There are only six isolated living giant panda populations, and a comprehensive understanding their genetic health status is crucial for the conservation of this vulnerable species. Liangshan Mountains is one of the main distribution areas of living giant pandas and is outside the newly established Giant panda national Park. In this study, 971 giant panda fecal samples were collected in the heartland of Liangshan Mountains (Mabian Dafengding Nature Reserve: MB; Meigu Dafengding Nature Reserve: MG; and Heizhugou Nature Reserve: HZG). Microsatellite makers and mitochondrial D-loop sequences were used to estimate population size and genetic diversity. We identified 92 individuals (MB: 27, MG: 22, HZG: 43) from the three reserves. Our results showed that: 1) Genetic diversity of three giant panda populations was medium-low; 2) Quite a few loci deviated significantly from the Hardy-Weinberg equilibrium and almost all these deviated loci showed significant heterozygote deficiencies and inbreeding; 3) Three giant panda populations have substantial genetic differentiation with the most differentiation between MB and the two other populations; 4) a large amount of giant panda feces outside the three reserves were found, implying the existence of protection gap. These results indicated that the giant panda population in Liangshan Mountains is at an risk of genetic decline or extinction given stochastic events and urgent need of human management. This study revealed that high attention should be paid to the protection of these giant panda populations outside the Giant panda national Park, to ensure them survival in their distribution areas.

The Tibetan macaque (Macaca thibetana) is an endemic macaque species in China belonging to the sinica group in genus Macaca. Here, we report the first chromosome-level genome assembly for the Tibetan macaque using PacBio long-read sequencing and Hi-C technology. The assembled Tibetan macaque genome was 2.82 Gbp in size with contig N50 of 48.75 Mbp and scaffold N50 of 150.62 Mbp, which was anchored to 22 chromosomes. Compared to the chromosome-level genome of rhesus macaque and cynomolgus macaque, the genome size of the Tibetan macaque is the smallest and the assembly quality is the best. A total of 22,485 protein-coding genes and 1.33 Gbp repeat sequences were annotated in the Tibetan macaque genome. Phylogenetic analysis indicated the Tibetan macaque was closely related to the stump-tailed macaque and diverged from a common ancestor 5.06 million years ago. A total of 977 positively selected genes were identified, which were enriched in pathways related to the thyroid, diabetes mellitus, fatty acid biosynthesis and metabolism. Among them, 11 genes associated with tail development and 9 genes associated with body size were found to be under positive selection, which might contribute to short tail and large body size of the Tibetan macaque. The structural variation (SV) analysis between the Tibetan macaque and other macaques identified 6,778 Tibetan macaque-specific SVs. Among them, three deletions and four insertions in six genes might be associated with tail development and body size. The high-quality genome of the Tibetan macaque will benefit further biological and evolutionary studies on primates.

The gut microbiomes of the host are large and complex communities, which helps to maintain homeostasis, improves digestive efficiency, and promotes the development of the immune system. The small mammals distributed in Sichuan Province are the most popular species for biodiversity research in Southwest China. However, the effects of different diets on the structure and function of the gut microbial community of these small mammals are poorly understood. In this study, whole-metagenome shotgun sequencing has been used to analyze the composition and functional structures of the gut microbiota of seven small mammals in Laojunshan National Nature Reserve, Sichuan Province, China. Taxonomic classification revealed that the most abundant phyla in the gut of seven small mammals were Bacteroides, Proteobacteria and Firmicutes. Moreover, Hafnia, Raoultella and Aeromonas were most abundant genus in the gut microbiomes of these seven species. At the functional level, we annotated a series of KEGG functional pathways, six Cazy categories and 46,163 AROs in the gut microbiomes of the seven species. Comparative analysis found that the difference in the gut microbiomes between the Soricidea and Muridae concentrated on the increase in the F/B (Firmicutes/Bacteroides) ratio in the Soricidea group, probably driven by the high fat and calorie digestive requirements due to their insectivorous diet. The comparative functional profiling revealed that functions related to metabolism and carbohydrates were significantly more abundant in Muridae group, which may be attributed to their high carbohydrate digestion requirements caused by their herbivorous diet. These data suggested that different diets in the host may play an important role in shaping the gut microbiota, and lay the foundation for teasing apart the influences of heritable and environmental factors on the evolution of gut microbial communities.