基于质体基因组学方法研究广义玄参科的系统发育

该研究利用GenBank数据库已公开发表的玄参科及相关类群的107属129个物种的质体基因组数据对广义玄参科的系统发育关系进行了分析。该文利用蛋白质编码基因构建了矩阵,并采用最大似然法及贝叶斯推断重建系统发育树。基于两种分析方法获得的系统发育树的拓扑结构完全一致且分辨率及支持率较高。在ML树中,总分支数为129个,其中支持率≥70%的分支数目为123个。结果表明：(1)广义玄参科不是一个单系类群,隶属于广义玄参科的51个物种(37属)分散于列当科、泡桐科、美丽桐科、通泉草科、母草科、狭义玄参科和车前科。(2)狭义玄参科为单系类群,除原隶属于广义玄参科的Bontia、Calamphoreus、Diocirea、Eremophila、Glycocystis、Leucophyllum、玄参属和毛蕊花属外,还包括了原隶属于马钱科的醉鱼草属和原隶属于苦槛蓝科的苦槛蓝属。(3)唇形目为一个单系,目下共形成了14个支持率高的单系分支,对应于14个科(其中美丽桐科和胡麻科仅包括一个物种,不包括在内),科间关系得到较好的解决,木犀科为最早分化出来的类群,其余的类群共同组成核心唇形目。在核心唇形目中,类群...     

广义报春苣苔属（苦苣苔科）的染色体新计数及其分类学意义

报道了广义报春苣苔属14种3变种和7个未定名种的染色体数目,并对其近缘属-广义石山苣苔属的3个种也进行了细胞学研究。结合最近的分类处理和系统发育假设,对所得结果和以前发表的染色体数据进行了综合分析,结果表明：广义报春苣苔属的染色体数目为2n=36,基数为x=18,表现出高度稳定性。染色体相对较小,以中间着丝粒和亚中间着丝粒染色体为主。尽管一些类群的染色体大小之间存在微小差异,但是染色体形态的均一性和染色体数目的一致性有力地支持分子系统学的研究结果。另外．相同的染色体数目及相似的染色体形态也表明广义报春苣苔属和广义石山苣苔属的亲缘关系较近,与分子系统学的结果一致。     

西北干旱区孑遗濒危植物四合木(Tetraena mongolica)叶绿体基因组特征研究及比较分析

四合木（Tetraena mongolica）是我国特有的蒺藜科（Zygophyllaceae）强旱生小灌木;因其起源古老、抗逆性强;所以可作为生物多样性起源和环境演变研究的理想对象;具有重要的学术研究价值。本研究采用Illumina双末端测序技术对四合木叶绿体基因组进行建库测序和分析。选取蒺藜目及牻牛儿苗目共计30个物种叶绿体基因组;与四合木进行系统发育关系分析探讨。结果表明:四合木叶绿体基因组长度为106 259 bp;其中反向重复区（IR区中）有7种基因;包括4种PCG基因;3种tRNA基因。叶绿体基因组共编码98种基因;包括65种蛋白编码基因、29种tRNA基因与4种rRNA基因。生物信息学表明;在四合木中共搜到92个SSR位点;其中包括74个单核苷酸重复基序;7个二核苷酸重复基序;1个三核苷酸重复基序;9个四核苷酸重复基序和1个五核苷酸基序。没有发现六核苷酸;其中单核苷酸重复在四合木的叶绿体基因组SSR中占比为80.1%。通过MEGA软件采用近邻结合法（neighbor-joining;NJ）对四合木等31个物种的叶绿体基因组进行聚类分析;发现四合木与蒺藜科三齿拉雷亚灌木为最近的姐妹种;其次为牻牛儿苗科智利白桦植物亲缘关系较近;与牻牛儿苗科天竺葵属和牻牛儿苗科高桂花属亲缘关系最远;说明四合木属于蒺藜科物种;这对于四合木的研究等具有一定的参考价值。     

