原核生物基因组三核苷酸转移概率偏倚的物种特异性及致病关联性

作为DNA序列的重要组成特征,基因组寡核苷酸使用模式及其偏倚的研究已被广泛应用于原核生物基因组的分析。然而,关于寡核苷酸使用模式的偏倚是否具有种群特异性并反映种群的功能这一问题,尚未阐明。我们基于一阶马尔可夫链模型,提出了一个度量寡核苷酸使用模式偏倚的新指标——基因组三核苷酸(trinucleotide,tri-)转移概率偏倚(transition probability bias,TPB)特征向量,或称之为三核苷酸转移概率最大偏倚分布,并分析比较了727条有代表性的原核生物基因组序列tri-TPB特征向量。结果表明,基因组tri-TPB特征向量具有物种特异性,亲缘关系越近的物种,它们的tri-TPB特征向量越相似;同种内的不同菌株具有几乎完全相同的tri-TPB特征向量,并且不依赖于基因组的GC含量;此外,基因组tri-TPB特征向量的相似性与菌株的致病性特征相关。本研究结果为基于全基因组寡核苷酸组成和分布信息的物种及其致病性进化分析提供了新的思路和方法。     

基于k-mer组分信息的系统发生树构建方法

随着越来越多基因组的测序完成,基于全基因组的非比对的系统发生分析已成为研究热点。不同的生物物种或个体基因组之间的核酸组分不完全相同。遗传语言-DNA序列的信息很大程度上反映在其k—mer频数中。基于基因组序列k-mer频数的系统发生树则从新的角度为我们提供物种之间的亲缘关系。本文定义基于k-mer,频数的信息参数,并用它表征基因组序列,计算不同基因组之间信息参数的距离,用邻接法对84个病毒构建了系统发生树,发现构建的系统发生树很大程度上与已有的系统发生树相吻合。     

基于全基因组的微生物亲缘关系与分类系统研究工具——CVTree

组分矢量构树(CVTree)方法是基于全基因组的、不用序列联配的物种亲缘关系研究方法。CVTree3是我们最新开发的CVTree网络服务器,它基于并行化的核心程序,以适应当前基因组数据的海量增加;它自动对比物种亲缘关系与分类系统,并在网页上以交互作用形式显示,从而使研究更加直观。使用CVTree3网络服务器,用户可以快速的对未知的全基因组序列进行亲缘关系分析,并对其分类地位进行初步鉴定。由于合理利用全基因组信息,CVTree方法能对种以下的亲缘关系与分类具有高分辨力。随着CVTree方法的深入与完善,希望其能成为阐明原核生物亲缘关系与分类系统的定义性的工具。     

细菌基因组重复序列PCR技术及其应用

细菌中散在分布的DNA重复序列近年来不断被报道,基因外重复回文序列和肠细菌基因间共有重复序列是两个典型的原核细胞基因组散在重复序列。重复序列在染色体上的分布和拷贝数具种间特异性,用它们的互补序列作为引物,以细菌基因组DNA为模板进行PCR扩增反应,反应产物的琼脂糖电泳可以提供非常清晰的DNA指纹图谱,使用此图谱既可对各种微生物进行快速分型及鉴定,又可对它们进行DNA水平上的遗传多样性分析。细菌基因组重复序列PCR技术具有简捷、快速、结果稳定等特点,可对细菌进行分子标记,用于菌株分型、分类鉴定和亲缘关系等方面的研究。     

致胰腺泛黄鸭1型甲肝病毒全基因组分子特征

【目的】揭示致胰腺泛黄鸭1型甲肝病毒(duck hepatitis A virus 1,DHAV-1)全基因组的分子特征。【方法】运用RT-PCR技术,扩增出致胰腺泛黄DHAV-1 MPZJ1206株全基因组序列,并与鸭甲肝病毒参考毒株基因组序列进行比对分析。【结果】致胰腺泛黄DHAV-1 MPZJ1206株基因组全长为7703 nt,(G+C)%为43.05%,包含一个大的开放阅读框,编码2249个氨基酸残基的多聚蛋白,基因组结构与其他DHAV-1参考毒株一致。序列比对结果显示,MPZJ1206株全基因组序列与GenBank数据库中DHAV-1参考毒株核苷酸序列同源性在93.5%-99.6%之间,氨基酸同源性在97.9%-99.6%之间,遗传距离均低于7%;分子系统进化分析显示与2011年分离的2株DHAV-1(Du/CH/LGD/111238和Du/CH/LGD/111239)亲缘关系最近。【结论】尽管MPZJ1206毒株感染雏番鸭引起的临床病变与传统DHAV-1差异明显,但其基因组分子特征与传统的DHAV-1毒株相似,病毒致病型的改变可能与其组织嗜性改变相关。     

