Comment on "Transitions to asexuality result in excess amino acid substitutions"

Paland and Lynch (Reports, 17 February 2006, p. 990) showed that in Daphnia pulex, the ratio of amino acid replacement to silent substitution in mitochondrial genes is higher in asexual lineages than in sexual lineages. If this base-composition bias is maintained by selection, it too should alter following transitions in reproductive mode. Analysis reveals no such change in the genomes of D. pulex.     

对虾科物种线粒体基因组特征和系统发育分析

综合分析对虾科(Penaeidae)21个物种线粒体基因组的全序列,发现其线粒体基因组的长度为15 893～16 071 bp, A+T含量为64.59%～70.61%。K_a/K_s分析表明,对虾科物种线粒体13个蛋白质编码基因(protein-coding genes, PCGs)中,atp8基因的K_a/K_s最高,表明在对虾科中atp8基因受到了较弱的选择压力;在差异位点的分析中,发现nd5和rrnL基因的差异位点比例较高,是理想的分子标记,可用于分析对虾不同群体之间的遗传多样性;在密码子的使用中,被编码的氨基酸均体现相似的偏好性。同时,采用ML(Maximum likelihood)和BI(Bayesian inference)方法构建系统发育树,结果显示,这两种方法构建的系统发育树拓扑结构完全一致,且同属物种也都归为一类或者单独归为一支。本研究为快速鉴定对虾科生物提供了可靠的分子标记,为分析对虾科物种遗传多样性提供理论依据。     

恶疫霉生长速率与同宗配合性状的遗传与变异

在实验室条件下，对不同地区和不同寄主来源的恶疫霉菌株的线性生长速率和同宗配合性状的遗传进行了研究。结果指出：恶疫霉菌株同宗配合性状在无性和有性后代均可稳定遗传，表明在供试恶疫霉菌株中上述性状的控制因子是纯合的。从试菌株生长速率的遗传情况十分复杂，至少存在3种类型：1．在单孢无性后代和自交后代均可稳定遗传；2．在单游动孢子后代稳定遗传而在自交后代发变异；3．在无性后代和有性后代均发生变异。表明该性状可能由细胞核纯合基因、也可能由细胞核杂合基因、还可能由细胞质因子调控。     

温州光唇鱼线粒体基因组结构及系统发育分析

采用已公布的鱼类线粒体基因组全序列,设计8对引物扩增、测定并注释温州光唇鱼(Acrossocheilus wenchowensis)线粒体基因组(GenBank登录号:KC_495074)。序列全长16 591 bp,包括13个蛋白质基因、22个tRNA基因、2个rRNA基因和1个非编码区,各基因的位置及组成与已公布的鲤科鱼类一致;37个基因中,1个蛋白质编码基因(ND6)和8个tRNA基因(tRNAGln、tRNAAla、tRNAAsn、tRNACys、tRNATyr、tRNASer(UCN)、tRNAGlu和tRNAPro)由L链编码,其余的均由H链编码。A、T、G、C碱基组成分别为30.92%、24.86%、16.41%、27.81%;除tRNASer(AGN)外,其它21个tRNA的二级结构均具有典型的三叶草结构;13个蛋白编码基因中,除COⅠ起始密码子为GTG外,其余均以ATG为起始密码子,而COⅡ、ND4和Cytb基因的终止密码子为不完整的T,其它10个基因均具有完整的终止密码子。利用鲤科共17属18种线粒体基因组13个蛋白质基因的氨基酸序列,从线粒体基因组水平探讨了温州光唇鱼在鲤科鱼类中的系统进化地位,为光唇鱼属乃至鲤科鱼类的系统分类学研究提供基础资料。     

The genome of black cottonwood, Populus trichocarpa (Torr. & Gray)

We report the draft genome of the black cottonwood tree, Populus trichocarpa. Integration of shotgun sequence assembly with genetic mapping enabled chromosome-scale reconstruction of the genome. More than 45,000 putative protein-coding genes were identified. Analysis of the assembled genome revealed a whole-genome duplication event; about 8000 pairs of duplicated genes from that event survived in the Populus genome. A second, older duplication event is indistinguishably coincident with the divergence of the Populus and Arabidopsis lineages. Nucleotide substitution, tandem gene duplication, and gross chromosomal rearrangement appear to proceed substantially more slowly in Populus than in Arabidopsis. Populus has more protein-coding genes than Arabidopsis, ranging on average from 1.4 to 1.6 putative Populus homologs for each Arabidopsis gene. However, the relative frequency of protein domains in the two genomes is similar. Overrepresented exceptions in Populus include genes associated with lignocellulosic wall biosynthesis, meristem development, disease resistance, and metabolite transport.     

