lineages.2,We identified 624 horn-specific genes and 761 antler-specific genes by the transcriptome data of multiple tissues.Both horn and antler were most highly co-expressed in bone,skin,testis and brain tissues.The 201 headgear-specific expression genes were shared by both antler and horn tissues,and these genes were enriched in bone development,skin development,and neurogenesis pathways.The gene expression results suggest that the development of both kinds of headgear involves similar gene expression profiles.3,We identified 240 genes were positively selected and 8,732 lineage-specific highly conserved elements in the pecorans with headgear.The positively selected genes(e.g.OLIG1,OTOP3),headgear-specific expression genes(e.g.SOX10,RXFP2,TFAP2A),lineage-specific highly conserved elements related genes(e.g.HOXD,SOX9,RXFP2)and horn-related genes were involved in neural crest cells migration pathway.Therefore,pecoran headgear likely shares a common cellular origin in neural crest stem cells.4,A total of 156 positively selected genes and 117 accelerated evolved conserved elements of Cervidae were identified.Both antler-specific expridentifiedession genes and cervid-specific HCE-associated genes are enriched in terms associated with the axon guidance pathway,these lines of evidence corroborate that neural processes are heavily involved in the unique process of annual antler regeneration.We found a higher correlation between the gene expression profiles of antler and osteocarcinoma(r~2=0.67-0.78)than between those of antler and normal bone tissues(r~2=0.33-0.47).Several proto-oncogenes and tumor suppressors,FOS,FAM83A,REL,PML and ADAMTS18 were under selection in Cervidae,which may play important roles in finely regulating antler growth,and as a byproduct confer cancer resistance in cervids.5,To explore the functional consequences of the cervid-specific PML amino acid changes,we constructed a human PML overexpression vector(pCDH-PML-human)and a cervid type PML vector(pCDH-PML-deer)by replacing the human alleles with unique cervid mutations.We found that overexpression of the native human PML gene can decrease cancer cell growth as expected,but significantly less strongly than the variant with cervid mutations.We also noticed that the PML-deer protein levels were all higher(1.49-1.84 times)than that of PML-human.Our mRNA and protein quantification results suggest that the deer-specific changes in PML may increase protein stability or gene translational efficiency,enhancing its efficiency as a cancer growth antagonist.In this study,we based on the results of comparative genomes and transcriptomes as well as cell experiment to explore the genetic basis of the origin and evolution of ruminantheadgear and the low cancer incidence of deers.