丝兰属6种植物叶绿体基因组特征分析

为了理清丝兰属（Yucca）叶绿体基因组特征和序列变异情况,进行丝兰属植物叶绿体比较基因组学分析,并构建基于叶绿体基因组的系统发育树。利用高通量测序技术获得无刺龙舌兰（Y. treculeana）叶绿体基因组序列,结合丝兰属现已发表的叶绿体基因组,使用生物信息学方法对6种丝兰属植物叶绿体全基因组进行基本结构、重复序列、边界收缩与扩张以及序列变异分析等在内的比较基因组学研究,并进行系统发育分析。结果表明：6种丝兰属植物叶绿体基因组大小、基因的类型及数目相近,种间基因组结构比较保守;从丝兰属植物叶绿体基因组中检测到多条重复序列,其中SSR位点多是由单核苷酸、双核苷酸和四核苷酸组成,且偏好使用A、T碱基;根据核酸多态性指数π≥0.008,在6种丝兰属植物叶绿体基因组中筛选出了psbK-psbl-trnS-GCU、rpl20-rps12和ccsA-ndhD 3个高变异区域;基于叶绿体全基因组和LSC+SSC区序列构建的系统发育关系基本一致,确定了6种丝兰属植物间的系统发育关系,其中无刺龙舌兰与克雷塔罗丝兰（Y. queretaroensis）的亲缘关系最近。本研究测序获得了无刺龙舌兰叶绿体基因组,揭示了6种丝兰属植物叶绿体基因组特征和序列变异情况,明确了各物种间的亲缘关系,研究结果可为后续丝兰属植物分子标记开发及系统发育研究提供参考。     

鸭圆环病毒全基因组克隆与序列分析

为研究鸭圆环病毒全基因组的分子生物学特性,运用重叠PCR技术从鸭组织脏器提取的DNA中扩增出2条核苷酸序列,拼接后对其核酸组成、基因组结构及病毒的遗传变异进行分析.结果表明所获病毒核酸为大小1 995nt的环型DNA,包含6个ORF,与登录在GenBank中克隆株MuDCV(AY228555)的同源性高达97.4%,可见所扩增的核酸序列为鸭圆环病毒基因组序列.     

绿豆Ty1／Copia类反转录转座子逆转录酶序列的克隆和分析

利用Ty1/copia类反转录转座子的保守位点设计简并引物,从绿豆(Vignaradiata(L.)Wilczek)基因组中扩增得到了反转录转座子的逆转录酶序列。对扩增得到的约270bp的片段进行分离和克隆,并随机挑选了40个克隆进行测序,结果得到了36个单独的核酸序列,其中18个含有移码突变或终止子。根据序列比对,这些克隆可分为9组以及单个的9种。这40个克隆中,核酸序列相似性从8%到100%,显示出其核酸序列的高度异质性。将这些克隆的核酸序列与来自其他种植物的相应序列进行谱系分析,发现有些克隆与来自其他种植物的相应序列的亲缘关系比这些克隆之间更为接近。斑点杂交显示Ty1/copia反转录转座子约占绿豆基因组的9.3%。     

中华鳖线粒体基因组序列分析

参照近源物种线粒体基因组序列,设计17对特异引物,采用PCR产物直接测序法测得中华鳖线粒体基因组全序列.初步分析其基因组特点和各基因的定位,用pDRAW32软件预测12种限制性酶对其的酶切图谱.结果表明,中华鳖线粒体基因组全长17364bp,核苷酸组成为35.23%A、27.26%T、25.73%C、11.78%G,包括13个蛋白质编码基因、2个rRNA基因、22个tRNA基因和1个非编码控制区.基于线粒体基因组编码的13个蛋白质的氨基酸序列,用NJ法和MP法构建系统进化树,分析6种龟鳖类动物之间的亲缘关系,与传统的系统分类基本一致,初步确定淡水龟科与海龟科的亲缘关系比与龟科的亲缘关系要近.     

绿豆Ty1/Copia类反转录转座子逆转录酶序列的克隆和分析

利用Ty1/copia类反转录转座子的保守位点设计简并引物,从绿豆(Vigna radiata(L.)Wilczek)基因组中扩增得到了反转录转座子的逆转录酶序列.对扩增得到的约270bp的片段进行分离和克隆,并随机挑选了40个克隆进行测序,结果得到了36个单独的核酸序列,其中18个含有移码突变或终止子.根据序列比对,这些克隆可分为9组以及单个的9种.这40个克隆中,核酸序列相似性从8%到100%,显示出其核酸序列的高度异质性.将这些克隆的核酸序列与来自其他种植物的相应序列进行谱系分析,发现有些克隆与来自其他种植物的相应序列的亲缘关系比这些克隆之间更为接近.斑点杂交显示Ty1/copia反转录转座子约占绿豆基因组的9.3%.     