水稻线粒体基因组水平上的蛋白质编码基因克隆方法研究

为探索适用于水稻线粒体基因的克隆方法,以水稻线粒体基因ccmB、nad9为例,分别选用3种不同的方法进行克隆。在对水稻线粒体基因组蛋白质编码基因进行比对分析的基础上,探讨了各种克隆方法的优劣及适用范围。结果表明:常规方法适用于Ⅰ类水稻线粒体基因的克隆,RT-PCR法适用于Ⅱ类水稻线粒体基因的克隆,简易方法只适用于Ⅲ类水稻线粒体基因的克隆。     

基于ND4基因部分片段探讨中国4个家驴品种的母系构成

为了分析中国家驴的遗传多样性,对保种和开发利用这一固有遗传资源提供有益帮助,并对其母性起源提供一些基础资料,作者对我国4个家驴品种(德州、凉州、云南、蒙古)209个个体的mtDNAND4基因编码区409bp片段进行了扩增、单链构象多态(SSCP)检测与测序分析,共检测到5种单倍型8个多态位点,其单倍型多样度为0.4699,核苷酸多样度为0.00308,表明我国家驴的遗传多态性比较丰富。通过对各单倍型序列按照脊椎动物线粒体编码规则翻译成氨基酸序列进行比对发现,部分核苷酸变异引起了氨基酸的变异。构建的简化加权中值网络聚类图显示,4个家驴品种的样品来自两个母系源头,并且,4个中国家驴品种都是由这两个母性世系混杂而成的,即未发现由同一种世系构成的品种。这与以前基于D-loop区序列对于中国家驴的研究结果相似,即地理位置、世系构成以及母性起源之间没有明显的相互关系。     

钱塘江三角鲂线粒体基因组测序及其结构特征分析

为了研究钱塘江流域三角鲂(Megalobrama terminalis Richardson)线粒体基因组结构特征及鲌亚科鱼类的系统进化关系,通过PCR扩增、测序、软件拼接获得了钱塘江三角鲂线粒体基因组全序列,GenBank登录号为MN725725。结果表明,钱塘江三角鲂线粒体基因组序列全长为16 621 bp,碱基组成分别为A(31.23%)、G(16.17%)、C(27.87%)和T(24.73%);共有13个蛋白编码基因,22个tRNA基因,2个rRNA基因,NAD6、tRNA-Gln、tRNA-Ala、tRNA-Asn、tRNA-Cys、tRNA-Tyr、tRNA-Ser^(UCN)、tRNA-Glu和tRNA-Pro等基因编码在L链上,其余基因均在H链上编码。钱塘江三角鲂线粒体基因组全序列与蛋白编码基因的A+T含量分别为55.97%和55.86%,具有明显的AT偏好性。线粒体基因中存在2个散在重复序列,分别位于线粒体控制区中终止结合序列区的前端和控制区3'的末端。在22个tRNA基因中,除了tRNA-Ser^(AGY)外,均具有典型的三叶草二级结构。基于BLAST比较,钱塘江三角鲂与黑龙江流域的三角鲂一致性为99.76%,与珠江流域三角鲂一致性为99.87%。基于15种隶属于7属的鲌亚科鱼类线粒体基因组全序列构建的系统进化树,鲂属与鳊属亲缘关系比与鲌属的亲缘关系上较近,与属、半属和细鳊属亲缘关系上较远。     

藤仓赤霉菌色素形成能力的遗传研究

通过菌株的无件继代培养和有性杂交方法,对藤仓赤霉菌(串珠镰孢霉)形成色素的能力及其遗传稳定性进行研究.试验结果表明,串珠镰孢霉产生色素的能力在无性后代中稳定遗传;从色素形成量不同的菌株间杂交试验结果,首次提出由单主效基因控制色素前体产生,而表型色素产生量的多少受一定数量微效基因控制,且这些微效基凶与色素产生量以及色素形成的快慢有关.     

Reproductive polyphenism and its advantages in aphids: Switching between sexual and asexual reproduction

Reproductive polyphenism, which allows one genotype to produce sexual and asexual morphs, is an extreme case of phenotypic plasticity and is commonly observed in aphids. Aphids are typical species that switch these reproductive modes, and the pathway orientation is triggered by the environmental conditions(mainly photoperiod and temperature). The typical annual life of aphids includes a succession of parthenogenetic generations during the spring and summer and a single sexual generation in autumn. In this review, we describe how the environmental cues orientate the reproductive mode of aphids from photoperiodic perception to endocrine regulation, and how juvenile hormones may act on the target cells(oocytes) to initiate the gametogenesis and embryogenesis in sexual and asexual reproduction. We also discuss the paradox of sex, especially the advantages of sexual reproduction in aphids. With the recent development of genomic resources in aphids, many potential genes involved in the reproductive polyphenism will enter the public's awareness. In particular, we describe a novel RNAi method in aphids, which may provide a molecular technique for determining the developmental fate and multiple reproductive strategies.     

