The Brassicaceae species Braya humilis shows broad adaptation to different climatic zones and latitudes. However, the molecular adaptation mechanism of B. humilis is poorly understood. In China, B. humilis is mainly d...The Brassicaceae species Braya humilis shows broad adaptation to different climatic zones and latitudes. However, the molecular adaptation mechanism of B. humilis is poorly understood. In China, B. humilis is mainly distributed on the QinghaiTibetan Plateau(QTP) and in the adjacent arid region. Previous transcriptome analysis of B. humilis has revealed that 39 salt and osmotic stress response genes are subjected to purifying selection during its speciation. To further explore the adaptation mechanism of B. humilis to an arid environment, OrthoMCL program was employed in this study and 6,268 pairs of orthologous gene pairs with high confidence were obtained between B. humilis and Arabidopsis thaliana. A comparative evolutionary analysis based on nonsynonymous to synonymous substitution ratio(Ka/Ks) was then conducted. There were 64 pairs exhibiting a Ka/Ks ratio more than 0.5 and among which, three instrumental candidate genes, T20487,T22576, and T23757, were identified with strong selection signatures(Ka/Ks >1). The corresponding A. thaliana orthologs are double-stranded RNA-binding domain protein, MADS-box family protein, and NADH-dehydrogenase subunit6, which is encoded by mitochondria genome. This report not only demonstrates the adaptation contribution of fast evolving nuclear genes, but also highlights the potential adaptive value of mitochondria gene to the speciation and adaptation of B. humilis toward the extreme environment in an arid region.展开更多
Thirteen cuticular protein （CP） families have been recognized in arthropods. In this study, 250 Anopheles sinensis CP genes were identified and named based on genome and transcriptome sequences. They were classified...Thirteen cuticular protein （CP） families have been recognized in arthropods. In this study, 250 Anopheles sinensis CP genes were identified and named based on genome and transcriptome sequences. They were classified into 10 families based on mo- tifs and phylogenetic analyses. In 11 other insect species, nine had CP numbers 〉 150 while Apis mellifera and Tribolium castaneum had CP numbers less than 52. The CPs of eight species occupied 〉 1.4% of the total genomic gene number, whereas in three species the CPs occupied 〈 1%. The phylogenies for each CP family in An. sinensis were constructed and discussed. The 250 CPs each had 1-8 exons with 144 CPs （57.6%） having two exons. The intron length ranged from 66--3888 bp with 174 introns （54.0%） being 66--100 bp long. Except for two CPs on two contigs, 248 CPs were mapped onto 28 scaffolds with 136 genes （54.4%） restricted to five scaffolds. A total of 107 CPs were clustered and located at 27 loci. The CPR family had the conserved motif GSYS- LVEPDGTVRTV. The RR- 1 subfamily had an additional 21 amino acid （aa） motifs with the YVADENGF sequence that is common in insects. The RR-2 subfamily had an additional 50 aa motifs with two additional regions RDGDWKG and G-x（3）-VV. A comparison with 115 orthologous counterparts of An. gambiae CPs suggested purifying selection for all of these genes. This study provides basic information useful for further studies on biological functions of An. sinensis CPs as well as for comparative genomics of insect CPs.展开更多
