线粒体基因组:结构特点和基因含量进化

线粒体具有其自身的遗传系统——一个来自内共生的α-变形细菌祖先的基因组。线粒体基因组的生物学功能非常保守,仅涉及与线粒体有关的5个方面的过程:呼吸和氧化磷酸化、翻译、转录、RNA成熟和蛋白运输。真核生物线粒体基因含量的变化异常显著,在包括被子植物在内的各种真核生物相对频繁地发生线粒体基因丢失的同时,动物和某些植物类群的线粒体基因含量相对来说则比较稳定。tRNA基因含量的变化反映了线粒体对来自核的tRNA在使用上的差异,而蛋白基因含量的变化主要是由于功能性的基因转移到核所造成的。对线粒体基因组学领域中有关基因组起源、结构和基因含量进化方面的研究进行综述。     

后生动物起源时间的分子钟研究

后生动物是起源于“寒武纪大爆发”还是经历了一个相对较长的前寒武时期一直是动物进化史上的不同解之谜。综述近年来出现的很多利分子数据推测后生动物起源时间的分子钟研究,并就研究中存在的无脊椎动物与脊劝物之的进化速率的校正、进化速率恒定基因的判断等问题进行讨论。     

糙刺参（Stichopus horrens）线粒体基因组及一种新的基因排列顺序

线粒体基因组序列在后口动物进化研究中有着重要的作用.本研究使用PCR方法获得糙刺参（Stichopus horrens）线粒体全基因组序列.该序列全长16257bp,包含13个蛋白编码基因,22个tRNA基因和2个rRNA基因.除了一个蛋白编码基因（nad6）和5个tRNA基因（tRNASer（UCN）,tRNAGln,tRNAAla,tRNAVal,tRNAAsp）在轻链上编码外,其余的基因都在重链上编码.糙刺参线粒体重链碱基有30.8%A,23.7%C,16.2%G,和29.3%T构成.假定的线粒体控制区长675bp.基因间间隔碱基长1～50bp,共227bp.11个基因间有重叠碱基,长1～10bp,共25bp.13个蛋白编码基因起始密码子均为ATG,终止密码子大多为TAA（nad3和nad4的为TAG）.亮氨酸编码频率最高（16.29%）,随后是丝氨酸（10.34%）和苯丙氨酸（8.37%）.所有的22个tRNA基因均能折叠成三叶草结构.通过和其他4种海参的线粒体基因排列顺序比较,本研究发现糙刺参的线粒体基因排列顺序是一种新的排列方式.     

动物与植物线粒体基因组结构的差异—两种进化途径

从进化的角度分析和综合多细胞动物、高等植物、原生动物、藻类和真菌的线粒体基因组的大小和各自的结构特点,并根据作者提出的重复序更与基因结构的起源和进货的模式与途径,得出线粒体通过内共生起源,也是从原始的线粒体基因组向小基因组和大基因组两种方向发展,并有着两种与核基因组的可比较的进货途径的结论。这两种进化途径能很好地说明不同类型的真核生理的线本基因组的结构差异和特点。本文还提出了一个关于重复序列、断列     

动物线粒体DNA在进化遗传学研究中的应用

介绍了进化遗传学研究的主要内容、基本的研究方法以及线粒体的结构和遗传特点;综述了近年来线粒体DNA在进化遗传研究上的主要应用情况。     

四川鹿属动物的线粒体DNA差异和系统进化关系研究

用聚合酶链反应,从水鹿,坡鹿,梅花鹿和马鹿等四种鹿属动物中分别扩增出线粒体ＤＮＡＲ的细胞色素ｂ基因片段,并测定得到了３６７ｂｐ的碱基序列,它们之间的序列差异在４．０９％￣７．０８％之间。     

动物中microRNA 的保守性和进化历程

microRNA 是一类长度约为22 个核苷酸的内源性非编码单链RNA, 在后生动物中普遍存在, 在转录后过程调控基因表达. miRNA 在个体发育过程中发挥着各种功能, 如发育时序调控和细胞分化、神经发育等. miRNA 在各种后生动物中具有保守性, 而且多个关键类群的出现皆伴随着大量新miRNA 的产生, 这些现象都表明miRNA 与动物的系统发生密切相关. 本文从miRNA 的产生和作用机制、在后生动物中的分布格局及其在个体发育中的调控功能3 个方面论述了miRNA 的保守性, 并结合miRNA 的发生和发展历程, 探讨了miRNA 在动物进化中起到的重要作用.     

