青藏高原不同海拔藏药独一味转录组分析

为了研究独一味(Phlomoides rotata)在不同海拔生境下基因表达差异及响应机制,本研究基于NR、 GO和KEGG等数据库进行差异表达基因(differentially expressed genes, DEGs)的注释,以及功能富集分析,获得独一味的DEGs,以及关联的代谢通路,并对注释获得的药用基因进行系统发育分析。结果显示,不同海拔独一味的DEGs,主要富集到植物激素信号转导、氨基酸的生物合成、萜类等次生代谢生物合成途径。其中,有4个基因在低温胁迫响应中起关键作用;鉴定出3个P5βR基因,其中2个基因编码环烯醚萜合成途径中的关键酶。系统发育结果显示,P5βR基因亚家族聚为两个分支(P5βR clusterⅠ和P5βR clusterⅡ)。本研究在转录组水平上发现独一味主要通过多种代谢途径,以及关键基因的调控表达来适应青藏高原高海拔生境。本研究为独一味不同海拔适应机制及独一味耐寒育种提供了数据支撑,为P5βR基因亚家族和环烯醚萜类生物合成的研究奠定基础。     

不同海拔饲育的麦洼牦牛肺脏组织转录组学分析

为了探讨牦牛适应高海拔低氧环境的基因表达特征与规律,对在高海拔（3 560 m）和低海拔地区（478 m）饲育4个月的2.5~3岁健康雄性麦洼牦牛肺组织进行转录组测序。转录组测序采用Illumina高通量测序平台(HiSeqTM2500/4000)进行,并以qRT-PCR验证差异表达基因的表达量。结果显示,高海拔组牦牛肺脏转录组平均每个测序样本得到约5.76亿条Clean Reads,低海拔组牦牛中得到约6.10亿条Clean Reads,比对到参考基因组上的Reads数分别占91.74%和91.28%以上,共发现了2 047个新转录本。低海拔组与高海拔组牦牛肺脏组织之间共有199个差异表达基因,其中含89个差异上调表达基因和110个差异下调表达基因。所得差异表达基因富集在297个GO条目和146个KEGG通路中,包含62个低氧适应相关的GO条目和35个低氧适应相关代谢通路。其中低氧适应相关GO条目在生物过程、细胞组成和分子功能三种类别中占比最多的分别为细胞粘附、蛋白复合物和钙离子结合。低氧适应相关KEGG通路中占比最多的为肿瘤坏死因子(TNF)信号通路,其次为低氧诱导因子1(HIF-1)信号通路。qRT-PCR验证结果显示,Ⅱ类人类白细胞抗原α链(HLA-DOA、HLA-DRA)、补体因子 (C2)和甘露糖结合凝集素相关丝氨酸蛋白酶1（MASP1）基因的表达量变化与转录组测序结果相符。本研究为全局和深入理解牦牛肺组织转录本表达对高海拔低氧的响应提供了有价值的切入点。     

栖息于青藏高原不同海拔环境的两种草原毛虫miRNA转录组的比较分析

有关动物适应异质性海拔环境的研究,已在表型、解剖学、生理学、基因组学和转录组学等方面广泛开展,但是很少关注小RNA(micro RNAs或miRNAs)的生态适应性功能.草原毛虫是青藏高原高寒草地的重要害虫,并对不同海拔环境产生了良好的适应性.为此,本研究以两种栖息于青藏高原不同海拔环境的黄斑草原毛虫和门源草原毛虫为研究对象,基于Illumina Hi Seq技术对这两种草原毛虫的miRNA转录组进行了高通量测序.结果表明,两种草原毛虫中共鉴定到109个成熟miRNAs,其中47个为保守miRNAs.在所有miRNAs种,共有9个miRNAs的表达水平在两种草原毛虫间存在显著差异性.对这9个差异性表达的miRNAs采用实时荧光定量PCR进行验证,发现8个基因的表达水平与高通量测序结果完全一致.功能分析表明,差异性表达的miRNAs共预测到93个靶基因.这些靶基因主要富集到脂、核酸和维生素等代谢或衰老相关的GO条目,并与代谢、抗寒和低氧等KEGG通路相关(如AMPK信号通路、Wnt信号通路和m TOR信号通路).这些研究表明,miRNAs在草原毛虫对异质性海拔环境的适应性进化过程中具有重要作用.该研究加深了对青藏高原特有昆虫适应高海拔环境的遗传基础的理解.     