An analysis of trypanosomatids kDNA minicircle by absolute dinucleotide frequency

Trypanosomatid mitochondrial DNA (kDNA) possesses thousands of copies of small circular molecules called minicircles. Due to a high level of nucleotide polymorphism among copies, sequence alignment for species or strain characterization is not appropriate. In this work we report dinucleotide absolute frequency as a method to analyze minicircle sequences heterogeneity in trypanosomatids. Using Trypanosoma rangeli and Leishmania guyanensis minicircles as example of sequence length heterogeneity, we show that dinucleotide frequency of minicircles whose length variation is less than to 10% is relatively constant. Dinucleotide frequencies in Leishmania genus point out three clusters of predominant dinucleotide profiles: GG/TT/TG for Old World species; ii) TT/AA/TA for New World species and iii) TT/GG(AA) TA(AT) for Sauroleishmania. Trypanosoma species displayed broad range composition and the highest frequency values. Their dinucleotide profile appears to be species specific, except for African trypanosomes which exhibit similar composition. The low number of sequences from Crithidia, Herpetomonas, Phytomonas and Wallaceina did not allow a generalized analysis, however some species present highly similar compositional profile, e.g., Wallaceina species. Distinct signatures for Trypanosomatidae family members can be generated by using values of absolute frequencies, range and composition of most/least frequent dinucleotides from minicircles. Each species can be graphically represented by a diagram of frequencies along with a box plot of summary statistics.     

完达山东部欧亚水獭种群数量及出现频次影响因素

水獭作为淡水生态系统健康的指示种和旗舰物种,在维持水生生态系统平衡与稳定中发挥着重要作用。然而目前对于完达山东部地区水獭种群数量、分布及其生境选择的影响因素的研究较为匮乏,严重影响了对该物种的野外保护与管理工作。于2021年12月至2022年4月冬季河流封冻期,采用沿河随机样线调查和红外相机监测相结合的方法对完达山东部地区8条主河和23条支流内的欧亚水獭(Lutra lutra)种群数量、分布现状进行了调查,并利用广义可加模型探究水獭出现频次与环境因子的关系。研究结果表明:(1)欧亚水獭在完达山东部水獭种群数量为571-661只,水獭种群密度为沿河(0.5559±0.2898)只/km,呈现中间高,四周低的趋势;(2)环境因子对水獭出现频次影响分析表明,河流深度、距农田距离、距居民区距离和距道路距离是影响水獭出现频次的关键因素。水獭出现频次与河流深度(0-40 cm)呈线性正相关,当河流深度达到40-50 cm时,水獭出现频次最高,之后随着河流深度的增加,出现频次降低;水獭出现频次与距农田距离(0-1.5 km)呈非线性正相关,在距农田距离为1.5-2 km范围内,水獭出现频次最高,之后降低;水獭出现频次与距居民区距离呈线性正相关;水獭出现频次与距道路距离呈非线性关系,当距离>7 km时,二者之间呈现为正相关,反之呈现为负相关。因此,水獭选择栖息地偏向于河流深(40-50 cm),远离农田(1.5-2 km)、居民区和道路(>7 km)的水域。研究为完达山东部欧亚水獭物种保护提供了基础数据和理论依据,建议通过河岸土地覆盖类型的管理、在河岸周围建立森林缓冲区及加强水獭保护宣传力度等措施实现对水獭物种及其栖息地的维持和保护。     

Autogenic-allogenic status affects interpond community similarity and species area relationship of macroparasites in the bluegill sunfish, Lepomis macrochirus, from a series of freshwater ponds in the Piedmont area of North Carolina

The effects of autogenic-allogenic status on the species-area relationship and the relationship between geographic distance and intercommunity dissimilarity were investigated in macroparasite communities of the bluegill sunfish Lepomis macrochirus. Rank correlation analyses were used to examine the relationship between pond surface area and species richness of all species collectively and of autogenic species and allogenic species separately. A positive relationship was found for allogenic species, whereas there was no association for all species, nor was there an association when the study was restricted to autogenic species. Mantel tests were used to determine the relationship between geographic distance and community dissimilarity for all species and for autogenic and allogenic species independently. Total community dissimilarity and allogenic dissimilarity were found to be influenced by geographic distance, whereas autogenic dissimilarity was random with regard to interpond distances. These findings serve to illustrate the importance of the autogenic-allogenic dichotomy and demonstrate that dispersal ability can influence commonly observed ecological patterns.     

