Yak Genome Assembly And Annotation Improvements

Domestic yak(Bos grunniens)is remarkable for its adaptation to high altitude and occupies a central place in the economies of the Qinghai-Tibet plateaus(QTP);for past thousands of years,yak regard as unique large livestock species endemic to QTP and for long-term nature selection,yak has fully adapted to the extreme environments of high altitude,such as low oxygen,high UV radiation and so on,it is of great research value to study species adapt to the plateau.For the nomadic people on the Tibetan Plateau,it not only contributes to the clothes,food,and fuel on which the survival depends.Transportation and transportation are also important carriers for the inheritance and development of Tibetan culture and religion.Due to long-term artificial selection and breeding,the economic traits of domestic yaks have been severely degraded,which has seriously affected the production and life of pastoralists in Tibetan areas and the stability and development of the agricultural and pastoral industries.Therefore,the current protection and improvement of yak genetic resources have become very practical,and the acquisition of high-quality yak genomic maps is a key means to achieve this goal.Our team had previously sequenced and published the draft genome of a female domestic yak using mainly short read sequencing data.However,limited by the short reads length of second-generation sequencing technology,further improving the assembly length and integrity of the yak genome,reducing the error rate,and improving the quality of gene annotation are necessary for follow-up studies.In this article we present an improved genome assembly and annotation generated using additional short reads,we re-sequencing additional 151.35 Gb clean reads,combined with the previously published and announced 212.77 Gb sequencing data,finally we used the total sequencing depth of 121 X data reassembled the yak genome.The final assembly result was called yak v2.0.Compared to yak v1.1,Scaffold N50 was upgraded from the original 1.5Mb to the current 4.9Mb,Contig N50 from the original 20 Kb to the current 40 Kb,the quality of genome assembly has greatly improved;it is helpful for subsequent gene annotation analysis;in addition,we use PacBio's third-generation single-molecule sequencing technology to focus on the heart tissue of domestic calves,liver tissue,spleen tissue,lung tissue,kidney tissue,skin tissue,and testis were all sampled,covering the main tissues and organs of calves.Using PacBio's technology to build library and perform full-length transcriptome sequencing,the resulting full-length transcriptome data was used for gene annotation analysis to improve the accuracy and reliability of annotation results.Finally,we identified 21,398 high-quality products.The protein-coding genes that match these genes to NCBI's Uniprot database have more than 99% of the genes can be mapped,indicating that our annotation results are of very reliable quality.We reassembled and annotated the yak genome in this study,this yak genome version called yak v2.0,it has been significantly improved in quality compared to the previously published version of yak v1.1,For example,in particular,the number of scaffolds was reduced by half on the original basis,and the average length of the annotated genes was increased by 50% from the original value,which is closer to the index of the genes of the cattle.the publication of yak v2.0 can provide a solid foundation for further annotating the gene function of bovine species,revealing its evolutionary status,and comparative genomics,and can also actively promote the breeding of bovine species.