海洋琼胶降解菌FG15基因组从头测序分析

为充分了解琼胶降解菌FG15的基因功能和代谢途径,本研究使用SOAP de novo 2.04对Illumina Hiseq2000平台测序产生的基因片段进行了拼接和组装,同时利用Glimmer 3.02来预测基因的开放性阅读框,并采用蛋白质直系同源基因簇(COG)、基因本体数据库(GO)以及京都基因和基因组百科全书(KEGG)的数据来预测其基因功能,获得了代谢途径.结果表明:FG15的基因组大小为5.10 Mb,G+C含量为44.58%,共有38条Scaffolds,4 922个开放性阅读框,82个tRNA,2个rRNA;通过COG分析可将菌株FG15注释到22种COG功能类型,主要包括细胞代谢、细胞信号转导等;利用GO注释可将FG15注释到3大类39个GO功能亚类上;KEGG分析能将其定位到154个代谢通路中,包括物质代谢、次生代谢产物的生物合成等.次生代谢产物的合成代谢途径精确显示,FG15能合成青霉素和头孢菌素,且其与抗生素抗性实验的结果一致.研究结果为FG15功能基因组学的研究和相关次级代谢产物的生物合成途径以及异源表达的研究提供了理论基础.     

黄精转录组特性分析及相关功能基因研究

分析黄精转录组数据,挖掘与黄精中多糖、皂苷元、黄酮生物合成途径相关的关键酶基因.利用Illumina HiSeq测序平台对黄精全株进行转录组测序,对测序结果进行注释分析.共获得146072个有效转录本,超过51.00％的转录本在NR、Swiss-Prot、KOG、GO、KEGG数据库中获得注释.β-呋喃果糖苷酶、己糖激...     

马克斯克鲁维酵母FIM1基因组分析

马克斯克鲁维酵母(Kluyveromyces marxianus)是一种富有潜力的新型细胞工厂宿主菌。K.marxianus FIM1(CGMCC No.10621)基因组组装与注释已于2019年完成并在NCBI上公布(GCA＿001854445.2),但在应用该基因组信息时发现其仍不完善。所以本研究使用重测序的DNA-seq数据校验了K.marxianus FIM1的基因组序列，随后补充了K.marxianus FIM1的注释，并使用比较基因组学的方法进一步完善了K.marxianus FIM1的基因组信息。根据重测序比对结果，删除了测序数据无法覆盖的位点61处，共4 910 bp。K.marxianus FIM1新序列总长为10 909 543 bp,可覆盖酵母目保守基因库中99.5%的基因。同时对K.marxianus FIM1的非编码RNA、次级代谢产物基因簇的也进行了补充注释。进一步，我们使用基因组共线性分析的方法分析了K.marxianus FIM1在物种分化过程中基因排列顺序保守的区域，并将K.marxianus FIM1与NCBI公布的11株K.marxianus进行了...     

黄连基因组勘测与分析

本研究基于下一代测序技术,对黄连基因组进行了勘测,构建了两个插入片段大小分别为200bp和500bp的文库,进行了深度约30X的测序。通过测序获得了54Gb的原始数据,过滤后得到44.8G数据。通过SOAP de nove软件组装后初步获得了contig和Scaffold序列,进一步分析结果显示其基因组大小为1,116Mb左右,大约具有1.1%的杂合度,说明要完成该物种的全基因测序可能在使用鸟枪法的同时,还应该联合BAC文库测序等多种方法.对这些数据进行了初步的组装,获得了130,381条scaffold序列.     

灰树花菌（Griflola frondosa）子实体原基转录组测序及分析

采用Illumina测序平台对灰树花菌（Griflola frondosa）原基进行转录组测序,获得了大量转录组信息.结显示果,测序得到38 189个非冗余Unigene,在Nr数据库中有31 454个Unigene被注释;与KEGG数据库比对,共有1 832个Unigene被注释,分属20条生物通路;在COG数据库中注释可划分为25类;与GO数据库进行注释可分为分子功能、细胞组分和生物过程3个主类和60个二级亚类.     

