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Mycoplasma capricolum subsp. Capricolum (Mcc) is an important member of the Mycoplasma mycoides cluster (Mm cluster) and causes caprine contagious agalactia. Mcc can infect goats of all age groups, especially pregnant ewes and kids. It can cause the abortion in pregnant ewes and the death of goat kids, leading to enormous losses in the goat breeding industry. To date, the prevalence of epidemic Mcc strains on Hainan Island, China, remains unclear. This study aimed to isolate and identify Mcc strains endemic to Hainan Island, China. Genome sequencing and comparative genomic analysis were performed to reveal the molecular characteristics and evolutionary relationships of the isolated strain. Mcc HN-B was isolated and identified in Hainan Island, China. The Mcc HN-B genome consists of a 1,117,925 bp circular chromosome with a 23.79% G + C content. It contains 912 encoding genes, 3 gene islands, and 14 potential virulence genes. The core genome with the features of the Mm cluster and the specific genes of Mcc HN-B were identified by comparative genomic analysis. These results revealed the evolutionary relationship between Mcc HN-B and other members of the Mm cluster. Our findings provide a reference for further studies on the pathogenic mechanism and local vaccine development of Mcc. [ABSTRACT FROM AUTHOR]

Goats have become one of the most adaptive and important livestock species distributed in developing countries in recent years. The Hainan Black goat is a native goat breed of the Hainan region that is generally well-liked by the local population and is thus raised in large numbers. However, the genomic diversity and selective signals of the Hainan Black goat have not been clearly elucidated yet. Therefore, in this study, we performed whole-genome resequencing of 16 Hainan Black goats and compared the results with those of 71 goats of 6 other breeds from different geographic regions. Principal component analysis (PCA) and phylogenetic analysis identified seven lineages for all goats. Hainan Black goats showed the most similarity with Leizhou goats and the least similarity with Boer goats. Selective sweep analysis identified candidate genes associated with various functions, including immune resistance to disease (TNFAIP2 (TNF alpha induced protein 2) and EXOC3L4 (exocyst complex component 3 like 4)), melanin biosynthetic process (CDH15 (cadherin 15), ASIP (agouti signaling protein), and PARD3 (par-3 family cell polarity regulator)), and light sensitivity (CNGB3 (cyclic nucleotide gated channel subunit beta 3) and CNBD1 (cyclic nucleotide binding domain containing 1)), underlying strong selection signatures in Hainan Black goats. The melanin biosynthetic process, circadian entrainment, regulation of cyclic adenosine 3,5-monophosphate (cAMP)-mediated signaling, and the Rap-1 signaling pathway were significantly enriched in Hainan Black and Alashan Cashmere goats. This result may be important for understanding each trait. Selection signature analysis revealed candidate single nucleotide polymorphisms (SNPs) and genes correlated with the traits of Hainan Black goats. Collectively, our results provide valuable insights into the genetic basis of specific traits correlated with the Hainan island climate, artificial selection in certain local goat breeds, and the importance of protecting breed resources. [ABSTRACT FROM AUTHOR]

• Investigate genetic diversity and unravel genomic regions potentially under selection for climatic conditions and geographic isolation in Hainan cattle. • The population structure revealed that Hainan cattle were originally from bos indicus and carried other ancestry. • The positive selection genes in Hainan cattle were mainly associated with immune pathways including bacterial invasion of epithelial cells, chemokine signaling pathway, and T cell receptor signaling pathway. The equatorial climate of Hainan Island has led to the evolution of Hainan cattle that are well adapted to the local conditions. This study aims to estimate the genetic diversity and selection signatures of Hainan cattle. After analyzing the whole-genome sequencing (WGS) data of 76 cattle from four representative populations of East Asian taurine cattle, India-Pakistan indicine cattle, Chinese indicine cattle, and Hainan locally adapted cattle, a total of 20,075,403 autosomal single nucleotide polymorphisms (SNPs) were detected. The Hainan cattle exhibited the highest level of genetic diversity (Ho=0.31, He=0.3). The increased genetic diversity observed in Hainan cattle population may be attributed to the admixture with Chinese indicine cattle population. The analysis of selective sweep, which was achieved through the utilization of Z F ST and log 2 π, indicated the detection of 92 potential loci in Hainan cattle, which encompassed 141 genes that underwent positive selection and were associated with immune pathways, including bacterial invasion of epithelial cells, the chemokine signaling pathway, and the T cell receptor signaling pathway. Mutations analysis revealed that two missense mutations in SKINT1 (c.458C>T, p.P153L and c.580G> A , p.D194N) and two missense mutations in BCAR1 (c.1765C>G, p.A589P and c.1150C>T, p.G384S) were the homozygous genotypes in Hainan cattle. This finding enhances our understanding of the polygenic basis underlying climatic adaptation in Hainan cattle and holds significant value for the preservation and utilization of these genetic resources. [ABSTRACT FROM AUTHOR]