沙葱萤叶甲卵滞育的转录组学分析

【目的】建立沙葱萤叶甲Galeruca daurica滞育卵转录组数据库,挖掘卵滞育相关的基因以及代谢和信号通路,在转录组水平探讨卵滞育的分子机制。【方法】采用Illumina NovaSeq6000高通量测序平台对沙葱萤叶甲滞育卵与解除滞育卵进行转录组测序,并进行生物信息学分析;利用DESeq软件分析沙葱萤叶甲滞育卵与解除滞育卵中的差异表达基因,对差异表达基因进行KEGG通路富集分析;利用qRT PCR技术对10个差异表达基因的表达模式进行验证。【结果】基于沙葱萤叶甲滞育卵与解除滞育卵转录组测序结果,共获得53 389个unigene,其中差异表达基因2 145个,24个差异表达基因与保幼激素信号及脂肪酸生物合成和降解相关。与解除滞育卵相比,滞育卵转录组中1 297个基因上调表达,富集于124条KEGG通路,其中核糖体通路显著富集;848个基因下调表达,富集于73条KEGG通路,其中MAPK信号通路和糖胺聚糖生物合成通路显著富集。qRT-PCR结果表明,随机选取的10个差异表达基因的表达趋势与RNA-Seq转录组测序结果完全一致。【结论】保幼激素,脂肪酸生物合成和降解,核糖体,MAPK信号及糖胺聚糖生物合成等通路可能在沙葱萤叶甲卵滞育调控中起着重要的作用。     

RNA-seq用于获得共轭亚油酸对贵妃鸡肌内脂肪代谢调控的关键基因

通过转录物组测序获得在贵妃鸡基础日粮中添加共轭亚油酸(CLA)对肌内脂肪代谢的差异表达基因,经生物信息学分析获得相关的信号通路及可能发挥重要作用的候选基因,为CLA对肌内脂肪沉积的分子机制奠定基础。本研究选用55日龄健康的贵妃鸡为试验动物,在基础日粮中添加CLA 0%、1%和2%,预饲期1周,正饲期6周。屠宰采集胸肌组织进行转录物组测序,对测序数据进行差异表达分析,差异表达基因GO功能和差异表达基因KEGG通路富集分析,筛选出与胸肌脂类代谢相关的差异表达基因,利用qRT-PCR对差异表达基因进行验证。结果显示,共获得1 065个差异表达基因,其中上调基因703个,下调基因362个。GO富集结果显示,差异表达基因主要富集在生物过程的细胞过程、单一生物过程、生物调节和代谢过程。KEGG信号通路富集显示,差异表达基因显著富集在黏着斑、不饱和脂肪酸生物合成、脂肪酸生物合成和类固醇生物合成等信号通路中,发现11个主要与肌内脂肪代谢相关的候选基因,分别是FADS1、FADS2、ELOVL5、ACOX2、SLC27A1、FABP5、LPL、LOC107050163、ENSGALG00000030996、ENSGALG00000005043和ENSGALG00000048882。并随机选取6个基因进行qRT-PCR验证,其相对表达量变化趋势与测序结果一致。本研究筛选到CLA影响贵妃鸡胸肌脂类代谢相关的差异表达基因,并对11个主要参与脂肪代谢相关的基因进行分析,为揭示CLA调控肌内脂肪沉积的分子机制奠定基础。     