一株多药耐药Comamonas kerstersii细菌的基因组分析（英文）

从1名尿路感染患者中分离出了1株多药耐药的Comamonas kerstersii(C.kerstersii)菌株121606,对其进行了抗微生物药敏试验(AST)和全基因组测序;然后将其与7个具有代表性的Comamonas菌株和Acidovorax菌种进行基因组比较分析,包括使用OrthoANI分析平均核苷酸同一性(ANI),以及通过snpTree网络服务器进行单核苷酸多态性(SNP)分析。最后,使用RAST服务器进行基因组序列,使用OrthoVenn软件对同源簇进行功能注释,通过CARD数据库对抗生素耐药基因(ARGs)进行预测,并利用CRISPR识别工具预测CRISPR,以及利用PHAST软件预测前噬菌体。结果表明：C.kerstersii 121606是一种多药耐药细菌,其遗传成分与其他7个Comamonas和Acidovorax菌种相似;其基因组中存在的ARGs有助于解释其多药耐药机制。这些发现为研究新型抗生素来控制多药耐药C.kerstersii感染提供了有价值的见解。     

Paenibacillus Shenyangensis的DNA序列拼接与组装

在已有测序数据基础上,利用三种常见的序列组装软件对Paenibacillus Shenyangensis全基因组测序结果进行拼接组装,分析比较了不同软件在各自最优参数条件下DNA序列的组装数据,并与NCBI数据库中类芽孢杆菌属其他近缘种进行基因比对与预测.结果表明,SOAPdenovo的组装结果最优,在k-mer为23时,组装基因组总长和N50分别为5 501 467和293 864 bp,预测的4 800个基因中有4 393个与NCBI-Nr数据库比对并注释成功.     

嗜麦芽糖寡氧单胞菌H002的基因组分析及对铀胁迫的转录组响应

为探究嗜麦芽糖寡氧单胞菌H002响应金属铀冲击的分子机制及生物修复铀污染的潜力，本研究从基因组和转录组两个层面进行了分析.基因组测序结果表明，H002基因组大小为5 099 056 bp,预测编码4780个蛋白；与其他6个近缘菌株相比，H002拥有344个独特的编码基因，涉及膜转运、细胞运动和分泌等功能.转录组分析显示，在铀胁迫的早期(1 h),差异基因主要富集于细胞运动、分泌、蛋白质和肽聚糖合成等KEGG途径.部分分泌通道相关基因的表达下调，可降低细胞对铀离子的摄取，进而减轻铀离子对细胞的毒性.在铀胁迫的后期(2 h和4 h),参与铀生物矿化的磷酸酶相关基因和能够提供还原电子的细胞色素c基因的表达上调，能以主动方式降低铀的细胞毒性.     

毛茛铁线莲叶绿体全基因组解析及系统发育分析

为了解析药用植物毛茛铁线莲的叶绿体全基因组特征及系统发育位置,利用高通量测序技术对毛茛铁线莲叶片样品进行测序,并对毛茛铁线莲叶绿体基因组进行组装、注释和特征分析,采用最大简约法(MP)、最大似然法(ML)及贝叶斯法(BI)构建分子系统发育树.结果表明,毛茛铁线莲的叶绿体基因组为典型的四分体结构,全长159 741 bp,共编码112个基因,包括79个蛋白编码基因、29个tRNA基因和4个rRNA基因;毛茛铁线莲叶绿体基因组共含有84个简单重复序列,以单核苷酸重复基序居多,共57个;毛茛铁线莲叶绿体基因组使用频次最高的氨基酸是亮氨酸;基于叶绿体全基因组构建的MP,ML和BI树,拓扑结构基本一致;铁线莲属是明显的单系类群,与银莲花属关系最近,毛茛铁线莲与绣球藤亲缘关系最近.     