蓖麻蚕线粒体基因组细胞色素氧化酶亚基Ⅲ的序列及其分子进化分析

测定了蓖麻蚕Samia cynthia ricini线粒体基因组(mtDNA)含完整的细胞色素氧化酶亚基Ⅲ(COX3)、tRNA-Gly和部分的NADH亚基Ⅲ(ND3)基因的DNA片段序列。COX3基因编码框包含789个核苷酸,编码262个氨基酸的蛋白质。通过同源性比较,发现COX3基因的3′端比5′端要保守,其编码的蛋白在C端有两个保守序列存在。COX3的下游为66 bp的tRNA-Gly基因。蓖麻蚕的COX3与家蚕COX3同源性最高,核苷酸和氨基酸序列同源性分别是80.2%和85.6%。根据COX3氨基酸序列进行了12种无脊椎动物的分子进化树分析,认为在采用线粒体基因序列进行分子进化分析时,应该综合考虑物种的繁殖模式及生态特点。     

四种犬科（Canidae）动物线粒体DNA分子进化

以９种限制性内切酶分析家犬,狼,赤狐,貉共７只动物的一粒体ＤＮＡ限制性片段长度多态性（ｍｔＤＮＡＲＦＬＰ）,通过双酶解法构建各种动物的限制性内切酶图谱,用ＵＰＧ法,ＮＪ法和简略法分析这些动物之间的遗传关系。结果表明,１．犬的个体差异小,而赤弧的个体间遗传分化程度非常高;２．犬和狼的亲缘关系很近,应是同一种动物;３．在属间关系中,犬属与狐属的关系较接近,貉属是一个较早分化的独立分支。     

植物基因起源进化研究取得新进展

动物基因中有很多逆转座基因,但长期以来,由于在拟南芥菜中发现很少的逆转座基因,因而形成了一种认为逆转座在植物基因和基因组进化中并不重要的观念。     

脊椎动物线粒体DNA的基因重排

将GenBank上已公布的321种脊椎动物mtDNA全序列,按纲整理归类,绘制基因排布图并进行比对。比对结果表明：81个物种的mtDNA中观察到基因重排现象,涉及脊椎动物各纲,其中9个物种同时存在基因顺序变化和基因倒置现象,所有的基因重排都涉及tRNA的变化。脊椎动物mtDNA基因顺序变化可分为3类：1)邻接的基因或片段的位置交换;2)接近于控制序列或轻链起始位点的基因或片段的位置变化,有时还伴随着控制序列的倍增;3)I-Q-M区域的变化。所有鸟类、蛇类、鳄类和有袋类的mtDNA具有各自独特的基因排列顺序。基因倒置现象常见于鱼类和哺乳类,且多表现为tRNA从轻链往重链上迁移。本文就这些基因重排现象、发生重排的机制和mtDNA基因重排在系统发生研究中的应用做一简要概述。     

Covariation of Mitochondrial Genome Size with Gene Lengths: Evidence for Gene Length Reduction During Mitochondrial Evolution

Reduction of genome size and gene shortening have been observed in a number of parasitic and mutualistic intracellular symbionts. Reduction of coding capacity is also a unifying principle in the evolutionary history of mitochondria, but little is known about the evolution of gene length in mitochondria. The genes for cytochrome c oxidase subunits I–III, cytochrome b, and the large and small subunit rRNAs are, with very few exceptions, always found on the mitochondrial genome. These resident mitochondrial genes can therefore be used to test whether the reduction in gene lengths observed in a number of intracellular symbionts is also seen in mitochondria. Here we show that resident mitochondrial gene products are shorter than their corresponding counterparts in -proteobacteria and, furthermore, that the reduction of mitochondrial genome size is correlated with a reduction in the length of the corresponding resident gene products. We show that relative genomic AT content, which has been identified as a factor influencing gene lengths in other systems, cannot explain gene length/genome size covariance observed in mitochondria. Our data are therefore in agreement with the idea that gene length evolves as a consequence of selection for smaller genomes, either to avoid accumulation of deleterious mutations or triggered by selection for a replication advantage.     

Plant Mitochondrial Genome Evolution and Cytoplasmic Male Sterility

Mitochondria are responsible for providing energy currency to life processes in the molecular form of ATP and are therefore typically referred to as the power factories of cells. Plant mitochondria are also relevant to the common phenomenon of cytoplasmic male sterility, which is agronomically important in various crop species. Cytoplasmic male sterility (CMS) is a complex trait that may be influenced by patterns of mitochondrial genome evolution, and by intergenomic gene transfer among the organellar and nuclear compartments of plant cells. Here, we review patterns and processes that shape plant mitochondrial genomes, some relevant interactions between organelles, and the general features shared by the majority of cytoplasmic male-sterile genes in plants to further the goal of understanding CMS.     

Universal Genome in the Origin of Metazoa: Thoughts About Evolution

Recent advances in paleontology, genome analysis, genetics and embryology raise a number of questions about the origin of Animal Kingdom. These questions include: (1) seemingly simultaneous appearance of diverse Metazoan phyla in Cambrian period, (2) similarities of genomes among Metazoan phyla of diverse complexity, (3) seemingly excessive complexity of genomes of lower taxons, and (4) similar genetic switches of functionally similar but non-homologous developmental programs. Here I propose an experimentally testable hypothesis of Universal Genome that addresses these questions. According to this model, (a) the Universal Genome that encodes all major developmental programs essential for various phyla of Metazoa emerged in a unicellular or a primitive multicellular organism shortly before the Cambrian period; (b) The Metazoan phyla, all having similar genomes, are nonetheless so distinct because they utilize specific combinations of developmental programs. This model has two major predictions, first that a significant fraction of genetic information in lower taxons must be functionally useless but becomes useful in higher taxons, and second that one should be able to turn on in lower taxons some of the complex latent developmental programs, e.g. a program of eye development or antibody synthesis in sea urchin. An example of natural turning on of a complex latent program in a lower taxon is discussed.     