杂交兰及其花艺突变体中类黄酮成分差异的代谢-转录组联合分析

为探索杂交兰花艺突变体变异的分子机理,该研究以杂交兰‘玉凤’及其花艺突变体‘双艺金龙’为材料,利用靶向代谢组学和转录组学鉴定两者中类黄酮化合物含量差异及其相关通路上的差异表达基因。结果表明：(1)代谢组分析发现,杂交兰‘玉凤’和‘双艺金龙’花瓣中共检测到271种类黄酮代谢物,其中黄酮醇类和黄酮类代谢物的相对含量约占总类黄酮的30%～50%;共检测到38个差异代谢物(15个上调,23个下调);‘玉凤’中差异最高的代谢物二氢山奈酚-7-O-葡萄糖苷(黄酮醇类)含量是‘双艺金龙’的124 444倍,‘双艺金龙’中差异最高的代谢物3,5,7,3′,4′-五羟基-5′-异戊二烯基黄酮(黄酮醇类)含量是‘玉凤’的7 244倍。(2)KEGG分析显示,差异代谢物显著富集在类黄酮、黄酮和黄酮醇生物合成途径。其中,在类黄酮生物合成途径上,根皮苷、黄腐醇、二氢山奈酚、二氢杨梅素和表没食子儿茶素含量升高,柚皮苷和二氢槲皮素含量降低;在黄酮和黄酮醇生物合成途径上,三叶豆苷和槲皮素含量均下降。(3)转录组分析共筛选到563个差异表达基因,与‘玉凤’相比,‘双艺金龙’中有220(39.1%)个基因上调表达,343...     

低压低氧对小鼠精子发生及其小RNA表达的影响

作为青藏高原最为关键的环境因子,低压低氧对高原非习服动物繁殖和生殖系统功能有不利影响。已有的研究表明,低氧环境会导致雄性生殖细胞凋亡、精子畸形率升高、精子质量下降,进而影响受精和早期胚胎发育,但目前缺乏低氧损伤精子功能的机理研究。小RNA (small RNA) 是在转录后及翻译水平上调控基因表达的重要功能分子,不同类型的small RNA通过诱导基因沉默或调控翻译等方式参与调节精子发生。本研究通过低压氧舱模拟海拔5 000 m处理4周建立缺氧小鼠模型,发现低氧处理导致小鼠曲精细管中生精细胞排列紊乱,精子数量未发生显著变化但畸形率增加17.5倍 (P < 0.001)。通过small RNA测序发现,低氧组小鼠精子中的small RNA碱基偏好性与对照组一致,第一碱基对尿嘧啶 (U) 有很强的偏好性。低氧组小鼠精子中21 nt长度的small RNA比例显著减少4.4% (P < 0.05)。低氧组小鼠精子中piRNA、tsRNA表达无差异,但miRNA表达上调21个,下调58个。对差异miRNAs靶基因与相同低氧处理小鼠睾丸组织差异基因比对,共比对到831个差异表达基因,其中上调miRNAs的靶基因中有429个差异表达基因;下调miRNAs的靶基因中有813个差异表达基因。此外,上调miRNAs的靶基因富集在FoxO信号通路、甲状腺激素信号通路、类固醇生物合成和HIF?1信号等通路,而下调miRNAs的靶基因富集在脂肪酸代谢等通路。本研究获得了缺氧小鼠精子small RNA变化图谱,对人类和其他动物在缺氧环境下精子表观遗传修饰变化的研究具有参考价值。     