鹿茸草全长转录组测序与次生代谢产物生物合成相关基因的挖掘

为获得鹿茸草的全长转录组信息,挖掘鹿茸草次生代谢化合物生物合成途径相关酶的基因,该文基于单分子测序技术,利用Pacbio高通量测序平台,对鹿茸草进行全长转录组测序,共获得48 005条去冗余的高质量转录本,与NR、Swiss-Prot、GO、KEGG等8个数据库进行BLAST比对,共有45 362个转录本被成功注释,注释率为94.50%.其中有389条转录本被注释到KEGG的10条标准次生代谢生物合成通路中.对转录组数据进一步分析发现：参与鹿茸草苯丙素类生物合成的转录本有194条,参与生物碱类生物合成的转录本有115条,参与类黄酮化合物生物合成的转录本有23条,参与其他次生代谢产物的转录本有57条,参与次生代谢后氧化与糖基化修饰的转录本有204条.鹿茸草全长转录组的获得极大地丰富了鹿茸草的遗传信息,初步揭示了参与鹿茸草次生代谢产物合成相关的基因通路,为深入研究鹿茸草次生代谢产物合成途径关键酶的功能及其调控机制奠定了基础.     

Advances in the study of helminth mitochondrial genomes and their associated applications

Helminths, including flatworms and roundworms, are abundant organisms that have a variety of life histories. Of these, the genera Schistosoma, Echinococcus, Trichinella are notable parasites of veterinary and medical importance, and cause substantial socio- economic losses throughout China and the rest of the world. Genetic markers in the mitochondrial (mt) genome have proven use- ful for systematic, ecological, evolutionary and population studies, and the growth of mt genomic research has increased in the last two decades. Technological improvements, such as the long-polymerase chain reaction method and high-throughput se- quencing have allowed minute amounts of DNA from single worms, biopsy samples or microscopic organisms to be used for whole mt genome characterization. To facilitate the retrieval, annotation and analyses of mitochondrial features, multiple data- bases and specific software have also been designed and established. This review focuses on current progress, applications and perspectives regarding helminth mt genomics. To date, the complete mt genomes for 93 species of helminths have been sequenced and analyzed. Analyses of the mt genes, including gene content, arrangement, composition and variation have revealed unique features among the helminths when compared with other metazoans. This provides important data concerning their functional and comparative mitochondrial genomics, molecular taxonomy and characterization, population genetics and systematics, and evolu- tionary history. Moreover, mt genome data for parasitic helminths are important for diagnosis, epidemiology and ecology of in- fections. Mitochondrial genome data offer a rich source of markers for the systematics and population genetics of socioeconomi- cally important parasitic helminths of humans and other animals.     

麂属动物小麂线粒体DNA文库的建立和序列分析

通过建立麂属动物小麂线粒体DNA文库，鸟枪法测序，我们获得了小麂线粒体基因组全序列的初步信息，这也是国内有关哺乳动物线粒体基因组全序列的首次报道，与其他哺乳动物线粒体基因组全库列的比较研究发现：全长为16354bp的小麂线粒体基因组同样编码13种蛋白、2种rRNA和22种tRNA，除了用于调控线粒体DNA复制和转录的D-Loop区以外，小麂线粒体基因组各基因长度，位置与其他哺乳动物相似，其编码蛋白质区域的rRNA基因与基因他哺乳动物具有很高的同源性，D－Loop区长度和序列的差异是导致各种哺乳动物线粒体差异的主要原因。     

A complete sequence and comparative analysis of a SARS-associated virus(Isolate BJ01)

Severe Acute Respiratory Syndrome (SARS) is a newly identified infectious disease[1—5]. The global outbreak of SARS has been threatening the health of people worldwide and has killed 353 people and infected more than 5462 in 27 countries, as reported by WHO on April 29, 2003 (http://www.who.int/csr/sarscountry/en). Although it has been recognized that a variant of virus from the family of coronavirus might be the candidate pathogen of SARS[1—5], its identity as the unique pathogen sti…     

A complete sequence and comparative analysis of a SARS-associated virus （Isolate BJO1）

