构巢曲霉与30种丝状子囊菌的基因组比较

为探讨丝状子囊菌的序列同源性,文章利用公开发表的真菌基因组序列构建本地基因组数据库,设置E值统计阈值为0.1,将构巢曲霉(Aspergillus nidulans)基因组的10560个注释基因分别与30种丝状子囊菌基因组比较。结果表明,同源匹配基因数量的多少可反映子囊菌之间的进化关系。构巢曲霉基因组的924个基因与这30种子囊菌基因组同时存在匹配序列,其中E值在10-5～0.1、10-30～10-5、10-100～10-30、0～10-100范围内都存在匹配序列的基因分别为6个、3个、6个和6个。ClustalX多序列比对分析显示,E值10-5～0.1的6组序列和E值10-30～10-5的3组序列均显示变异性过大而E值0～10-100的6组序列过于保守,E值介于10-100～10-30之间的6组同源序列可用于本研究的31种子囊菌系统学分析。     

基于直向同源序列的比较基因组学研究

直向同源序列在不同的物种中具有相近甚至相同的功能、相似的调控途径, 扮演相似甚至相同的角色, 而且, 绝大多数核心生物功能就是由相当数量的直向同源基因所承担, 它是基因组序列的功能注释与分析中最可靠的选择, 其特殊的生物学特性决定: 利用直向同源序列开展比较基因组学研究, 必将为探测不同生物在进化过程中重要功能基因的出现、表达和丢失提供线索。文章从直向同源基因的基本特性、直向同源序列与比较基因组学的关系、应用直向同源序列开展比较基因组学相关研究方法、现状等展开综述。关键词: 直向同源; 比较基因组学; 生物学特性; 数据库     

中国菌生非地衣型子囊菌资源

菌生真菌是指以其他真菌为宿主的真菌,是重要的自然生物资源.它们不是系统学上的分类群,而是特殊生境真菌,包括子囊菌、担子菌和接合菌的种类.其中菌生子囊菌是动植物以及其他真菌的内生菌、寄生菌或腐生菌,少数种己用于植物病害的生物防治,对其进行研究具有重要的理论意义和应用潜力.作者汇总了我国丰富的非地衣型菌生子囊菌资源,目前己报道该类真菌132种,其中以担子菌为宿主的约63种,以子囊菌为宿主的38种,其余或对基物的选择性不强或宿主真菌的分类地位不详,部分种类表现出对基物真菌或者宿主真菌的选择性.同时,对菌生真菌与宿主真菌相互作用方式、菌生子囊菌在植物病害防控中的应用以及少数种类对食用菌栽培的为害进行了简要概述.     

痢疾志贺氏菌亚群的比较基因组学研究与进化分析

利用大肠杆菌K12 MG1655株全基因组ORFs和痢疾志贺氏菌A1型Sd51197株特异性ORFs探针制备的芯片, 研究了痢疾志贺氏菌13个血清型代表株的基因组组成. 结果显示, 该血清群成员的基因组中包含有2654个保守的源于大肠杆菌ORFs; 共同缺失了219个涉及前噬菌体基因、分子伴侣、特异性O抗原合成等大肠杆菌原有的基因; 并通过水平转移获得了一些特异性基因, 如Ⅱ型分泌系统相关组分、铁转运相关因子等. 根据基因组组成所作的进化树, 发现A1, A2, A8和A10这四型菌与其他痢疾志贺氏菌亲源关系较远. 研究所得结果为进一步深入探索痢疾志贺氏菌的生理过程、致病性和进化奠定了基础.     

痢疾志贺氏菌亚群的比较基因组学研究与进化分析

利用大肠杆菌K12MG1655株全基因组ORFs和痢疾志贺氏菌A1型Sd51197株特异性ORFs探针制备的芯片,研究了痢疾志贺氏菌13个血清型代表株的基因组组成.结果显示,该血清群成员的基因组中包含有2654个保守的源于大肠杆菌ORFs;共同缺失了219个涉及前噬菌体基因、分子伴侣、特异性O抗原合成等大肠杆菌原有的基因;并通过水平转移获得了一些特异性基因,如Ⅱ型分泌系统相关组分、铁转运相关因子等.根据基因组组成所作的进化树,发现A1,A2,A8和A10这四型菌与其他痢疾志贺氏菌亲源关系较远.研究所得结果为进一步深入探索痢疾志贺氏菌的生理过程、致病性和进化奠定了基础.     