广义报春苣苔属 (苦苣苔科) 的染色体新计数及其分类学意义

报道了广义报春苣苔属14种3变种和7个未定名种的染色体数目,并对其近缘属——广义石山苣苔属的3个种也进行了细胞学研究。结合最近的分类处理和系统发育假设,对所得结果和以前发表的染色体数据进行了综合分析, 结果表明：广义报春苣苔属的染色体数目为2n=36,基数为x=18,表现出高度稳定性。染色体相对较小,以中间着丝粒和亚中间着丝粒染色体为主。尽管一些类群的染色体大小之间存在微小差异,但是染色体形态的均一性和染色体数目的一致性有力地支持分子系统学的研究结果。另外,相同的染色体数目及相似的染色体形态也表明广义报春苣苔属和广义石山苣苔属的亲缘关系较近,与分子系统学的结果一致。     

广义竹叶青蛇属Trimeresurus (sensu lato)的分类和系统学研究进展

广义的竹叶青蛇属于Trimeresurus(sensu lato)包含有40多个物种,广泛分布在南亚和东南亚国家和地区。目前,该类群已经相继被划分为6个属：Trimeresurus(sensu stricto)、Tropidolaemus、Ovophis Protobothrops,Triceratolepidophis,Zhaoermia本文从形态、细胞以及分了系统学等方面对Trimeresurus(sensu lato)的分类和系统学研究进行综述。     

Using next-generation sequencing for molecular reconstruction of past Arctic vegetation and climate

Palaeoenvironments and former climates are typically inferred from pollen and macrofossil records. This approach is time-consuming and suffers from low taxonomic resolution and biased taxon sampling. Here, we test an alternative DNA-based approach utilizing the P6 loop in the chloroplast trnL (UAA) intron; a short (13–158 bp) and variable region with highly conserved flanking sequences. For taxonomic reference, a whole trnL intron sequence database was constructed from recently collected material of 842 species, representing all widespread and/or ecologically important taxa of the species-poor arctic flora. The P6 loop alone allowed identification of all families, most genera (>75%) and one-third of the species, thus providing much higher taxonomic resolution than pollen records. The suitability of the P6 loop for analysis of samples containing degraded ancient DNA from a mixture of species is demonstrated by high-throughput parallel pyrosequencing of permafrost-preserved DNA and reconstruction of two plant communities from the last glacial period. Our approach opens new possibilities for DNA-based assessment of ancient as well as modern biodiversity of many groups of organisms using environmental samples.     

Evidence for frequent OspC gene transfer between Borrelia valaisiana sp. nov. and other Lyme disease spirochetes

IMP-1 metallo-beta-lactamase is a transferable carbapenem-hydrolyzing enzyme found in some clinical isolates of Pseudomonas aeruginosa, Serratia marcescens and Klebsiella pneumoniae. Bacteria that express IMP-1 show significantly reduced sensitivity to carbapenems and other beta-lactam antibiotics. A series of thioester derivatives has been shown to competitively inhibit purified IMP-1. As substrates for IMP-1, the thioesters yielded thiol hydrolysis products which themselves were reversible competitive inhibitors. The thioesters also increased sensitivity to the carbapenem L-742,728 in an IMP-1-producing laboratory stain of Escherichia coli, but will need further modification to improve their activity in less permeable organisms such as Pseudomonas and Serratia. Nonetheless, the thioester IMP-1 inhibitors offer an encouraging start to overcoming metallo-beta-lactamase-mediated resistance in bacteria.     

Plastid genome sequencing,comparative genomics,and phylogenomics:Current status and prospects

More than 190 plastid genomes have been completely sequenced during the past two decades due to advances in DNA sequencing technologies.Based on this unprecedented abundance of data,extensive genomic changes have been revealed in the plastid genomes.Inversion is the most common mechanism that leads to gene order changes.Several inversion events have been recognized as informative phylogenetic markers,such as a 30-kb inversion found in all living vascular plants minus lycopsids and two short inversions putat...     