不同海拔高原鼠兔个性特征与SERT基因多态性关联

个性特征是指动物个体间稳定、可遗传的行为差异,与相关基因多态性有关,反映了动物对环境的适应模式,探究个性相关基因变异,将有助于更好地理解动物对环境的适应与进化机制。本文以高原鼠兔 (Ochotona curzoniae) 为对象,研究了5个不同海拔地区高原鼠兔的个性 (探究性、勇敢性和温顺性) 差异特征,并检测了个性相关基因5-羟色胺转运体 (SERT) 的单核苷酸多态性 (SNP) 和mRNA表达。结果发现,高海拔地区高原鼠兔的探究性和勇敢性显著高于低海拔地区,而高海拔地区高原鼠兔SERT基因mRNA表达量显著低于低海拔地区,提示不同海拔高原鼠兔个性特征差异可能与SERT基因mRNA表达有所关联。进一步检测不同海拔地区高原鼠兔SERT基因多态性及其分布差异情况,发现该基因存在6个SNP (其中5个位于外显子3,1个位于外显子5 );不同海拔地区鼠兔基因分布差异分析显示外显子5的c.A1063C 同义突变与海拔之间存在显著相关,高海拔地区该位点CC基因型分布频率显著高于低海拔地区;c.A1063C的基因型虽然与探究性、勇敢性无显著相关,但与温顺性显著相关。综上所述,随着海拔升高,高原鼠兔探究性和勇敢性增加,这有利于动物获取更多的食物资源,进而增加其生存机会。与此同时,SERT基因多态性显示与不同海拔地区的生存环境相适应的特征,且与温顺性有关,暗示不同海拔高原鼠兔个性差异可能与SERT基因SNP的差异有关。本研究从基因表达与突变的角度尝试阐述高原鼠兔适应不同海拔环境的行为差异,显示了不同海拔地区高原鼠兔行为生存策略潜在的分子机制。     

基于单细胞转录组数据探究不同海拔牦牛心肌细胞通讯和基因表达差异

心脏作为血液循环最重要的器官在动物环境适应中发挥着重要的作用。心肌细胞是心脏主要的功能细胞,然而高海拔地区牦牛心肌细胞基因表达变化及细胞间通讯关系尚不清楚。为此,本研究以高海拔地区牦牛(青海祁连,海拔4 000 m)和低海拔地区牦牛(青海循化,海拔2 600 m)为研究对象,基于心脏组织10×单细胞转录组测序数据,对心肌细胞和心脏其他细胞进行细胞通讯及配体-靶基因调控预测,同时对高、低海拔牦牛心肌细胞差异表达基因进行功能注释分析,以期探究心肌细胞在牦牛适应高原环境过程中的作用。结果显示,牦牛心肌细胞与内皮细胞、上皮细胞的关联最强,心肌细胞-树突状细胞及心肌细胞-巨噬细胞两个“细胞对”中CD74＿COAP和CD74＿APP配受体表达量相对较高;配受体活力在TNF信号通路中相对较强;在免疫相关通路发挥重要作用的配体PTPRC、PECAM1、ITGB2、ANXA1、BDNF等对所有“细胞对”影响明显,且PI3K-Akt信号通路在配体-靶基因调控中潜力分值最高;高、低海拔牦牛心肌细胞中差异表达基因功能主要富集在代谢途径,其中氧化磷酸化、糖酵解代谢通路相关的基因表达明显增强。本研究结果提示,牦牛...     

不同海拔下烤烟碳氮代谢相关酶基因的表达差异分析

为探讨贵州乌蒙烟区不同海拔的烤烟特色形成的分子机理,本文利用实时荧光定量PCR技术对的烤烟碳氮代谢相关酶基因的表达进行检测。结果表明,液泡转化酶(VIN)基因在烤烟移栽后50 d的中海拔表达较强,移栽后60 d高海拔表达比较活跃,烤烟成熟期低海拔表达略强。蔗糖合成酶(SS)和蔗糖磷酸合成酶(SPS)基因在烤烟旺长期高海拔表达较强,烤烟成熟期低海拔表达较强,中海拔表达较弱。在4个取样时期,海拔越高,蔗糖磷酸化酶(SPP)基因表达越强,高海拔地区烟叶的颗粒结合型淀粉合成酶(GBSSI)基因表达均最强。淀粉分支酶(SBE)基因在烤烟移栽后50、60和70 d高海拔下表达较强,在移栽后80 d低海拔下表达相对较强。从同一时期不同海拔的结果分析,烤烟硝酸还原酶(NR)基因表达强度随海拔降低而逐渐增强。谷氨酰胺合成酶(GS1-3和GS1-5)基因表达在4个取样时期表现为低海拔强于中、高海拔的。     