The genome sequence of the Severe Acute Respiratory Syndrome (SARS)-assoclated virus provides essential information for the identification of pathogen(s), exploration of etiology and evolution, interpretation of transmission and pathogenesis, development of diagnostics, prevention by future vaccination, and treatment by developing new drugs.We report the complete genome sequence and comparative analysis of an isolate (B J01) of the coronavirus that has been recognized as a pathogen for SARS. The genome is 29725 nt in size and has 11 ORFs (Open Reading Frames). It is composed of a stable region encoding an RNA-dependent RNA polymerase (composed of 20RFs) and a variable region representing 4 CDSs (coding sequences) for viral structural genes (the S, E, M, N proteins) and 5 PUPs (putative uncharacterized proteins). Its gene order is identical to that of other known coronaviruses. The sequence alignment with all known RNA viruses places this virus as a member in the family of Coronaviridae. Thirty putative substitutions have been identified by comparative analysis of the 5 SARS-associated virus genome sequences in GenBank. Fifteen of them lead to possible amino acid changes (non-synonymous mutations) in the proteins. Three amino acid changes, with predicted alteration of physical and chemical features, have been detected in the S protein that is postulated to be involved in the immunoreactions between the virus and its host.Two amino acid changes have been detected in the M protein,which could be related to viral envelope formation. Phylogenetic analysis suggests the possibility of non-human origin of the SARS-associated viruses but provides no evidence that they are man-made. Further efforts should focus on identifying the etiology of the SARS-associated virus and ruling out conclusively the existence of other possible SARS-related pathogen(s).     

柳树痂囊腔菌的基因组测序和比较基因组分析

【目的】报道柳树痂囊腔菌(Elsinoë murrayae)的全基因组序列,与甜橙痂囊腔菌杨树致病型的基因组进行比较分析,为阐述柳树痂囊腔菌的致病和适应性机制提供参考。【方法】采用Illumina HiSeq 2500 测序仪对柳树痂囊腔菌的全基因组序列进行测序,预测蛋白编码基因,筛选与致病相关的碳水化合物活性酶基因、小分泌蛋白基因和次生代谢产物基因簇。根据痂囊腔属真菌基因的直系同源关系,筛选柳树痂囊腔菌和甜橙痂囊腔菌杨树致病型之间共有特异性的基因和二者之间差异基因,并进行GO富集分析。鉴定柳树痂囊腔菌的交配类型位点,使用特异性引物进行PCR,检测分离株的交配类型。【结果】组装获得了1个20.7 Mb基因组,完整度99%;预测出8 256个蛋白编码基因,其中包括486个碳水化合物活性酶基因,193个小分泌蛋白基因和16个次生代谢产物基因簇 (GenBank登录号:NKHZ00000000)。系统进化和共线性分析显示柳树痂囊腔菌和甜橙痂囊腔菌杨树致病型亲缘关系最近,两者之间具有12个在其他痂囊腔菌中没有的共有特异性基因。两个真菌的比较基因组分析,筛选出752和1 746个差异基因,主要参与碳水化合物代谢和毒素代谢的生物学过程。已有分离株的交配类型均为MAT1-2。【结论】获得柳树病原真菌-柳树痂囊腔菌的基因组,筛选出痂囊腔菌中负责寄主适应性的候选基因,分析了柳树痂囊腔菌交配系统,这可为柳树病害防治和柳树-病原真菌相互作用研究提供关键信息。     

Widespread horizontal transfer of mitochondrial genes in flowering plants

Horizontal gene transfer--the exchange of genes across mating barriers--is recognized as a major force in bacterial evolution. However, in eukaryotes it is prevalent only in certain phagotrophic protists and limited largely to the ancient acquisition of bacterial genes. Although the human genome was initially reported to contain over 100 genes acquired during vertebrate evolution from bacteria, this claim was immediately and repeatedly rebutted. Moreover, horizontal transfer is unknown within the evolution of animals, plants and fungi except in the special context of mobile genetic elements. Here we show, however, that standard mitochondrial genes, encoding ribosomal and respiratory proteins, are subject to evolutionarily frequent horizontal transfer between distantly related flowering plants. These transfers have created a variety of genomic outcomes, including gene duplication, recapture of genes lost through transfer to the nucleus, and chimaeric, half-monocot, half-dicot genes. These results imply the existence of mechanisms for the delivery of DNA between unrelated plants, indicate that horizontal transfer is also a force in plant nuclear genomes, and are discussed in the contexts of plant molecular phylogeny and genetically modified plants.     