Pervasive properties of the genomic signature

Background  

The dinucleotide relative abundance profile can be regarded as a genomic signature because, despite diversity between species, it varies little between 50 kilobase or longer windows on a given genome. Both the causes and the functional significance of this phenomenon could be illuminated by determining if it persists on smaller scales. The profile is computed from the base step "odds ratios" that compare dinucleotide frequencies to those expected under the assumption of stochastic equilibrium (thorough shuffling). Analysis is carried out on 22 sequences, representing 19 species and comprised of about 53 million bases all together, to assess stability of the signature in windows ranging in size from 50 kilobases down to 125 bases.     

Premature chromosme condensation in the bone marrow of Chinese hamster after application of bleomycin in vivo.

The Chinese hamster bone marrow was used as a test system in vivo to analyse the chromosome-danaging effect of bleomycin. Both chromosome and chromatid aberrations were found. Mitoses with aberrations (Ma) show a linear dose-effect relationship after a recovery time of 24 h, the same hold true for cells with micronuclei (Cm) and for mitoses with premature chromosome condensation (PCC). The dose-effect relationships for Ma, Cm and PCC run parallel to each other with Ma at the highest and PCC at the lowest level (Ma greater than Cm greater than PCC). The time-effect relationships for Ma, Cm and PCC show that after 12 h recovery time there are no PCCs but the highest frequencies of Ma and Cm indicating that most cells are in their first post-treatment mitoses or Gi-phases at this fixation time. In addition to the frequency determinations autoradiographic analysis were performed to clarigy the nature of the PCCs. The results are interpreted as follows: bleomycin induces chromosomal aberrations that in turn give rise to micronuclei by means of lagging chromatin, main and micronuclei eventually become asynchronous in their cell cycles and mitosing main nuclei induce PCC in the micronuclei.     

Local similarity analysis reveals unique associations among marine bacterioplankton species and environmental factors

MOTIVATION: Characterizing the diversity of microbial communities and understanding the environmental factors that influence community diversity are central tenets of microbial ecology. The development and application of cultivation independent molecular tools has allowed for rapid surveying of microbial community composition at unprecedented resolutions and frequencies. There is a growing need to discern robust patterns and relationships within these datasets which provide insight into microbial ecology. Pearson correlation coefficient (PCC) analysis is commonly used for identifying the linear relationship between two species, or species and environmental factors. However, this approach may not be able to capture more complex interactions which occur in situ; thus, alternative analyses were explored. RESULTS: In this paper we introduced local similarity analysis (LSA), which is a technique that can identify more complex dependence associations among species as well as associations between species and environmental factors without requiring significant data reduction. To illustrate its capability of identifying relationships that may not otherwise be identified by PCC, we first applied LSA to simulated data. We then applied LSA to a marine microbial observatory dataset and identified unique, significant associations that were not detected by PCC analysis. LSA results, combined with results from PCC analysis were used to construct a theoretical ecological network which allows for easy visualization of the most significant associations. Biological implications of the significant associations detected by LSA were discussed. We also identified additional applications where LSA would be beneficial. AVAILABILITY: The algorithms are implemented in Splus/R and they are available upon request from the corresponding author.     

phrA, the major photoreactivating factor in the cyanobacterium Synechocystis sp. strain PCC 6803 codes for a cyclobutane-pyrimidine-dimer-specific DNA photolyase

A new broad-host-range plasmid, pSL1211, was constructed for the over-expression of genes in Synechocystis sp. strain PCC 6803. The plasmid was derived from RSF1010 and an Escherichia coli over-expression plasmid, pTrcHisC. Over-expressed protein is made with a removable N-terminal histidine tag. The plasmid was used to over-express the phrA gene and purify the gene product from Synechocystis sp. strain PCC 6803. PhrA is the major ultraviolet-light-resistant factor in the cyanobacterium. The purified PhrA protein exhibited an optical absorption spectrum similar to that of the cyclobutane pyrimidine dimer (CPD) DNA photolyase from Synechocuccus sp. strain PCC 6301 (Anacystis nidulans). Mass spectrometry analysis of PhrA indicated that the protein contains 8-hydroxy-5-deazariboflavin and flavin adenine dinucleotide (FADH2) as cofactors. PhrA repairs only cyclobutane pyrimidine dimer but not pyrimidine (6-4) pyrimidinone photoproducts. On the basis of these results, the PhrA protein is classified as a class I, HDF-type, CPD DNA photolyase.     

