Knowledge about the impact of different geographical environments on rhesus macaque gut microbiota is limited. In this study, we compared the characteristics of gut microbiota in six different Chinese rhesus macaque populations, including Hainan, Nanning, Guizhou, Xichang, Jianchuan and Tibet. Through the composition analysis of operational taxonomic units (OTUs), we found that there were significant differences in the abundance of core overlapping OTUs in the six Chinese groups. Specifically, the Tibet population exhibited the highest gut microbial diversity and the most unique OTUs. Statistically significant differences in the composition of gut microbiota among the six groups at phylum and family level were evident. Specifically, Tibet had higher abundances of Firmicutes and lower abundances of Bacteroidetes than the other geographical groups, and the higher abundance of Firmicutes in the Tibetan group was mainly caused by a significant increase in the family Ruminococcaceae and Christensenellaceae. Phylogenetic investigation of communities by reconstruction of unobserved state analysis showed that the enrichment ratio for environmental information processing and organismal systems was the highest in the Tibet population. Additionally, our results suggested that in the adaptation process of rhesus macaques to different geographical environments, the abundance of the core common flora of the intestinal microbes had undergone varying degree of change and produced new and unique flora, both of which helped to reshape the gut microbiota of rhesus macaques. In particular, this change was more obvious for animals in the high-altitude environments.

Erianthus arundinaceus is a valuable source of agronomic traits for sugarcane improvement such as ratoonability, biomass, vigor, tolerance to drought and water logging, as well as resistance to pests and disease. To investigate the introgression of the E. arundinaceus genome into sugarcane, five intergeneric F1 hybrids between S. officinarum and E. arundinaceus and 13 of their BC1 progeny were studied using the genomic in situ hybridization (GISH) technique. In doing so, we assessed the chromosome composition and chromosome transmission in these plants. All F1 hybrids were aneuploidy, containing either 28 or 29 E. arundinaceus chromosomes. The number of E. arundinaceus chromosomes in nine of the BC1 progeny was less than or equal to 29. Unexpectedly, the number of E. arundinaceus chromosomes in the other four BC1 progeny was above 29, which was more than in their F1 female parents. This is the first cytogenetic evidence for an unexpected inheritance pattern of E. arundinaceus chromosomes in sugarcane. We pointed to several mechanisms that may be involved in generating more than 2n gametes in the BC1 progeny. Furthermore, the implication of these results for sugarcane breeding programs was discussed.

Background N 6-methyladenosine (m6A) is the most prevalent internal form of modification in messenger RNA in higher eukaryotes and potential regulatory functions of reversible m6A methylation on mRNA have been revealed by mapping of m6A methylomes in several species. m6A modification in active gene regulation manifests itself as altered methylation profiles in a tissue-specific manner or in response to changing cellular or species living environment. However, up to date, there has no data on m6A porcine transcriptome-wide map and its potential biological roles in adipose deposition and muscle growth.MethodsIn this work, we used methylated RNA immunoprecipitation with next-generation sequencing (MeRIP-Seq) technique to acquire the first ever m6A porcine transcriptome-wide map. Transcriptomes of muscle and adipose tissues from three different pig breeds, the wild boar, Landrace, and Rongchang pig, were used to generate these maps.ResultsOur findings show that there were 5,872 and 2,826 m6A peaks respectively, in the porcine muscle and adipose tissue transcriptomes. Stop codons, 3′-untranslated regions, and coding regions were found to be mainly enriched for m6A peaks. Gene ontology analysis revealed that common m6A peaks in nuclear genes are associated with transcriptional factors, suggestive of a relationship between m6A mRNA methylation and nuclear genome transcription. Some genes showed tissue- and breed-differential methylation, and have novel biological functions. We also found a relationship between the m6A methylation extent and the transcript level, suggesting a regulatory role for m6A in gene expression.ConclusionThis comprehensive map provides a solid basis for the determination of potential functional roles for RNA m6A modification in adipose deposition and muscle growth.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-017-3719-1) contains supplementary material, which is available to authorized users.

Background: The mammal intestinal microbiota is involved in various physiological processes and plays a key role in host environment adaption. However, for non-human primates (NHPs), little is known about their gut microbial community in high-altitude environments and even less about their adaption to such habitats. We characterised the gut microbial community of rhesus macaques from multiple high-altitude environments and compared it to those of low-altitude populations. Results: We collected faecal samples of rhesus macaques from four high-altitude populations (above 3000 m) and three low-altitude populations (below 500 m). By calculating the alpha diversity index, we found that high-altitude populations exhibited a higher diversity. Statistical analysis of beta diversity indicated significant differences between high-and low-altitude populations. Significant differences were also detected at the phylum and family levels. At the phylum level, the high-altitude gut microbial community was dominated by Firmicutes (63.42%), while at low altitudes, it was dominated by Bacteroidetes (47.4%). At the family level, the high-altitude population was dominated by Ruminococcaceae (36.2%), while the low-altitude one was dominated by Prevotellaceae (39.6%). Some families, such as Christensenellaceae and Rikenellaceae, were consistently higher abundant in all high-altitude populations. We analysed the overlap of operational taxonomic units (OTUs) in high-altitude populations and determined their core OTUs (shared by all four high-altitude populations). However, when compared with the lowaltitude core OTUs, only 65% were shared, suggesting a divergence in core OTUs. Function prediction indicated a significant difference in gene copy number of 35 level-2 pathways between high-and low-altitude populations; 29 of them were higher in high altitudes, especially in membrane transport and carbohydrate metabolism. Conclusions: The gut microbial community of high-altitude rhesus macaques was significantly distinct from that of low-altitude populations in terms of diversity, composition and function. High-altitude populations were dominated by Firmicutes and Ruminococcace, while in low-altitude populations, Bacteroidetes and Prevotellaceae were dominant. The difference in gut microbiota between these two populations may be caused by differences in host diet, environmental temperature and oxygen pressure. These differentiated gut microbial microorganisms may play a critical role in the adaptive evolution of rhesus macaques to high-altitude environments.