鹅耳枥属树种叶绿体基因组结构及变异分析

【目的】了解鹅耳枥属(Carpinus)树种叶绿体基因组基因组成及结构特征,为鹅耳枥属的系统发育及基因组进化研究提供参考。【方法】获取鹅耳枥属16个树种的叶绿体基因组,对其进行基因注释,利用生物信息学方法比较叶绿体基因组间的结构特征与变异程度,并以麻栎(Quercus acutissima)为外类群分析了鹅耳枥属的系统发育关系。【结果】鹅耳枥属16个树种的叶绿体基因组均为双链环形结构,均包含1个长单拷贝区(LSC)、1个短单拷贝区(SSC)以及2个反向重复区(IRa和IRb)。叶绿体基因组大小差异较小,最大差异仅1 902 bp。基因排列顺序基本一致,各基因数量相对保守,其中核糖体RNA(rRNA)数量最为保守,所有树种均为8个。此外,鹅耳枥属树种叶绿体基因组在序列长度、基因组成以及GC含量等方面相对保守,但4个边界存在明显的多样性。鹅耳枥属叶绿体基因组中非基因编码区存在较大差异,变异程度较高,而基因编码区差异较小,具有较高的保守性。在叶绿体基因组4个部分中,LSC区的变异程度最高,IRa区的变异程度最低。鹅耳枥属叶绿体基因组中psbA、rps16、atpA、rps19、ndhF、ndhI以及ycf1等基因的编码区存在显著差异。此外,ycf3-trnS, trnS-rps4, trnH-psbA, psbZ-trnfM, matK-rps16, rps16-trnQ, trnQ-psbK, ccsA-ndhD, accD-psaI, ndhC-trnV, trnT-trnL, trnF-ndhJ, atpB-rbcL, trnT-psbD, trnE-trnT, trnD-trnY, rpl32-trnl等基因间隔区的非编码区差异较大。绝大部分基因的编码区长度十分保守,含内含子的蛋白编码基因长度变异主要来源于内含子长度或编码区长度。系统发育分析结果将鹅耳枥属划分为鹅耳枥组与千金榆组,此外由于地理隔离导致欧洲鹅耳枥(C. betulus)、美洲鹅耳枥(C. caroliniana)与鹅耳枥属其他树种表现出较远的亲缘关系。【结论】鹅耳枥属树种叶绿体基因组具有较高的保守性,其基因排列顺序基本一致,未检测到大规模的倒位或基因重排,但其IR区与单拷贝区(SC)边界存在明显的多样性。基于叶绿体基因组构建的系统发育树在一定程度上可以揭示鹅耳枥属树种的系统发育关系。     

Analysis of the genome sequence of the flowering plant Arabidopsis thaliana

The flowering plant Arabidopsis thaliana is an important model system for identifying genes and determining their functions. Here we report the analysis of the genomic sequence of Arabidopsis. The sequenced regions cover 115.4 megabases of the 125-megabase genome and extend into centromeric regions. The evolution of Arabidopsis involved a whole-genome duplication, followed by subsequent gene loss and extensive local gene duplications, giving rise to a dynamic genome enriched by lateral gene transfer from a cyanobacterial-like ancestor of the plastid. The genome contains 25,498 genes encoding proteins from 11,000 families, similar to the functional diversity of Drosophila and Caenorhabditis elegans--the other sequenced multicellular eukaryotes. Arabidopsis has many families of new proteins but also lacks several common protein families, indicating that the sets of common proteins have undergone differential expansion and contraction in the three multicellular eukaryotes. This is the first complete genome sequence of a plant and provides the foundations for more comprehensive comparison of conserved processes in all eukaryotes, identifying a wide range of plant-specific gene functions and establishing rapid systematic ways to identify genes for crop improvement.