卡波氏肉瘤(Kaposi sarcoma,KS)在全球范围内是人免疫缺陷病毒感染者第二易患的肿瘤。本研究旨在确定KS中差异表达的关键微小RNA(microRNA,miRNA)及其靶基因和相关途径,为深入了解该疾病的分子机制提供理论基础。本研究通过测序获得KS...卡波氏肉瘤(Kaposi sarcoma,KS)在全球范围内是人免疫缺陷病毒感染者第二易患的肿瘤。本研究旨在确定KS中差异表达的关键微小RNA(microRNA,miRNA)及其靶基因和相关途径,为深入了解该疾病的分子机制提供理论基础。本研究通过测序获得KS组织及瘤旁组织中的差异miRNA,借助starBase数据库预测差异表达miRNA的靶基因,同时用基因本体论(Gene Ontology,GO)数据库、京都基因与基因组百科全书(Kyoto Encyclopedia of Genes and Genomes,KEGG)、Reactome通路富集和转录因子注释分析差异miRNA的靶基因,最后用实时荧光定量PCR(Quantitative Real⁃time PCR,qRT⁃PCR)验证下调最明显的三个miRNA。结果显示,上、下调差异miRNA分别为39个和67个。GO和KEGG富集分析显示,上调的差异miRNA靶基因主要富集在组蛋白修饰、核染色质、DNA−结合转录激活因子活性等生物学功能,主要通过cAMP信号通路和长时程增效等通路参与KS的疾病进程;下调的差异miRNA主要与组蛋白修饰、细胞前沿和蛋白丝氨酸/苏氨酸激酶的活性有关,主要通过FoxO及Hippo等信号通路参与KS的疾病进程。Reactome富集显示,差异miRNA多集中在受体酪氨酸激酶信号、信号转导疾病和PI3K⁃Akt等信号通路。转录因子注释结果显示,肿瘤蛋白P53(Tumor Protein P53,TP53)、叉头框转录因子O亚族1(Forkhead Box Protein O1,FOXO1)和叉头框转录因子O亚族3(Forkhead Box Protein O3,FOXO3)等转录因子可能和KS的发生发展密切相关。qRT⁃PCR结果显示,测序中下调最明显的三个miRNA在KSHV感染细胞中均显著下调。总之,本研究筛选出了KS组织中差异表达的miRNA,对其靶基因进行了一系列生物信息学分析,并初步发现miR⁃651⁃3p,miR⁃223⁃3p及miR⁃186⁃5p通过Hippo、FoxO及PI3K⁃AKT信号通路可能在KS的疾病进程中发挥重要作用。这些研究均为探寻KS的发病机制和靶向干预提供了有力的理论基础。展开更多
基金supported by National Natural Science Foundation of China (No. 41201048)by the Youth Innovation Promotion Association of Chinese Academy of Sciences (2018463)
文摘The Brassicaceae species Braya humilis shows broad adaptation to different climatic zones and latitudes. However, the molecular adaptation mechanism of B. humilis is poorly understood. In China, B. humilis is mainly distributed on the QinghaiTibetan Plateau(QTP) and in the adjacent arid region. Previous transcriptome analysis of B. humilis has revealed that 39 salt and osmotic stress response genes are subjected to purifying selection during its speciation. To further explore the adaptation mechanism of B. humilis to an arid environment, OrthoMCL program was employed in this study and 6,268 pairs of orthologous gene pairs with high confidence were obtained between B. humilis and Arabidopsis thaliana. A comparative evolutionary analysis based on nonsynonymous to synonymous substitution ratio(Ka/Ks) was then conducted. There were 64 pairs exhibiting a Ka/Ks ratio more than 0.5 and among which, three instrumental candidate genes, T20487,T22576, and T23757, were identified with strong selection signatures(Ka/Ks >1). The corresponding A. thaliana orthologs are double-stranded RNA-binding domain protein, MADS-box family protein, and NADH-dehydrogenase subunit6, which is encoded by mitochondria genome. This report not only demonstrates the adaptation contribution of fast evolving nuclear genes, but also highlights the potential adaptive value of mitochondria gene to the speciation and adaptation of B. humilis toward the extreme environment in an arid region.
文摘Thirteen cuticular protein （CP） families have been recognized in arthropods. In this study, 250 Anopheles sinensis CP genes were identified and named based on genome and transcriptome sequences. They were classified into 10 families based on mo- tifs and phylogenetic analyses. In 11 other insect species, nine had CP numbers 〉 150 while Apis mellifera and Tribolium castaneum had CP numbers less than 52. The CPs of eight species occupied 〉 1.4% of the total genomic gene number, whereas in three species the CPs occupied 〈 1%. The phylogenies for each CP family in An. sinensis were constructed and discussed. The 250 CPs each had 1-8 exons with 144 CPs （57.6%） having two exons. The intron length ranged from 66--3888 bp with 174 introns （54.0%） being 66--100 bp long. Except for two CPs on two contigs, 248 CPs were mapped onto 28 scaffolds with 136 genes （54.4%） restricted to five scaffolds. A total of 107 CPs were clustered and located at 27 loci. The CPR family had the conserved motif GSYS- LVEPDGTVRTV. The RR- 1 subfamily had an additional 21 amino acid （aa） motifs with the YVADENGF sequence that is common in insects. The RR-2 subfamily had an additional 50 aa motifs with two additional regions RDGDWKG and G-x（3）-VV. A comparison with 115 orthologous counterparts of An. gambiae CPs suggested purifying selection for all of these genes. This study provides basic information useful for further studies on biological functions of An. sinensis CPs as well as for comparative genomics of insect CPs.
