We report the sequencing at 131× coverage, de novo assembly and analyses of the genome of a female Tibetan wild boar. We also resequenced the whole genomes of 30 Tibetan wild boars from six major distributed locations and 18 geographically related pigs in China. We characterized genetic diversity, population structure and patterns of evolution. We searched for genomic regions under selection, which includes genes that are involved in hypoxia, olfaction, energy metabolism and drug response. Comparing the genome of Tibetan wild boar with those of neighboring Chinese domestic pigs further showed the impact of thousands of years of artificial selection and different signatures of selection in wild boar and domestic pig. We also report genetic adaptations in Tibetan wild boar that are associated with high altitudes and characterize the genetic basis of increased salivation in domestic pig.

Edible plant-derived exosome-like nanoparticles (EPDELNs) are novel naturally occurring plant ultrastructures that are structurally similar to exosomes. Many EPDELNs have anti-inflammatory properties. MicroRNAs (miRNAs) play a critical role in mediating physiological and pathological processes in animals and plants. Although miRNAs can be selectively encapsulated in extracellular vesicles, little is known about their expression and function in EPDELNs. In this study, we isolated nanovesicles from 11 edible fruits and vegetables and subjected the corresponding EPDELN small RNA libraries to Illumina sequencing. We identified a total of 418 miRNAs—32 to 127 per species—from the 11 EPDELN samples. Target prediction and functional analyses revealed that highly expressed miRNAs were closely associated with the inflammatory response and cancer-related pathways. The 418 miRNAs could be divided into three classes according to their EPDELN distributions: 26 “frequent” miRNAs (FMs), 39 “moderately present” miRNAs (MPMs), and 353 “rare” miRNAs (RMs). FMs were represented by fewer miRNA species than RMs but had a significantly higher cumulative expression level. Taken together, our in vitro results indicate that miRNAs in EPDELNs have the potential to regulate human mRNA.

It is evident that epigenetic factors, especially DnA methylation, have essential roles in obesity development. Here, using pig as a model, we investigate the systematic association between DnA methylation and obesity. We sample eight variant adipose and two distinct skeletal muscle tissues from three pig breeds living within comparable environments but displaying distinct fat level. We generate 1,381 Gb of sequence data from 180 methylated DnA immunoprecipitation libraries, and provide a genome-wide DnA methylation map as well as a gene expression map for adipose and muscle studies. The analysis shows global similarity and difference among breeds, sexes and anatomic locations, and identifies the differentially methylated regions. The differentially methylated regions in promoters are highly associated with obesity development via expression repression of both known obesity-related genes and novel genes. This comprehensive map provides a solid basis for exploring epigenetic mechanisms of adipose deposition and muscle growth.

Uncovering genetic variation through resequencing is limited by the fact that only sequences with similarity to the reference genome are examined. Reference genomes are often incomplete and cannot represent the full range of genetic diversity as a result of geographical divergence and independent demographic events. To more comprehensively characterize genetic variation of pigs (Sus scrofa), we generated de novo assemblies of nine geographically and phenotypically representative pigs from Eurasia. By comparing them to the reference pig assembly, we uncovered a substantial number of novel SNPs and structural variants, as well as 137.02-Mb sequences harboring 1737 protein-coding genes that were absent in the reference assembly, revealing variants left by selection. Our results illustrate the power of whole-genome de novo sequencing relative to resequencing and provide valuable genetic resources that enable effective use of pigs in both agricultural production and biomedical research.

Background: MicroRNAs (miRNAs), a large family of short endogenous RNAs known to post-transcriptionally repress gene expression, participate in the regulation of almost every cellular process. Changes in miRNA expression are associated with many pathologies. Ovarian folliculogenesis and testicular spermatogenesis are complex and coordinated biological processes, in which tightly regulated expression and interaction of a multitude of genes could be regulated by these miRNAs. Identification and preliminary characterization of gonad-specific miRNAs would be a prerequisite for a thorough understanding of the role that miRNA-mediated posttranscriptional gene regulation plays in mammalian reproduction.Method: Here, we present the identification of a repertoire of porcine miRNAs in adult ovary and testis using deep sequencing technology. A bioinformatics pipeline was developed to distinguish authentic mature miRNA sequences from other classes of small RNAs represented in the sequencing data.Results: Using this approach, we detected 582 precursor hairpins (pre-miRNAs) encoding for 732 mature miRNAs, of which 673 are unique. Statistically, 224 unique miRNAs (out of 673, 33.28%) were identified which had significant differential expression (DE) between ovary and testis libraries (P < 0.001). Most of DE miRNAs located on the X chromosome (X-linked miRNAs) (24 out of 34, 70.59%) significantly up-regulated in ovary versus testis (P < 0.001). Predictably, X-linked miRNAs are expressed in a testis-preferential or testis-specific pattern. To explore the potential for co-expression among genomic location clusters of X-linked miRNAs, we surveyed the relationship between the distance separating miRNA loci and the coordinate expression patterns of 32 high confidence X-linked miRNAs in seven normal pig tissues using the real-time quantitative PCR (q-PCR) approach. Our results show that proximal pairs of miRNAs are generally co-expressed implying that miRNAs within 50 kb of genomic bases are typically derived from a common transcript.Conclusions: The present study characterizes the miRNA transcriptome of adult porcine gonads, with an emphasis on the co-expression patterns of X-linked miRNAs. Our report should facilitate studies of the organ-specific reproductive roles of miRNAs.