Response of the soil fungal community to multi-factor environmental changes in a temperate forest

Both environmental and climatic changes are known to influence soil microbial biomes in terrestrial ecosystems. However, there are limited data defining the interactive effects of multi-factor environmental disturbances, including N-deposition, precipitation, and air temperature, on soil fungal communities in temperate forests. A 3-year outdoor pot experiment was conducted to examine the temporal shifts of soil fungal communities in a temperate forest following N-addition, precipitation and air temperature changes. The shifts in the structure and composition of soil fungal communities were characterized by denaturing gradient gel electrophoresis and DNA sequencing. N-addition regimen induced significant alterations in the composition of soil fungal communities, and this effect was different at both higher and lower altitudes. The response of the soil fungal community to N-addition was much stronger in precipitation-reduced soils compared to soils experiencing enhanced precipitation. The combined treatment of N-addition and reduced precipitation caused more pronounced changes in the lower altitude versus those in the higher one. Certain fungal species in the subphylum Pezizomycotina and Saccharomycotina distinctively responded to N fertilization and soil water control at both altitudes. Redundancy discrimination analysis showed that changes in environmental factors and soil physicochemical properties explained 43.7% of the total variability in the soil fungal community at this forest ecosystem. Variations in the soil fungal community were significantly related to the altitude, soil temperature, total soil N content (TN) and pH value (P < 0.05). We present evidence for the interactive effects of N-addition, water manipulation and air temperature to reshape soil fungal communities in the temperate forest. Our data could provide new insights into predicting the response of soil micro-ecosystem to climatic changes.     

棉花单核苷酸多态性标记研究进展

单核苷酸多态性标记已在农作物研究中得到广泛应用并取得重大进展。为了便利棉花SNP(Single nucleotide polymorphism)标记的研究和应用,介绍了利用基因芯片、简化基因组测序、重测序等在棉花中开发SNP标记的方法 ,综述了SNP标记在棉花遗传图谱构建、数量位点的定位和分子标记辅助育种、基因组测序以及系统进化等研究中的应用。并对异源四倍体棉花中SNP标记开发时,同源序列位点和部分同源序列位点上的SNP标记辨别问题进行了系统探讨,对其快捷的开发、检测方式和在数量基因定位中的应用前景进行了展望。     

Differentially expressed genes identified through RNA‐seq with extreme values of principal components for beef fatty acid in Nelore cattle

The aim of this study was to identify differentially expressed genes (DEG) in the Longissimus thoracis muscle of Nelore cattle related to fatty acid (FA) profile through RNA sequencing and principal component analysis (PCA). Two groups of 10 animals each were selected containing PC1 and PC2 extreme DEG values (HIGH × LOW) for each FA group. The intramuscular fat (IMF) was compared between cluster groups by ANOVA, and only the sum of monounsaturated FA (MUFA) and ω3 showed significant differences (p < .05). Interestingly, the highest percentage (95%) of phenotypic variation explained by the sum of the first two PC was observed for ω3, which also displayed the lowest number of DEG (n = 1). The lowest percentage (59%) was observed for MUFA, which also revealed the largest number of DEG (n = 66). Since only MUFA and ω3 exhibited significant differences between cluster groups, we can conclude that the differences observed for the remaining groups are not due to the percentage of IMF. Several genes that have been previously associated with meat quality and FA traits were identified as DEG in this study. The functional analysis revealed one KEGG pathway and eight GO terms as significant (p < .05), in which we highlighted the purine metabolism, glycolytic process, adenosine triphosphate binding and bone development. These results strongly contribute to the knowledge of the biological mechanisms involved in meat FA profile of Nelore cattle.     

甘肃省兴隆山区域丛枝菌根真菌多样性初探

本研究采用Illumina HiSeq分子测序技术,探究了兴隆山东山丛枝菌根(Arbuscular mycorrhizal,AM)真菌多样性及其在不同海拔高度的分布特征。结果表明:1)自兴隆山东山土壤分离获得AM真菌共52种,隶属于4目8科13属,其中球囊霉属(Glomus)和原囊霉属(Archaeospora)为主要物种,分别为20种和9种,共占总物种的55.77%;2)各海拔梯度AM真菌种属分布结果表明,优势属球囊霉属(Glomus)和类球囊霉属(Paraglomus)随海拔变化呈现规律性分布,其余各属均匀分布于不同海拔梯度;球状巨孢囊霉(Gigaspora margarita)、蜜色无梗囊霉(Acaulospora mellea)、白色球囊霉(Glomus albidum)、球囊霉属的Glomus sp.1和Glomus sp.4,还有弯丝硬囊霉(Sclerocystis sinuosa)仅在部分海拔梯度出现,为不同海拔特有种;3)AM真菌丰富度分析表明,从低海拔到高海拔,ACE和Chao1指数总体上表现出“单峰”变化曲线,且部分海拔间差异性显著(P<0.05)。Spearman相关性分析发现,该地区AM真菌种属分布受海拔因子影响较小,两者间不具有显著相关性。综上,兴隆山东山AM真菌资源丰富,物种繁多,具有较大的应用潜力。     

