中国科学院昆明动物研究所机构知识库

面对环境变化或环境胁迫时，生物体可能会在不同的层面发生应对机制。针对生物体应对环境的机制，本研究以高原鼢鼠和猪为研究对象，对高原鼢鼠应对高海拔环境相关的基因间长非编码RNA(long intergenic noncoding RNA, lincRNA)和猪应对不同饲养环境相关的肠道微生物进行解析。高原鼢鼠是青藏高原特有的啮齿动物，在高原环境中受到高寒、高辐射、低氧的环境胁迫。本研究以lincRNA为切入点，研究高原鼢鼠应对高海拔环境的机制。通过分析来自多海拔多组织的高原鼢鼠样本的RNA-seq数据，得到了14024条lincRNA基因，然后鉴定了高海拔特异表达的lincRNA基因，并且对编码基因和lincRNA基因进行了共表达分析，鉴定了和海拔变化相关的共表达模块，这些模块内的lincRNA基因和高海拔特异表达的lincRNA基因均可以视为高原鼢鼠适应高原环境相关的候选lincRNA基因。然后对lincRNA基因和编码基因进行相互作用关系的初步探索，在这其中关注了高海拔特异表达的lincRNA基因和邻近编码基因的相互作用关系，以及模块内重要的编码基因和lincRNA基因的相互作用关系。本研究注释了高原鼢鼠基因组中的lincRNA基因部分，发现了与高原鼢鼠应对高海拔环境相关的lincRNA基因，并对部分lincRNA基因和编码基因的相互作用关系进行了初步探索，对于高原鼢鼠适应高海拔机制的研究具有重要意义。 肠道微生物可以影响宿主的食物消化、营养吸收、能量供应、脂肪代谢、免疫调节等方面。本研究通过对多品种不同饲养环境下的猪肠道微生物宏基因组数据进行分析，分析猪应对不同饲养环境相关的肠道微生物，样品来源包括中国的放牧藏猪，也包括法国、丹麦和中国圈养的猪，且后三者包含多种猪品种。研究得到了猪肠道微生物的8190个MAGs(Metagenome-assembled Genomes)和其对应的1113个SLGs(Species-level Genomes)，对SLGs进行解析，找到了不同饲养环境下相关的SLGs，并分析得到了在不同群体中富集的碳水化合物活性酶基因(Carbohydrate-Active Enzymes, CAZymes)，特别是相对法国、丹麦和中国圈养猪来讲，中国放牧的藏猪的肠道微生物中富集与果胶、半纤维素、几丁质等物质降解相关的CAZymes。目前，关于猪肠道微生物的高通量的宏基因组研究十分有限，数据库中的微生物资源多来自人和小鼠，尚未有研究系统地大规模地挖掘猪肠道微生物的参考基因组信息，本研究得到的MAGs和SLGs可作为后续猪肠道微生物研究的参考基因组资源，也发现了与猪应对不同饲养环境相关的SLGs和Cazymes，对猪的生产养殖有一定的借鉴意义。

Faced to different environments or pressures from environments, organisms will response at different levels. For exploring the mechanisms of organisms adapting to environments, this study use plateau zokor to analyze long intergenic noncoding RNAs(lincRNAs) associated with high altitude adaptation and use pig to analyze gut microbes associated with different environments. Plateau zokor belongs to rodents, homed to Tibet Plateau. There is pressure of coldness, high radiation, and hypoxia. This study focuses on lincRNAs to study the mechanism of plateau zokor’s response to altitudes. By analyzing RNA-seq data of plateau zokor from many altitudes and many tissues, 14024 lincRNAs are identified in the genome. LincRNA genes specially expressed at high altitudes are identified after that. Co-expressed relationships of lincRNA genes and coding genes are also analyzed. Co-expressed modules related with altitudes changes are identified too. LincRNA genes from those modules and lincRNA gens specially expressed at high altitudes are regarded as candidate genes related with high altitude adaptation. After that, the interactions between lincRNA genes and other coding genes are explored preliminarily. In that analysis, interactions between lincRNA genes and their nearest genes and interactions between important coding genes and lincRNA genes in modules are focused. This study annotated lincRNA gens in plateau zokor genome and discovered lincRNA genes associated with plateau zokor’s response to high altitudes. The interactions between lincRNA genes and other genes are also explored preliminarily. Gut microbes can affect food digestion, nutrient absorption, energy supply, fat metabolism, immune regulation, et al. This study analyzed metagenomic data of pigs of many breeds from different environments to analyze gut microbes associated with pig’s response to different environments. 8190 MAGs (Metagenome-assembled Genomes) and representative 1113 SLGs (Species-level Genomes) are obtained. By analyzing SLGs, SLGs associated different populations from different environments are obtained. Carbohydrate-Active Enzymes (CAZymes) were enriched in different populations were also obtained. Especially, CAZymes associated with digestion of pectin, hemicellulose, and chitin are enriched in China’s grazed Tibetan pigs. By now, few researches about high-throughput metagenome are published. The microbes in databases mainly come from human or mouse. There is no research mining information about pig’s gut microbes in large scale. Therefore, the MAGs and SLGs obtained in this research can be genome reference for later research about pig’s gut microbes. SLGs and Cazymes related with different feeding environments are also found. This study gives inspiration for feeding pigs.