Deep genomic analysis of the Chlorella sorokiniana SAG 211-8k chloroplast

The chloroplast genome contains information that is applicable in many scientific fields, such as plant systematics, phylogenetic reconstruction and biotechnology, because its features are highly conserved among species. To date, several complete green algal chloroplast genomes have been sequenced and assembled. In this study, the nucleotide sequence of the chloroplast genome (cpDNA) of Chlorella sorokiniana SAG 211-8k is reported and compared for the first time to the chloroplast genomes of 10 Chlorellaceae. The recently updated Chlorella sorokiniana cpDNA sequence, assembled as a circular map of 109?811 bp, encodes 113 genes. Similar to other Chlorella strains, this chloroplast genome does not show a quadripartite structure and lacks the large rRNA operon-encoding Inverted Repeat (IR). The Chlorella sorokiniana plastid encodes the tRNA(Ile)-lysidine synthetase (tilS), which is responsible for modifying the CAU anticodon of a unique tRNA. Gene ordering and clustering highlight the close relationships among Chlorella clade members and the preservation of crucial gene clusters in photosynthetic strains. The features of Chlorella sorokiniana presented here reinforce the monophyletic character of Chlorellaceae and provide important information that sheds light on chloroplast genome evolution among species of Chlorella.     

硬皮肿腿蜂属线粒体基因组特征及系统发育位置研究

【目的】硬皮肿腿蜂属Sclerodermus物种是我国林业蛀干害虫重要的天敌寄生蜂。本研究旨在明确硬皮肿腿蜂属在针尾部(Aculeata)中的分类地位;对4种硬皮肿腿蜂的线粒体基因组进行测序;分析其线粒体基因组结构和系统发育位置。【方法】利用Illumina HiSeq对硬皮肿腿蜂属4个种(松褐天牛肿腿蜂Sclerodermus alternatusi、白蜡吉丁肿腿蜂Sclerodermus pupariae、川硬皮肿腿蜂Sclerodermus sichuanensis和苹小吉丁肿腿蜂Sclerodermus sp.)线粒体基因组进行测序;然后对其进行组装和注释;分析其结构特点和碱基组成;在NCBI下载膜翅目(Hymenoptera)其他46个种的注释完整的线粒体基因组与本研究获得的4种硬皮肿腿蜂线粒体基因组;基于13个蛋白编码基因(protein-coding genes, PCGs)序列;利用贝叶斯法(Bayesian inference, BI)和最大似然法(maximum likelihood, ML)构建系统发育树;分析肿腿蜂科(Bethylidae)在针尾部中的系统发育位置。【结果】 4种硬皮肿腿蜂线粒体基因组全长为15 000~16 000 bp;由37个基因组成;包括13个PCGs、 2个rRNA基因和22个tRNA基因及1个非编码控制区。13个PCGs中;使用频率较高的4种氨基酸为Ile, Leu, Phe和Met。22个tRNA基因中;仅trnS1缺失DHU臂;其余21个tRNA基因都能形成典型的三叶草结构。37个基因中共有17个基因发生基因重排;包括15个tRNA基因和2个PCGs。与其余细腰亚目(Apocrita)昆虫相比;4种硬皮肿腿蜂线粒体基因组中trnT-trnP发生基因洗牌的同时;trnT发生了基因倒置。系统发育分析结果表明;肿腿蜂科具有单系性;且硬皮肿腿蜂属和头甲肿腿蜂属Cephalonomia的亲缘关系最近。【结论】本研究提供了4种硬皮肿腿蜂的线粒体基因组特征;发现基因重排现象复杂;系统发育分析表明硬皮肿腿蜂属隶属于肿腿蜂科;支持传统形态学分类结果;肿腿蜂科具有单系性;与蚁蜂科(Mutillidae)互为姐妹群。本研究的结果为后续肿腿蜂科分类和系统发育研究奠定了基础。     