序列同源性比较软件Blast的本地化实现及VB接口程序的编制

美国国家生物技术信息中心（ＮａｔｉｏｎａｌＣｅｎｔｅｒｆｏｒＢｉｏｔｅｃｈｎｏｌｏｇｙＩｎｆｏｒｍａｔｉｏｎ,ＮＣＢＩ）的Ｂｌａｓｔ软件是进行核酸序列和蛋白质序列同源性比较的有力工具［１,２］．通过访问ＮＣＢＩ的主页（ｈｔｔｐ：／／ｗｗｗ．ｎｃｂｉ．ｎｌｍ．ｎｉｈ．ｇｏｖ）进行Ｂｌａｓｔ同源性比较是常用的分析方法．然而在很多场合需要在脱机状态下使用Ｂｌａｓｔ进行同源性比较,所以,Ｂｌａｓｔ软件的本地化实现有其必要性．本文介绍实现Ｂｌａｓｔ本地化过程的经验,同时用ＶｉｓｕａｌＢａｓｉｃ５．０（以下…     

五株克雷伯氏菌噬菌体的生物学特性及比较基因组学研究

【目的】耐药性克雷伯氏菌属(Klebsiella)的细菌作为人类感染的重要病原,是临床治疗重要的挑战。本研究对多株克雷伯氏菌裂解性噬菌体的生物学特性和基因组特征进行比较分析,为其应用提供更多科学数据。【方法】使用双层平板法从人类和动物新鲜粪便、污水中分离纯化裂解性克雷伯氏菌噬菌体;通过磷钨酸染色和透射电镜观察其形态;采用双层平板噬菌斑法确定其宿主范围,测定温度和pH稳定性、一步生长曲线和体外抑菌效果等生物学特性;基于全基因组测序对分离株进行比较基因组学分析;通过体内抑菌试验评估噬菌体对多重耐药变栖克雷伯氏菌(Klebsiella variicola)BS375-3感染的大蜡螟(Galleria mellonella)幼虫的保护作用。【结果】5株噬菌体分别属于Schitoviridae(pKP-BM327-1.2)、Autographiviridae(pKP-M186-2.1、pKP-M186-2.2和pKV-BS375-3.1)、Drexlerviridae(pKP-BS317-1.1)家族;噬菌体pKV-BS375-3.1可裂解受试菌中的8株,pKP-BM327-1.2可裂解受试菌中的3株,pKP-M186-2.1、pKP-M186-2.2和pKP-BS317-1.1则分别裂解受试菌中的1株;5株噬菌体感染10–20 min后即进入指数增长期,在–20–37℃、pH 6–10环境下均能够保持稳定活性;感染变栖克雷伯氏菌BS375-3后经噬菌体pKV-BS375-3.1处理[感染复数(multiplicity of infection,MOI)=100]的大蜡螟幼虫96 h内存活率达到80%(8/10);5株噬菌体基因组长度在42–77 kb之间,未携带抗生素抗性基因和毒力基因,基于内溶素(endolysin)的溯源分析显示该蛋白在克雷伯氏菌噬菌体中呈现多样性,属内呈保守性。【结论】5株克雷伯氏菌噬菌体均具有较好的体外抑菌活性,生物学特性稳定,endolysin在噬菌体属内呈现保守性。宿主谱宽、潜伏期短的噬菌体pKV-BS375-3.1在治疗Klebsiella pneumoniae和K.variicola临床感染方面具有潜在应用前景。     

来自大别山的子囊菌4个中国新记录种

依据形态分类学和分子系统学相结合的方法对采集于大别山的子囊菌标本进行物种鉴定的结果,本研究报道了4个中国新记录种：蚤褐炭团菌Hypoxylonpulicicidum、提契诺炭团菌H.ticinense、双滴瓶头霉Phialocephalabiguttulata和近木根平盘菌Rhizodiscinalignyota,基于作者所研究的标本对这4个种进行了描述及图示。在基于ITS序列和(或) LSU序列、采用贝叶斯法和最大似然法构建的系统发育树中,新记录种均得到分子数据的支持。凭证标本保存于南京师范大学真菌标本室(Herbarium of Fungi of Nanjing Normal University, HFNNU)。     