藏北燕麦草地持续利用与撂荒对高寒草甸土壤特征的影响

为研究不同利用方式对藏北高寒草甸建植一年生燕麦（Avena sativa Linn.）人工草地的土壤理化性质及土壤细菌群落的影响,本试验于8月份植物生长旺季,在持续利用人工草地（AG）、撂荒人工草地（AC）和对照天然草地（NG）采集土壤样品,分析了土壤理化性质、土壤细菌群落组成和结构特征变化。结果表明,AG样地土壤有机质、全钾含量和pH与NG样地相比无显著性变化,土壤全氮、速效氮和速效钾含量显著降低;AC样地与NG样地相比土壤pH显著升高,土壤有机质、全氮、速效氮和速效钾含量显著降低。AG样地土壤细菌群落Chao1,Shannon和Pielou均匀度指数显著高于NG样地,AC样地酸杆菌门和变形菌门丰度显著升高。土壤理化性质是土壤细菌群落结构组成门、属相对丰度变化主要影响因子。综上所述,高寒草甸一年生燕麦人工草地长期利用应科学补充肥料,保持土壤肥力;草地撂荒需谨慎,应及时采取恢复措施避免草地发生退化。     

Randomly primed,strand-switching,MinION-based sequencing for the detection and characterization of cultured RNA viruses

RNA viruses rapidly mutate, which can result in increased virulence, increased escape from vaccine protection, and false-negative detection results. Targeted detection methods have a limited ability to detect unknown viruses and often provide insufficient data to detect coinfections or identify antigenic variants. Random, deep sequencing is a method that can more fully detect and characterize RNA viruses and is often coupled with molecular techniques or culture methods for viral enrichment. We tested viral culture coupled with third-generation sequencing for the ability to detect and characterize RNA viruses. Cultures of bovine viral diarrhea virus, canine distemper virus (CDV), epizootic hemorrhagic disease virus, infectious bronchitis virus, 2 influenza A viruses, and porcine respiratory and reproductive syndrome virus were sequenced on the MinION platform using a random, reverse primer in a strand-switching reaction, coupled with PCR-based barcoding. Reads were taxonomically classified and used for reference-based sequence building using a stock personal computer. This method accurately detected and identified complete coding sequence genomes with a minimum of 20× coverage depth for all 7 viruses, including a sample containing 2 viruses. Each lineage-typing region had at least 26× coverage depth for all viruses. Furthermore, analyzing the CDV sample through a pipeline devoid of CDV reference sequences modeled the ability of this protocol to detect unknown viruses. Our results show the ability of this technique to detect and characterize dsRNA, negative- and positive-sense ssRNA, and nonsegmented and segmented RNA viruses.     

狼山鸡高、低近交组卵巢组织转录组差异分析

为了探究近交对繁殖效应的影响,本研究以国家级地方鸡种基因库保存的狼山鸡为素材,结合分子标记和系谱信息,组建高、低近交两个试验组,记录高、低近交组的繁殖性能数据。选取高、低近交组中正常个体各3只,采取卵巢组织进行RNA-seq测序,并对差异基因进行功能注释。结果在高、低近交组中共获得差异转录本1 114个,其中783个基因获得注释,307个上调,476个下调。GO和KEGG分析表明,差异基因主要富集在核糖体的生物合成、炎性反应、繁殖、生长、免疫系统过程、代谢过程等生物学过程,Pathway显著富集在叶酸的生物合成、卵母细胞成熟和代谢等生物学通路。功能分析发现,筛选出的差异基因（如GGH、CPEB1、GNMT和PIWIL等）与繁殖功能相关。此外,还包括一些与应激和免疫相关的基因（如APOC3、HSP70、CD38和LGMN等）。研究结果有助于了解狼山鸡繁殖性状近交衰退相关的基因及其调控机制,为家禽特定性状近交衰退分子机理提供参考。     

MSTN基因编辑牛肌肉转录组测序及生物信息学分析

为探究肌生长抑制素（myostatin,MSTN）基因对牛肌肉发育的具体调控机制,本研究选取同一牛场健康鲁西黄牛10头,其中通过转基因技术得到的基因编辑牛MSTN^-/-和同种非转基因野生型牛各5头。分别采集两组牛腿臀肌肉样品,利用IIlumina HiSeq高通量测序技术进行转录组测序分析,通过生物信息学方法比较两组样本间的差异表达基因,并进行GO和KEGG富集分析,最后利用实时荧光定量PCR验证转录组测序数据。结果显示,基因编辑型牛和野生型牛之间共检测到18 071个基因。在log₂|FoldChange|≥ 1.48条件下,筛选出406个差异表达基因,其中347个显著上调,59个显著下调。GO功能富集分析显示,MSTN基因编辑后显著影响915个功能类别（P<0.05）,差异基因主要参与结合、生物系统调节、免疫系统等相关功能。KEGG通路富集分析结果共涉及211个通路,差异基因主要富集在细胞黏附分子、趋化因子信号通路、细胞因子互作等信号通路上,进一步从中筛选出可能参与细胞生长、肌肉发育的差异基因（CD14、KIT、CSF1R、FBP1、DUSP4、ULBP21、PRKCB、SPN、CHAD、SRC）。实时荧光定量PCR检测结果显示,所选差异基因表达水平与转录组表达水平一致,证明测序结果的可靠性。本研究结果表明,MSTN基因发挥作用后可以介导多个下游基因表达,从而影响相关信号通路及生物学过程;同时,所筛选出的差异表达基因可作为进一步研究骨骼肌调控机制的候选靶标。     

Effects of lncRNA-GTL2 Transgenosis on Gut Microbiota Composition in Mice

This research was aimed to study whether the lncRNA would have effects on the structure and constitution of the intestinal microbial colonies in mice.High throughout sequencing was used to sequence and analyze the intestinal microbial colonies in both transgenic and non-transgenic mice of three months old.We conducted comparison and t-test at the level of phylum and genus.The result showed that transferred into long non-coding RNA genes GTL2 (lncRNA-GTL2),the mouse intestinal microbial colony structure and composition had no significant differences in the overall,within the same gender,but there were individual differences.Therefore,this study didn't find that long non-coding RNA transfered had a significant impact on the intestinal microflorain the phylum and genus level.