The gut microbiota helps the host to absorb nutrients and generate immune responses that can affect host behavior, development, reproduction, and overall health. However, in most of the previous studies, microbiota was sampled mainly using feces and intestinal contents from mammals but not from wild reptiles. Here, we described the bacterial profile from five different gastrointestinal tract (GIT) segments (esophagus, stomach, small intestine, large intestine, and cloaca) of three wild Rhabdophis subminiatus using 16S rRNA V4 hypervariable amplicon sequencing. Forty‐seven bacterial phyla were found in the entire GIT, of which Proteobacteria, Firmicutes, and Bacteroidetes were predominant. The results showed a significant difference in microbial diversity between the upper GIT segments (esophagus and stomach) and lower GIT segments (large intestine and cloaca). An obvious dynamic distribution of Fusobacteria and Bacteroidetes was observed, which mainly existed in the lower GIT segments. Conversely, the distribution of Tenericutes was mainly observed in the upper GIT. We also predicted the microbial functions in the different GIT segments, which showed that microbiota in each segments played an important role in higher membrane transport and carbohydrate and amino acid metabolism. Microbes in the small intestine were also mainly involved in disease‐related systems, while in the large intestine, they were associated with membrane transport and carbohydrate metabolism. This is the first study to investigate the distribution of the gut microbiota and to predict the microbial function in R. subminiatus . The composition of the gut microbiota certainly reflects the diet and the living environment of the host. Furthermore, these findings provide vital evidence for the diagnosis and treatment of gut diseases in snakes and offer a direction for a model of energy budget research.

The oriental fruit fly, Bactrocera dorsalis, is a serious pest of fruits and vegetables in South‐east Asia, and, because of quarantine restrictions, impedes international trade and economic development in the region. Revealing genetic variation in oriental fruit fly populations will provide a better understanding of the colonization process and facilitate the quarantine and management of this species. The genetic structure in 15 populations of oriental fruit fly from southern China, Laos and Myanmar in South‐east Asia was examined with a 640‐bp sequence of the mitochondrial cytochrome oxidase subunit I (COI) gene. The highest levels of genetic diversity were found in Laos and Myanmar. Low to medium levels of genetic differentiation (FST ≤ 0.134) were observed among populations. Pooled populations from mainland China differed from those in Laos and Myanmar (FST = 0.024). Genetic structure across the region did not follow the isolation‐by‐distance model. The high genetic diversity observed in Laos and Myanmar supports the South‐east Asian origin of B. dorsalis. High genetic diversity and significant differentiation between some populations within mainland China indicate B. dorsalis populations have been established in the region for an extended period of time. High levels of genetic diversity observed among the five populations from Hainan Island and similarity between the Island and Chinese mainland populations indicate that B. dorsalis was introduced to Hainan from the mainland and has been on the island for many years. High genetic diversity in the recently established population in Shanghai (Pudong) suggests multiple introductions or a larger number of founders.

Erianthus arundinaceus (E. arundinaceus) has many desirable agronomic traits for sugarcane improvement, such as high biomass, vigor, rationing ability, tolerance to drought, and water logging, as well as resistance to pests and disease. To investigate the introgression of the E. arundinaceus genome into sugarcane in the higher generations, intergeneric BC2 and BC3 progeny generated between Saccharum spp. and E. arundinaceus were studied using the genomic in situ hybridization (GISH) technique. The results showed that the BC2 and BC3 generations resulted from n + n chromosome transmission. Furthermore, chromosome translocation occurred at terminal fragments from the E. arundinaceus chromosome in some progeny of Saccharum spp. and E. arundinaceus. Notably, the translocated chromosomes could be stably transmitted to their progeny. This study illustrates the characterization of chromosome inheritance of the intergeneric BC2 and BC3 progeny between Saccharum spp. and E. arundinaceus. This work could provide more useful molecular cytogenetic information for the germplasm resources of E. arundinaceus, and may promote further understanding of the germplasm resources of E. arundinaceus for sugarcane breeders to accelerate its progress in sugarcane commercial breeding.

The complete mitochondrial genome of Eurasian lynx (Lynx lynx) from China has been described in this study. It has a circular genome of 16,996 bp with a higher A þ T content of 58.65%, and the base composition is A: 32.31%, G: 14.29%, T: 26.35%, C: 27.06%. When compared with the reported individual (KR919624) from China, there are 81 variations and 58 base deletion between the two sequences. The phylogenetic analysis indicated our sequence separated clearly from Eurasian lynx individuals in the previous publications. These results could provide more molecular information for the conservation of Eurasian lynx genetic resources.