Annotation Of Functional Regions And Application Of Mapping Structural Polymorphisms In Pig Genome

Two independent wild boar populations diverged from Southeast Asia and invaded the entire Eurasian mainland around 1 mya.Since then,multiple admixture and divergence events occurred among Sus species inhabiting Eurasian mainland,either by natural dispersal or by human intervention,eventually leading to the formation of genetic diversity and traits of pig species.To date,the domestic pig is one of the most popular livestock species predominately raised for human consumption worldwide.Besides its socio-economic importance,pig has been generally recognized as a valuable model species for studying human biology and disease.However,a lack of the complete pig annotation of functional regions and genetic polymorphisms have left a gap in our knowledge of the pig genome and have restricted the feasibility of using pigs as a biomedical model.We herein performed the genome annotation at multi-omics and the identification and application of genomic polymorphisms to providing valuable insights and a rich resource for enhancing studies of pig genomics and biology.The study here includes six parts,as follows:1)We presented the landscape of a tissue-based transcriptome for pigs.Our findings not only offer confirmatory evidence for 55,328 annotated transcripts corresponding to 20,401 existing protein-coding genes(PCGs)deposited in the NCBI annotation,but also supplemented 136,537 potentially novel alternatively spliced transcripts corresponding to 15,385 PCGs.Further profiling expression feature of these PCGs,we respectively identified 5,592 tissue-enriched PCGs,948 group-enriched PCGs,and 5,147 ubiquitously expressed PCGs in pig transcriptome.Besides,Comparison of transcriptomic profiling between human and pig.These common genes with similar expression patterns can be speculated to play similar roles in both human and pigs.Meanwhile,we found that most gene expression in human which is much higher than that in pigs is mainly related to the brain and nervous system,while 1,607 pig-dominated genes were enriched in allograft rejection and the olfactory transduction pathway,reflecting substantial differences in overall genomic functions and evolution history.2)We performed a tissue-based long Non-coding RNA(lncRNA)profiling via exploiting 32,212 non-redundant lncRNA isoforms corresponding to 18,676 IncRNA loci across 34 normal pig tissues using high-throughput sequencing.We deposited those with high-confidence(98%)in the publicly available NONCODE database,providing a valuable resource for facilitating pig non-coding genomic studies.Among these lncRNAs,ubiquitously expressed IncRNA appeared at a higher level compared to tissue-specific one.Furthermore,the potential relationship between our identified lncRNAs and PCGs were globally assessed via a comprehensive computation-based strategy,developing a genome-wide lncRNA-targeted genome draft for further functional studies on non-coding genes.3)We improved the genome annotation for 7,319 unknown protein isoforms,which includes 3,703 novel protein isoforms,669 protein isoforms from 460 genes symbolized beginning with LOC,and 2,947 protein iso forms without clearly NCBI annotation in current pig genome.Further combining the well-annotated gene that having parallel expression pattern and subcellular witness,we predicted the tissue related subcellular components and potential function for these unknown proteins.At last,we effectively identified 3,656 orthologous genes for 49.95%of unknown protein isoforms across multiple species,referring to 65 KEGG pathways and 15 disease signaling pathways.These findings provide valuable insights and a rich resource for enhancing studies of pig genomics and biology as well as biomedical model application to human medicine.4)We identified the genetic variations,including single nucleotide polymorphisms(SNPs),insertions and deletions(InDels)and copy number variations(CNVs),of 32 Meishan pigs,35 Duroc pigs and 30 Tibetan wild boars to mine in depth the genomic polymorphisms contributing to the breed features of pigs.On basis of SNPs with other 29 representative pig individuals,We systematically analyzed their global population structure,genetic divergence and demographic history.Finally,we constructed the first CNVR map in Meishan population and found 4 duplication CNVs near the exon 3-8 of AR gene were potentially associated with litter size.5)We found that the domestication of Meishan pigs occurred in the Taihu Basin area between the Majiabang and Liangzhu Cultures,during which 300 protein-coding genes underwent positive selection.Notably,enrichment of the FoxO signaling pathway and IGF1R were likely associated with high fertility of Meishan pigs.Moreover,NFKB1 exhibited strong selective sweep signals and positively participated in hyaluronan biosynthesis as the key gene of NF-kB signaling,which may have resulted in the wrinkled skin and face of Meishan pigs.Particularly,three population-specific synonymous single-nucleotide variants(SNVs)occurred in PYROXD1,MC1R,and FAM83G,of which the T305C substitution in MCIR explained the black coat in Meishan pigs well.In addition,the shared haplotypes between Meishan and Duroc breeds confirmed previous Asian-derived introgression and demonstrated the specific contribution of Meishan pigs.6)We performed high-precision structure variation(S V)detection using 13 pig assembly genomes and further validated the TE-related SVs through large scale sequencing data of 423 geographically representative pigs.Combining these haplotype-related TEs and the known evolutionary relationships between Sus species,allowed detecting the formation of a unique X chromosome pattern,which improves our understanding of admixture events in Sus species.We found that the formation of haplotype-related TEs independently occurred in 42 Mb regions of chromosome X in the early Middle Pleistocene in European and Asian wild boars.In the late Middle Pleistocene,introgression between European and North Asian wild boars resulted in two novel heterozygous haplotypes(12 Mb and 30 Mb).Around 0.2 million years ago,Tibetan wild boars with a heterozygous haplotype diverged from North Asian wild boars,and Tibetan wild boars in the Yunnan province gradually formed the South Asian pig haplotype due to introgression of South Asian pigs.Our findings revealed unknown introgression events of Eurasian wild boars in the Middle Pleistocene and showed that TEs are practical,useful markers for the study of pig ancestry and admixture.In conclusion,we constructed the annotation of functional regions and maps of structural polymorphisms in pig genome,contributing to the improvement of pig genome annotation and development of pig functional genome in future.