Genetic diversity of the Sichuan snub-nosed monkey (Rhinopithecus roxellana) in Shennongjia National Park, China using RAD-seq analyses

Ecological Health Assessment of Chinese National Parks Based on Landscape Pattern: A Case Study in Shennongjia National Park

Assessing the health of the ecosystem based on the landscape pattern of national parks can facilitate policy makers in formulating more targeted conservation policies to better manage national park ecosystems. To analyze the landscape patterns and characteristics of the national park, the ecosystem health evaluation index system of the national park was constructed using the vigor-organization-resilience (VOR) model to evaluate the health status. In this study, the Shennongjia National Park in China was selected as a case study area to be assessed using the index system. The results revealed that the patches of construction land and farmland are the largest in number and the most complex in shape, reflecting the obvious fragmentation of construction land and farmland patches. All patch types in this national park were evenly distributed. The results of the analysis showed that the comprehensive index of national park heath, according to the VOR model, is 0.74, indicating that the ecosystems in this study area were in a good state of health. Ecosystems in strictly protected areas of this park had the highest ecosystem health index levels, while the traditional utilization areas had the lowest. Ecosystem health levels were characterized by significant spatial agglomeration characteristics, with high-high aggregation distribution areas, mainly clustered in strictly protected areas, and low-low aggregation distribution, mainly clustered in traditional utilization areas and marginal areas. This study provided a set of ecosystem health assessment systems and their practical use in China’s newly established national parks.

Identification and expression profile of microRNA in seven tissues of the Golden snub-nosed monkey (Rhinopithecus roxellanae)

MicroRNAs (miRNAs) are key in the post-transcriptional regulation of gene expression and thus characterization of miRNAs and investigation of the relative abundance and specificity of tissue expression are essential for understanding gene expression in the golden snub-nosed monkey (GSM, Rhinopithecus roxellanae). Here, we report the first dataset of GSM miRNAs where we identified 460 miRNAs in seven tissues, with 246 conserved known mature miRNAs and 214 novel mature miRNAs. We determined miRNA abundance and expression in the seven tissues using a Tissue Specificity Index score and found that most novel GSM miRNAs showed a highly tissue-specific expression pattern. In particular, 67 novel miRNAs and the miR-34 family were expressed in abundance only in the lung. Five known miRNAs were highly abundant in digestive organs such as the pancreas and liver, and four novel miRNAs were highly expressed in the heart and muscle. Annotation of target genes of GSM miRNAs indicated that target genes were enriched in many important pathways, such as the HIF-1 signaling pathway and xenobiotic biodegradation-related pathways. Collectively, these results emphasize that miRNAs play important roles in GSM diet and high-elevation adaptation regulation. In summary, this study provides essential information on GSM miRNAs and will benefit further investigations of the function and mechanism of miRNAs in controlling gene expression in the GSM.

Genome-wide SNP discovery and genetic diversity evaluation of Liangshan cattle in China

Liangshan cattle are a very small indigenous breed with adult weight of less than 300 Kg and have been mainly distributed in the Liangshan Yi Autonomous Prefecture of Southwestern Sichuan, China. Due to its long-term adaptation to local environments, Liangshan cattle is a valuable genetic resource and should be paid with more attentions. However, the genetic diversity of Liangshan cattle have not been specifically investigated yet, which would be required when designing the appropriate conservation and utilization programs. In this study, we successfully employed the restriction-site-associated DNA sequencing (RAD-seq) approach to explore a total of 84,854 genome-wide and high-confidence SNPs of Liangshan cattle. All these SNPs were evenly distributed through all chromosomes with an average of 98 SNPs per 1-Mb region. The nucleotide diversity, expected heterozygosity, polymorphism information content of Liangshan cattle were 0.227, 0.223 and 0.183, respectively. Furthermore, there was no obvious difference on the genetic diversity among the three studied geographical populations. In conclusion, we provided a list of SNPs that could be used in the follow-up studies for Liangshan cattle and revealed a relatively high genetic variation in this gene pool.