子囊菌交配型基因MAT1-1的系统发育

子囊菌具有无性态与有性态的复杂性,以及人们对其系统发育和亲缘关系了解的局限性,进而导致菌物学家对子囊菌分类尚持不同意见。子囊菌的交配型基因（MAT）进化保守,且编码的蛋白质调控子囊菌的有性生殖过程。核盘菌Sclerotinia sclerotiorum (Lib.) de Bary隶属于子囊菌门Ascomycota、盘菌纲Discomycete,是一种典型丝状同宗配合真菌,控制该菌有性生殖的交配型基因MAT1-1和MAT1-2紧密连锁,且该菌并无有性态与无性态的复杂性。故此,本文根据所克隆的核盘菌交配型基因MAT1-1,利用PAUP*软件将82种含有Alpha-box交配型基因的子囊菌进行了系统进化分析,通过核苷酸及氨基酸水平的系统发育分析,并结合Ainsworth（1973）分类系统及最新的Deep Hyphae（2006）分类系统的对比研究,发现所构建的系统进化树与传统分类所表现的进化关系基本一致,且核盘菌交配型基因MAT1-1在进化过程中功能相对保守,该分析结果有助于对其他子囊菌交配型基因的克隆、系统分类与进化研究,同时对核盘菌的亲缘关系、病害预测及防治等具有重要意义。     

林木比较基因组学研究进展

比较基因组学是基因组研究的重要内容。林木比较基因组学研究发现林木基因组中存在广泛的共线性或同线性及微共线性,在进化过程中呈现高度保守性。本文概述了林木比较基因组学研究的进展状况,探讨了该领域的发展趋势,以期为我国林木基因组学研究提供有益的参考。     

Phylogenetic relationships of ascomycetes and basidiomycetes based on comparative genomics analysis

The relationship between ascomycetes and basidiomycetes, the two main phyla of non-flagellated fungi, has rarely been investigated. In this study, we performed a comparative genomics analysis of genome sequences of 55 ascomycetes and 26 basidiomycetes species and detected 81 universal markers, 875 homologous genes and a conserved contig in the glucose-regulated protein gene. In dendrograms based on simple sequence repeat markers and homologous genes, ascomycetes and basidiomycetes formed distinct clusters, with each set of taxa having a high coefficient of relatedness. Ascomycetes and basidiomycetes also constituted distinct groups in a phylogenetic tree based on a conserved contig in the glucose-regulated protein gene. These results provide evidence that basidiomycetes may be derived from ascomycetes but are definitely genetically differentiated at the genomic level. The phylogenetic relationships of ascomycetes and basidiomycetes uncovered in this study provide new insights for future research related to fungal classification and evolution.     

Homology modeling, comparative genomics and functional annotation of Mycoplasma genitalium hypothetical protein MG_237

Mycoplasma genitalium is a human pathogen associated with several sexually transmitted diseases. The complete genome of M. genitalium G37 has been sequenced and provides an opportunity to understand the pathogenesis and identification of therapeutic targets. However, complete understanding of bacterial function requires proper annotation of its proteins. The genome of M. genitalium consists of 475 proteins. Among these, 94 are without any known function and are described as 'hypothetical proteins'. We selected MG_237 for sequence and structural analysis using a bioinformatics approach. Primary and secondary structure analysis suggested that MG_237 is a hydrophilic protein containing a significant proportion of alpha helices, and subcellular localization predictions suggested it is a cytoplasmic protein. Homology modeling was used to define the three-dimensional (3D) structure of MG-237. A search for templates revealed that MG_237 shares 63% homology to a hypothetical protein of Mycoplasma pneumoniae, indicating this protein is evolutionary conserved. The refined 3D model was generated using (PS)(2)-v2 sever that incorporates MODELLER. Several quality assessment and validation parameters were computed and indicated that the homology model is reliable. Furthermore, comparative genomics analysis suggested MG_237 as non-homologous protein and involved in four different metabolic pathways. Experimental validation will provide more insight into the actual function of this protein in microbial pathways.     

The animal in the genome: comparative genomics and evolution

Comparisons between completely sequenced metazoan genomes have generally emphasized how similar their encoded protein content is, even when the comparison is between phyla. Given the manifest differences between phyla and, in particular, intuitive notions that some animals are more complex than others, this creates something of a paradox. Simplistic explanations have included arguments such as increased numbers of genes; greater numbers of protein products produced through alternative splicing; increased numbers of regulatory non-coding RNAs and increased complexity of the cis-regulatory code. An obvious value of complete genome sequences lies in their ability to provide us with inventories of such components. I examine progress being made in linking genome content to the pattern of animal evolution, and argue that the gap between genomic and phenotypic complexity can only be understood through the totality of interacting components.     