Genetic structure in the species-pair Silene vulgaris and S. uniflora (Caryophyllaceae) on the Baltic island of Öland

Allozyme data were used to assess the genetic structure between 37 sympatric populations of the species-pair Stlene vulgaris and S uniflora ssp petraea, and to infer levels of intra- and interspecific gene flow in the two species Silene vulgaris is a geographically widespread weed of disturbed habitats whereas S uniflora ssp petraea is endemic to the Baltic islands of Oland and Gotland On Oland, Silene vulgaris forms extensive linear populations along roads while S uniflora ssp petraea occurs in sparse and spatially-separated populations in open limestone habitats Despite the differences in population size and structure between the two species, both species show extremely low levels of between-population differentiation Between-site differences account for <2% of the total allozyme diversity within Oland in S vulgaris, and < 1% in S uniflora ssp petraea Indirect estimates of gene flow are high for both species (Nm = 11 and 27, respectively) There is no relationship between genetic distance and geographic distance within either species, and the lack of genetic structure is consistent with the pollination biology of the species - both of which are predominantly moth-pollinated The two species hybridize in intermediate habitats, and the geographic distribution of species-characteristic alleles indicates a potential for spatially extensive interspecific gene flow Nevertheless, there are significant differences in allele frequencies between the two species and multivariate analyses show no overlap between populations of the two species The species are ecologically separated by their different habitat preferences and by differences in their flowering phenology There is no evidence that the endemic S uniflora ssp petraea is threatened by genetic contamination or assimilation by the widespread weed, S vulgaris     

Insular black files (Diptera: Simuliidae) of North America: tests of colonization hypotheses

Aim To understand factors that facilitate insular colonization by black flies, we tested six hypotheses related to life‐history traits, phylogeny, symbiotes, island area, and distance from source areas. Location Four northern islands, all within 150 km of the North American mainland, were included in the study: Isle Royale, Magdalen Islands, Prince Edward Island, and Queen Charlotte Islands. Methods Immature black flies and their symbiotes were surveyed in streams on the Magdalen Islands, and the results combined with data from similar surveys on Isle Royale, Prince Edward Island, and the Queen Charlotte Islands. Black flies were analysed chromosomally to ensure that all sibling species were revealed. Tests of independence were used to examine the frequency of life‐history traits and generic representation of black flies on islands vs. source areas. Results A total of 13–20 species was found on each of the islands, but no species was unique to any of the islands. The simuliid faunas of the islands reflected the composition of their source areas in aspects of voltinism (univoltine vs. multivoltine), blood feeding (ornithophily vs. mammalophily), and phylogeny (genus Simulium vs. other genera). Five symbiotic species were found on the most distant island group, the Magdalen Islands, supporting the hypothesis that obligate symbiotes are effectively transported to near‐mainland islands. An inverse relationship existed between the number of species per island and distance from the source. The Queen Charlotte Islands did not conform to the species–area relationship. Main conclusions The lack of precinctive insular species and an absence of life‐history and phylogenetic characteristics related to the presence of black flies on these islands argue for gene flow and dispersal capabilities of black flies over open waters, possibly aided by winds. However, the high frequency of precinctive species on islands 500 km or more from the nearest mainland indicates that at some distance beyond 100 km, open water provides a significant barrier to colonization and gene exchange. An inverse relationship between number of species and distance from the source suggests that as long as suitable habitat is present, distance plays an important role in colonization. Failure of the Queen Charlotte Islands to conform to an area–richness trend suggests that not all resident species have been found.     

The evolution of nonhuman primate loud calls: Acoustic adaptation for long-distance transmission

Many nonhuman primates produce species-typical loud calls used to communicate between and within groups over long distances. Given their observed spacing functions, primate loud calls are likely to show acoustic adaptations to increase their propagation over distance. Here we evaluate the hypothesis that primates emit loud calls at relatively low sound frequencies to minimize their attenuation. We tested this hypothesis within and between species. First, we compared the frequencies of loud calls produced by each species with those of other calls from their vocal repertoires. Second, we investigated the relationship between loud call frequency and home range size across a sample of primate species. Comparisons indicated that primates produce loud calls at lower frequencies than other calls within their vocal repertoires. In addition, a significant negative relationship exists between loud call frequency and home range size among species. The relationship between call frequency and range size holds after controlling for the potentially confounding effects of body size and phylogeny. These results are consistent with the hypothesis that nonhuman primates produce loud calls at relatively low frequencies to facilitate their transmission over long distances.