文摘目的禽流感疫情的爆发和传播受到多种自然因素的影响。今欲尝试将地理信息系统与基因进化树分析相结合，以建立一种基于基因序列变异追踪中国禽流感病毒地理传播的技术。方法禽流感病毒基因来源于美国国立医学图书馆（National Library for Medicine，NLM）数据库，所获得的基因组数据利用E—Utilities软件包转化为结构体后，可用Matlab软件阅读。结构体主要字段包括PB2、PBl、PA、HA、NP、HA、M1和NSl8个片段，分别代表流感病毒的8个不同的基因片段。基于结构体字段，利用计算生物学的方法比较不同传播能力禽流感病毒的同义突变／非同义突变基因（Ka／Ks）比例，确定不同选择压力之下A型禽流感病毒的基因突变模式。进而选择Ka／Ks比例最大的基因片段，采用Jukes—Cantor算法估计氨基酸序列变异的进化距离，然后对不同爆发点的H5N1型禽流感进行进化树聚类。将聚类信息输入Google Earth，并利用不同图层地理信息对影响爆发点分布的因素做单因素分析。结果比较分析A型禽流感所有的8个基因序列可以看出，NSl、HA和NA蛋白的Ka／Ks比值较大。三者中，HA基因的Ka／Ks比值最大，可以代表病毒的传播能力。利用分级聚类的思路对HA基因转录的氨基酸相似程度进行比较，发现自2003年以来亚洲地区爆发的H5N1型禽流感之间的关系可以表示为一个由30个节点构成的进化树，其中14个节点为分支节点，16个节点为叶子结点。把分支树的前三个节点作为分类标准，可以把所有16个病毒株分为四类。这四类病毒在地理空间的分布呈现一定规律。计算发现禽流感爆发相关地理因素排序分别为：内陆水体〉主要铁路交通线〉家禽密度。结论对中国HSNl病毒株基因序列变异的地理分布分析显示，禽流感病毒爆发与候鸟迁徙、家禽运输密切相关。
文摘卡波氏肉瘤(Kaposi sarcoma,KS)在全球范围内是人免疫缺陷病毒感染者第二易患的肿瘤。本研究旨在确定KS中差异表达的关键微小RNA(microRNA,miRNA)及其靶基因和相关途径,为深入了解该疾病的分子机制提供理论基础。本研究通过测序获得KS组织及瘤旁组织中的差异miRNA,借助starBase数据库预测差异表达miRNA的靶基因,同时用基因本体论(Gene Ontology,GO)数据库、京都基因与基因组百科全书(Kyoto Encyclopedia of Genes and Genomes,KEGG)、Reactome通路富集和转录因子注释分析差异miRNA的靶基因,最后用实时荧光定量PCR(Quantitative Real⁃time PCR,qRT⁃PCR)验证下调最明显的三个miRNA。结果显示,上、下调差异miRNA分别为39个和67个。GO和KEGG富集分析显示,上调的差异miRNA靶基因主要富集在组蛋白修饰、核染色质、DNA−结合转录激活因子活性等生物学功能,主要通过cAMP信号通路和长时程增效等通路参与KS的疾病进程;下调的差异miRNA主要与组蛋白修饰、细胞前沿和蛋白丝氨酸/苏氨酸激酶的活性有关,主要通过FoxO及Hippo等信号通路参与KS的疾病进程。Reactome富集显示,差异miRNA多集中在受体酪氨酸激酶信号、信号转导疾病和PI3K⁃Akt等信号通路。转录因子注释结果显示,肿瘤蛋白P53(Tumor Protein P53,TP53)、叉头框转录因子O亚族1(Forkhead Box Protein O1,FOXO1)和叉头框转录因子O亚族3(Forkhead Box Protein O3,FOXO3)等转录因子可能和KS的发生发展密切相关。qRT⁃PCR结果显示,测序中下调最明显的三个miRNA在KSHV感染细胞中均显著下调。总之,本研究筛选出了KS组织中差异表达的miRNA,对其靶基因进行了一系列生物信息学分析,并初步发现miR⁃651⁃3p,miR⁃223⁃3p及miR⁃186⁃5p通过Hippo、FoxO及PI3K⁃AKT信号通路可能在KS的疾病进程中发挥重要作用。这些研究均为探寻KS的发病机制和靶向干预提供了有力的理论基础。