The influence of altitude and topography on genetic structure in the long-toed salamander (Ambystoma macrodactulym)

A primary goal of molecular ecology is to understand the influence of abiotic factors on the spatial distribution of genetic variation. Features including altitudinal clines, topography and landscape characteristics affect the proportion of suitable habitat, influence dispersal patterns, and ultimately structure genetic differentiation among populations. We studied the effects of altitude and topography on genetic variation of long-toed salamanders (Ambystoma macrodactylum), a geographically widespread amphibian species throughout northwestern North America. We focused on 10 low altitude sites (< 1200 m) and 11 high-altitude sites in northwestern Montana and determined multilocus genotypes for 549 individuals using seven microsatellite loci. We tested four hypotheses: (1) gene flow is limited between high- and low-altitude sites; and, (2) gene flow is limited among high-altitude sites due to harsh habitat and extreme topographical relief between sites; (3) low-altitude sites exhibit higher among-site gene flow due to frequent flooding events and low altitudinal relief; and (4) there is a negative correlation between altitude and genetic variation. Overall F(ST) values were moderate (0.08611; P < 0.001). Pairwise F(ST) estimates between high and low populations and a population graphing method supported the hypothesis that low-altitude and high-altitude sites, taken together, are genetically differentiated from each other. Also as predicted, gene flow is more prominent among low-altitude sites than high-altitude sites; low-altitude sites had a significantly lower F(ST) (0.03995; P < 0.001) than high altitude sites (F(ST) = 0.10271; P < 0.001). Use of Bayesian analysis of population structure (BAPS) resulted in delineation of 10 genetic groups, two among low-altitude populations and eight among high-altitude populations. In addition, within high altitude populations, basin-level genetic structuring was apparent. A nonequilibrium algorithm for detecting current migration rates supported these population distinctions. Finally, we also found a significant negative correlation between genetic diversity and altitude. These results are consistent with the hypothesis that topography and altitudinal gradients shape the spatial distribution of genetic variation in a species with a broad geographical range and diverse life history. Our study sheds light on which key factors limit dispersal and ultimately species' distributions.     

Genetic adaptation to high altitude in the Ethiopian highlands

Background

Genomic analysis of high-altitude populations residing in the Andes and Tibet has revealed several candidate loci for involvement in high-altitude adaptation, a subset of which have also been shown to be associated with hemoglobin levels, including EPAS1, EGLN1, and PPARA, which play a role in the HIF-1 pathway. Here, we have extended this work to high- and low-altitude populations living in Ethiopia, for which we have measured hemoglobin levels. We genotyped the Illumina 1M SNP array and employed several genome-wide scans for selection and targeted association with hemoglobin levels to identify genes that play a role in adaptation to high altitude.

Results

We have identified a set of candidate genes for positive selection in our high-altitude population sample, demonstrated significantly different hemoglobin levels between high- and low-altitude Ethiopians and have identified a subset of candidate genes for selection, several of which also show suggestive associations with hemoglobin levels.

Conclusions

We highlight several candidate genes for involvement in high-altitude adaptation in Ethiopia, including CBARA1, VAV3, ARNT2 and THRB. Although most of these genes have not been identified in previous studies of high-altitude Tibetan or Andean population samples, two of these genes (THRB and ARNT2) play a role in the HIF-1 pathway, a pathway implicated in previous work reported in Tibetan and Andean studies. These combined results suggest that adaptation to high altitude arose independently due to convergent evolution in high-altitude Amhara populations in Ethiopia.     