Effects of purifying and adaptive selection on regional variation in human mtDNA

A phylogenetic analysis of 1125 global human mitochondrial DNA (mtDNA) sequences permitted positioning of all nucleotide substitutions according to their order of occurrence. The relative frequency and amino acid conservation of internal branch replacement mutations was found to increase from tropical Africa to temperate Europe and arctic northeastern Siberia. Particularly highly conserved amino acid substitutions were found at the roots of multiple mtDNA lineages from higher latitudes. These same lineages correlate with increased propensity for energy deficiency diseases as well as longevity. Thus, specific mtDNA replacement mutations permitted our ancestors to adapt to more northern climates, and these same variants are influencing our health today.     

Functional divergence of former alleles in an ancient asexual invertebrate

Theory suggests it should be difficult for asexual organisms to adapt to a changing environment because genetic diversity can only arise from mutations accumulating within direct antecedents and not through sexual exchange. In an asexual microinvertebrate, the bdelloid rotifer, we have observed a mechanism by which such organisms could acquire the diversity needed for adaptation. Gene copies most likely representing former alleles have diverged in function so that the proteins they encode play complementary roles in survival of dry conditions. One protein prevents desiccation-sensitive enzymes from aggregating during drying, whereas its counterpart does not have this activity, but is able to associate with phospholipid bilayers and is potentially involved in maintenance of membrane integrity. The functional divergence of former alleles observed here suggests that adoption of asexual reproduction could itself be an evolutionary mechanism for the generation of diversity.     

云南地区扁穗雀麦繁殖对策研究

对云南野生种牧草扁穗雀麦的繁殖对策进行了初步研究,结果表明:有性繁殖和营养繁殖效果都很好,种子产量可以达到270.00 g/m2,且种子发芽率在无任何处理的情况下也能达到80%以上,总繁殖效力平均为34.24%。扁穗雀麦有性繁殖苗期生长缓慢,生长速率为0.361 cm/d,但分蘖以后生长速率加大,抽穗开花期达最大;扁穗雀麦营养繁殖成活率较高,为89.7%,生长速度比有性繁殖快,并且随植株长大,生长速率呈下降趋势;种子产量随地上生物量的增加而增加。     

Rarity of males in pea aphids results in mutational decay

When females can reproduce without males, do males become an evolutionarily weaker sex whose genes experience mutational decay? We addressed this hypothesis in aphids, whose reproduction alternates between parthenogenetic and sexual forms: Over the course of a year, there can be 10 to 20 generations of asexual females but only a single, if any, generation with males. We used microarray analyses to identify male-biased, asexual female-biased, and neutral genes. Interspecific comparisons reveal accelerated evolution of male-biased genes, and intraspecific polymorphisms exhibit a significant excess of nonsynonymous coding variation in male-biased genes. We conclude that the ability of females to reproduce asexually without males reduces selection constraints on male-based genes, resulting in their mutational decay.     

The Xist RNA gene evolved in eutherians by pseudogenization of a protein-coding gene

The Xist noncoding RNA is the key initiator of the process of X chromosome inactivation in eutherian mammals, but its precise function and origin remain unknown. Although Xist is well conserved among eutherians, until now, no homolog has been identified in other mammals. We show here that Xist evolved, at least partly, from a protein-coding gene and that the loss of protein-coding function of the proto-Xist coincides with the four flanking protein genes becoming pseudogenes. This event occurred after the divergence between eutherians and marsupials, which suggests that mechanisms of dosage compensation have evolved independently in both lineages.     