玄参科植物叶绿体基因组特征及系统发育分析

目的 探究玄参科（Scrophulariaceae）叶绿体基因组（chloroplast DNA, cpDNA）的特征及其系统发育关系。 方法 对湖北玄参进行DNA测序;通过组装与注释获得了其叶绿体基因组序列;并从GenBank下载46条玄参科植物叶绿体基因组序列进行比较分析。 结果 玄参科叶绿体基因组长度在142 336-154 710 bp;GC含量为37.7%-38.1%;展现出典型的四分体结构;其中大单拷贝区长度为83 531-97 103 bp;小单拷贝区为17 375-18 600 bp;反向重复区为13 497-25 695 bp。通过对玄参科叶绿体基因组成的比较;揭示了在进化过程中获得与丢失的模式。此外;共线性分析发现;玄参科叶绿体基因组排列较为保守;但也存在基因组重排事件。长重复序列分析结果显示;玄参科叶绿体基因组大多数是正向重复和回文重复;而简单重复序列分析则鉴定了117-156个SSR位点;其中以A/T组成的单核苷酸重复次数最多;占比高达85.50%-91.50%。通过相对同义密码子使用度（RSCU）分析;筛选出25个最优密码子;绝大部分以A/U结尾。分化时间分析表明;玄参科的共同祖先与近缘物种大约在70.5百万年前（MYA）分开;并在约52.4 MYA形成了一个单系分支;绝大多数玄参科物种出现在近50 MYA。 结论 玄参科叶绿体基因组虽具有相似的结构特征;但在其进化历程中;基因的获得与丢失以及基因组的重排现象亦有所发生。基于叶绿体基因组;构建了更为精细的玄参科系统发育树。此外;分化时间的研究表明;玄参科物种的快速分化主要发生在大约50百万年前。     

Current approaches to whole genome phylogenetic analysis

It has long been known that evolutionary trees (phylogenies) can be estimated by comparing the DNA or protein sequences of homologous genes across different organisms. More recently, attempts have been made to estimate phylogenies by comparing entire genomes. These attempts have focused largely on comparisons of gene content and gene order. Many different methods have been proposed for making these comparisons. These include primarily maximum parsimony and distance methods, although more recently maximum likelihood and Bayesian methods are being developed. This paper discusses each of these approaches in turn, including their merits and limitations, and any software which is available to make use of them.     

毛茛科和芍药科叶绿体基因组密码子特征和系统发育比较

为研究和比较毛茛科和芍药科叶绿体基因组密码子使用模式和系统进化关系,以完成测序的毛茛科33种植物、芍药科7种植物叶绿体基因组为材料,采用分析软件CodonW在线软件CUSP和R软件对叶绿体基因进行密码子特征分析。用MAFFT软件,MEGA软件进行系统发育分析。研究结果表明芍药科植物叶绿体基因组和毛茛科植物（耧斗菜属除外）叶绿体基因组高频密码子一致性高,具有29个高频密码子,基本偏向与于A/U结尾,但最优密码子存在差异。毛茛科和芍药科叶绿体基因组密码子偏好性的形成因素主要受自然选择的影响,且芍药科叶绿体基因组密码子偏好性受自然选择的影响大于毛茛科。基于叶绿体基因组全序列和基于叶绿体基因组CDS序列的系统进化关系表明,芍药科基于叶绿体基因组全序列和基于叶绿体基因组CDS序列的系统进化关系虽然部分不同,但都可以被划分为芍药组和牡丹组。毛茛科基于叶绿体基因组的系统进化关系不符合中国植物志分类关系,但支持把毛茛科划分为4亚科14族。系统进化分析结果也支持芍药科独立于毛茛科和毛茛目,被划分到虎耳草目,同时证明了叶绿体基因组作为超级DNA条形码的可行性。