Consensus folding of aligned sequences as a new measure for the detection of functional RNAs by comparative genomics

Facing the ever-growing list of newly discovered classes of functional RNAs, it can be expected that further types of functional RNAs are still hidden in recently completed genomes. The computational identification of such RNA genes is, therefore, of major importance. While most known functional RNAs have characteristic secondary structures, their free energies are generally not statistically significant enough to distinguish RNA genes from the genomic background. Additional information is required. Considering the wide availability of new genomic data of closely related species, comparative studies seem to be the most promising approach. Here, we show that prediction of consensus structures of aligned sequences can be a significant measure to detect functional RNAs. We report a new method to test multiple sequence alignments for the existence of an unusually structured and conserved fold. We show for alignments of six types of well-known functional RNA that an energy score consisting of free energy and a covariation term significantly improves sensitivity compared to single sequence predictions. We further test our method on a number of non-coding RNAs from Caenorhabditis elegans/Caenorhabditis briggsae and seven Saccharomyces species. Most RNAs can be detected with high significance. We provide a Perl implementation that can be used readily to score single alignments and discuss how the methods described here can be extended to allow for efficient genome-wide screens.     

Hallmarks of mycolic acid biosynthesis: a comparative genomics study

Mycolic acids, which render unique qualities to mycobacteria, are known to be important for mycobacterial growth, survival, and pathogenicity. It is of interest to understand the evolutionary origins of the mycolic acid pathway (MAP), as well as the common minimum principles critical for generating the capability of mycolic acid biosynthesis. The recent curation of a comprehensive model of the MAP in Mycobacterium tuberculosis and the availability of a large number of genome sequences make it feasible to carry out detailed sequence and phylogenetic analyses, to address these questions. A comprehensive phylogenetic pathway profile analysis was carried out for 318 fully sequenced bacterial genomes, for each of the proteins present in the MAP. The organisms were clustered on the basis of co-occurrence of the MAP proteins in their proteome, while the proteins were clustered on the basis of their phylogenetic profiles. The MAP proteins were also searched against the nonredundant sequence database, to identify similar proteins from other phyla. The pathway profiles indicate that four proteins and certain protein domains stand out as more characteristic to mycolate producing organisms. Further analysis leads to the identification of the desaturases DesA1 and DesA2 and certain domains of Fas and Pks13 as hallmarks of the pathway. The roles of these proteins in some other organisms, as well as the distribution of these proteins across all known genome sequences are also briefly discussed. The clustering of organisms, carried out to group organisms with similar profiles, provides a means of obtaining finer classification as compared to the standard taxonomic method. The results indicate that the MAP and hence the capacity of mycolic acid production in mycobacteria is an example of an emergent property that has come about by recruiting enzymes from unrelated pathways in plants, presumably through lateral gene transfer. The understanding of the hallmarks of mycolic acid biosynthesis will also find application in evaluating drug targets.     

基因芯片在细菌基因组学和细胞微生物学研究中的应用

利用基因芯片可以鉴定病原菌在不同宿主微环境中受到差异调节的基因、直接或间接由转录因子控制的基因,以及编码多步骤代谢和生物合成途径中各种组分的基因;通过比较基因组学研究,评价相关菌种和菌株的自然群体内遗传多样性的范围和特性,并在ORF水平描述病原体和共生体之间的差异;同时也可进行感染组织细胞基因表达分析,研究病原体和宿主之间复杂的相互作用关系。     

基于高通量测序的群体基因组学——植物病原真菌研究新方向

群体基因组学能够从全基因组水平揭示种群结构与进化、物种形成、适应性机制等。随着高通量技术的不断发展,基因组测序成本不断降低,大规模测序已成为可能。近几年被全基因组测序的真菌数量迅速增加,极大地促进了真菌群体基因组学的发展,加深了人们对植物病原真菌起源、遗传多样性、选择作用、致病性、毒力因子、杀菌剂抗药性、寄主专化型等生物学特性的认识。本文简要介绍了植物病原真菌的全基因测序以及比较基因组学的研究进展,重点综述了基于高通量测序的病原真菌群体基因组学的最新研究动态。群体基因组学将成为植物病原真菌一个新的研究方向。