青花菜线粒体基因组组装与序列特征分析

为更好地从分子水平了解青花菜,对青花菜进行线粒体基因组组装,并对其序列特征进行分析。青花菜线粒体基因组大小为219 964 bp,GC含量为45.25%。线粒体基因组注释到61个基因,包括33个编码蛋白基因,23个tRNA基因,3个rRNA基因和2个假基因。其中8个基因的核苷酸多样性较高;24个基因无核酸多样性。变异数量最多的基因是 rrn26、 rrn18和 atp1,其变异数量分别为326、277和136。密码子偏好性分析结果显示RSCU值>1的密码子有29个,大多以A/U碱基结尾,表明其密码子更偏向于A/U结尾。基因组序列中共检测到345个重复序列,包括170个正向重复序列和175个回文重复序列。青花菜与花椰菜的线粒体基因组具有极好的共线性,且基因的位置基本一致。青花菜线粒体和叶绿体基因组中共检测到22条同源片段。同源片段总长度为13 355 bp,平均607 bp。     

四川稻瘟病菌遗传宗谱的地理分布及与寄主品种的相关性研究

本研究应用rep-PCR分子指纹技术,对2000~2002年采自四川6个自然生态稻作区的137个稻瘟病菌菌株进行了DNA指纹谱型分析。以0.19遗传相似水平将供试菌株划分成37个遗传宗谱,层次较为丰富。结果表明,各稻作区稻瘟病菌遗传宗谱丰富,它们既有相同的遗传宗谱(即宗谱SCL36、37),又具有自己的特异性宗谱。在杂交稻和常规稻上检测出8个共同稻瘟病菌遗传宗谱,表明它们之间具有一定的亲缘关系;不同的宗谱在杂交稻与常规稻上的分布存在差异,有着自己的优势寄主。     

紫貂线粒体基因组全序列结构及其进化

利用PCR方法和直接测序技术获得的紫貂线粒体基因组全长为16523bp,包含13个蛋白质编码基因、2个rRNA基因、22个tRNA基因和1个非编码基因控制区(D-Loop区),碱基组成为A32.0%、C27.6%、G14.7%、T25.8%;在编码蛋白质基因的密码子第3位点处具有AC高偏向性(72.6%),并且频繁利用不完全终止密码子T或TA(7个)。将紫貂线粒体基因组序列提交到GenBank,并获得检索号为FJ429093。结合GenBank中已公布的鼬科其他6种动物的线粒体基因组全序列及貂属6种D-Loop区部分序列,分别以虎和狗獾为外类群,应用最大简约法构建鼬科和貂属物种的系统进化树。结果表明:鼬科7个物种分成3大支系,分别为水獭亚科和臭鼬亚科群、日本貂和貂熊群以及紫貂和狗獾群,说明鼬科并非是一个单系群,紫貂与鼬科中的獾亚科亲缘关系较近,而与貂属中的美洲貂和石貂亲缘关系最近。     

青藏高原高寒草地退化与人工恢复过程中植物群落的繁殖适应对策

以三江源区不同退化程度高寒草甸和不同恢复年限人工草地作为研究对象,通过野外调查与采样、实验室分析,探究了高寒地区退化天然草地与人工恢复草地的植被群落繁殖构件数量变化。结果表明：在群落水平上,天然草地退化和人工草地建植会对植物繁殖构件的数量和生物量产生影响。随着天然草地退化程度的增加,营养枝数量和生物量则明显下降,而繁殖枝的数量和生物量明显升高（P<0.05）;随着人工草地恢复年限的增加,营养枝的数量和生物量逐渐增加,而繁殖枝的数量和生物量则逐渐降低（P<0.05）;随着恢复年限的增加,人工草地繁殖构件的变化逐渐接近未退化天然草地。在功能群水平上,植物繁殖构件数量亦随草地退化程度和人工恢复年限而变化。随着恢复年限的增加,禾本科、莎草科、杂类草的营养枝数量和生物量均呈现显著增加（P<0.05）,而繁殖枝数量和生物量则显著下降,禾本科的繁殖构件数量远远大于莎草科和杂类草;随着退化程度的增加,三大功能群的营养枝枝数和生物量显著增加（P<0.05）,而繁殖枝则呈现相反的趋势。本研究实证了草地退化和人工恢复改变植物群落繁殖分配对策的科学假设,为高寒草地植被恢复重建技术的发展和更新提供理论支撑。     

Temporal fragmentation of speciation in bacteria

Because bacterial recombination involves the occasional transfer of small DNA fragments between strains, different sets of niche-specific genes may be maintained in populations that freely recombine at other loci. Therefore, genetic isolation may be established at different times for different chromosomal regions during speciation as recombination at niche-specific genes is curtailed. To test this model, we separated sequence divergence into rate and time components, revealing that different regions of the Escherichia coli and Salmonella enterica chromosomes diverged over a approximately 70-million-year period. Genetic isolation first occurred at regions carrying species-specific genes, indicating that physiological distinctiveness between the nascent Escherichia and Salmonella lineages was maintained for tens of millions of years before the complete genetic isolation of their chromosomes.