Gene Expression Variability within and between Human Populations and Implications toward Disease Susceptibility

Variations in gene expression level might lead to phenotypic diversity across individuals or populations. Although many human genes are found to have differential mRNA levels between populations, the extent of gene expression that could vary within and between populations largely remains elusive. To investigate the dynamic range of gene expression, we analyzed the expression variability of ∼18, 000 human genes across individuals within HapMap populations. Although ∼20% of human genes show differentiated mRNA levels between populations, our results show that expression variability of most human genes in one population is not significantly deviant from another population, except for a small fraction that do show substantially higher expression variability in a particular population. By associating expression variability with sequence polymorphism, intriguingly, we found SNPs in the untranslated regions (5′ and 3′UTRs) of these variable genes show consistently elevated population heterozygosity. We performed differential expression analysis on a genome-wide scale, and found substantially reduced expression variability for a large number of genes, prohibiting them from being differentially expressed between populations. Functional analysis revealed that genes with the greatest within-population expression variability are significantly enriched for chemokine signaling in HIV-1 infection, and for HIV-interacting proteins that control viral entry, replication, and propagation. This observation combined with the finding that known human HIV host factors show substantially elevated expression variability, collectively suggest that gene expression variability might explain differential HIV susceptibility across individuals.     

Major-histocompatibility-complex gene markers and restriction-fragment analysis of steroid 21-hydroxylase (CYP21) and complement C4 genes in classical congenital adrenal hyperplasia patients in a single population

The gene CYP21B, encoding the steroid 21-hydroxylase enzyme of adrenal steroid biosynthesis, has been mapped to the human major histocompatibility complex (MHC). Deficiency of this enzyme leads to congenital adrenal hyperplasia (CAH). We report the phenotypes of the HLA and complement C4 and Bf genes, which are closely linked to the CYP21B gene, together with a detailed analysis of the CYP21 and C4 RFLP, in 17 Finnish families with CAH. The RFLP analysis with six restriction enzymes suggested that, altogether, 35% of the affected chromosomes had a CYP21B + C4B gene deletion, 9% an obvious gene conversion of the CYP21B gene to a CYP21A-like gene, and 3% a CYP21A + C4B duplication. The remaining 53% gave the RFLP patterns also found in nonaffected chromosomes. We also found that a 14.0-kb EcoRI RFLP marker of the CYP21 genes was strongly associated with the presence of a short C4B gene, suggesting that some of the RFLP markers found with the CYP21 probe may actually derive from C4B gene polymorphism. Three particular MHC haplotypes, each with a characteristic RFLP pattern, were found in many unrelated families. These three haplotypes accounted for 59% of the affected chromosomes in our study group, the rest (41%) of the affected chromosomes being distributed among various subtypes. The results suggest that, within a single, well-defined population such as in Finland, only a few CYP21B gene defects may constitute a substantial part of the affected chromosomes. This finding will help in genetic studies of CAH in such populations.     

蒺藜苜蓿糖基转移酶基因SMALL AND EMERALD1的克隆和功能研究

类黄酮代谢对于植物生长发育和植物-环境互作至关重要,其中糖基转移酶介导的糖基化修饰在类黄酮代谢中发挥着重要作用。为了研究蒺藜苜蓿中糖基转移酶的生物学功能,通过定向筛选蒺藜苜蓿Tnt1逆转座子插入突变体库,获得了一类植株矮小、叶片深绿的突变体small and emerald1 (se1)。通过基因表型连锁性分析成功克隆了SE1基因,该基因编码1个糖基转移酶,与拟南芥中调控类黄酮生物合成的AtUGT84A1氨基酸同源性为52.8%。对野生型和se1突变体叶片的类黄酮含量进行测定发现类黄酮总量在se1突变体中显著降低(P<0.01)。进一步研究发现在se1突变体中类黄酮合成途径关键基因CHS、F3H和F3’H表达水平下降。亚细胞定位显示SE1可能在细胞质和细胞核中发挥生物学功能。研究表明糖基转移酶基因SE1可能参与蒺藜苜蓿类黄酮合成代谢调控,进而影响其生长发育。此外,研究还发现SE1基因对于叶绿素合成可能具有负向调控作用。