藏鸡线粒体全基因组序列的测定和分析

通过PCR扩增,测序,拼接,获得藏鸡（Tibetan Chicken）线粒体全基因组序列并进行数据分析处理。藏鸡线粒体全基因组序列全长16783bp,共有13个蛋白质编码基因、2个rRNA基因、22个tRNA基因和1个D-loop区。模拟电子酶切结果显示,藏鸡DraI酶的酶切结果和先前报道的原鸡,茶花鸡,尼西鸡和大理漾濞黄鸡的酶切结果都不相同,为藏鸡特有。基于D-loop区全序列和13个蛋白质编码基因序列,采用N-J算法与原鸡属4个种,3个亚种和3个家鸡品系构建系统进化树：初步确定藏鸡起源于红原鸡,与家鸡中的来航鸡、白洛克鸡亲缘关系最近,但是藏鸡的进化与来航鸡、白洛克鸡这两个家鸡品系又显得相对独立。推测可能原因是藏鸡的祖先在进入高原以后处于相对封闭的环境,从而形成了独特群体遗传特性。     

Meiofauna and the origins of the Metazoa*

Possible alternative habitats and life-styles of the original metazoan are considered. It is argued from the dominance of the benthic habitat in present-day groups that the original metazoan habitat was benthic rather than planktonic. Similarly, plesiomorphic metazoan taxa tend to be holobenthic rather than pelago-benthic. It is therefore probable that the early Metazoa were holobenthic. The concept of plesiohabitats and apohabitats in the evolution of taxa is presented. This leads to the proposition that the early metazoans were interstitial bionts of fine sand. Finally, the controversy concerning the aerobic or anaerobic origin of the Metazoa is considered. It is shown that competition theory predicts that plesiomorphic taxa are likely to remain in plesiohabitats. Diagrams showing the possible evolution of major taxa in relation to available habitats are presented. It is concluded that the earliest Metazoa could have evolved in anaerobic marine sand and that the early Plathelminthomorpha and Aschelminthes did so.     

基于线粒体基因片段核苷酸多态性的亚洲栽培稻起源进化研究

亚洲栽培稻的祖先是普通野生稻,已成为世界公认的观点,然而亚洲栽培稻的2个亚种:粳稻和籼稻是一次起源还是二次起源仍存在很大争议,其起源地是国内还是国外依然是国际学者间争论的焦点。本文通过对184份亚洲栽培稻和203份普通野生稻3段基因序列cox3、cox1、orf 224和2段基因间序列ssv-39/178、rps2-trnfM的多样性研究,验证了以下观点:1)粳稻起源于中国,籼稻起源于中国和国外;2)亚洲栽培稻的起源为二次起源,即普通野生稻存在偏籼和偏粳2种类型,亚洲栽培稻的2个亚种籼稻和粳稻在进化过程中分别由偏籼型的普通野生稻和偏粳型的普通野生稻进化而来。     

线粒体DNA聚合酶的起源研究

随着新的DNA聚合酶A家族成员的加入,家族内部的系统发育关系需要重新检查。分析显示：在真核生物演化的不同阶段,线粒体DNA聚合酶基因可能通过水平基因转移方式起源于不同类群的生物。原始真核生物线粒体DNA聚合酶基因可能来源于细菌,植物线粒体DNA聚合酶基因可能从质粒获得,而真菌和动物线粒体DNA聚合酶基因可能起源于T3/T7相关噬菌体。     

Organization of the Mitochondrial Genome of a Deep-Sea Fish, Gonostoma gracile (Teleostei: Stomiiformes): First Example of Transfer RNA Gene Rearrangements in Bony Fishes

We determined the complete nucleotide sequence of the mitochondrial genome (except for a portion of the putative control region) for a deep-sea fish, Gonostoma gracile. The entire mitochondrial genome was purified by gene amplification using long polymerase chain reaction (long PCR), and the products were subsequently used as templates for PCR with 30 sets of newly designed, fish-universal primers that amplify contiguous, overlapping segments of the entire genome. Direct sequencing of the PCR products showed that the genome contained the same 37 mitochondrial structural genes as found in other vertebrates (two ribosomal RNA, 22 transfer RNA, and 13 protein-coding genes), with the order of all rRNA and protein-coding genes, and 19 tRNA genes being identical to that in typical vertebrates. The gene order of the three tRNAs (tRNA^Glu, tRNA^Thr, and tRNA^Pro) relative to cytochrome b, however, differed from that determined in other vertebrates. Two steps of tandem duplication of gene regions, each followed by deletions of genes, can be invoked as mechanisms generating such rearrangements of tRNAs. This is the first example of tRNA gene rearrangements in a bony fish mitochondrial genome. Received August 5, 1998; accepted February 19, 1999.