植物叶绿体DNA与线粒体DNA的遗传变异

植物叶绿体和线粒体含有DNA,它们表现出不同的遗传变异特性。叶绿体基因组的保守性强,含有特征性重复顺序,它的遗传形式多样而以母系遗传为主,在组织培养和体细胞杂交中具有稳定性强,单亲遗传的特点。线粒体基因组变异性很强,含有主基因组和随体DNA,它的遗传形式是母系遗传,但在体细胞杂交中有时表现为双亲本遗传,并有mtDNA重组,mtDNA在组织培养中发生极大的变异性。在细胞核和线粒体、叶绿体之间存在DNA互相运动的现象。     

植物叶绿体与线粒体基因组DNA特异性比较研究

研究不同植物间叶绿体和线粒体基因组DNA的差异,探讨其在法庭科学中的应用价值.根据叶绿体和线粒体基因组DNA核苷酸序列的特点,分别设计了一系列相应的引物,经PCR扩增后,电泳鉴别不同的植物.结果表明在设计的一系列引物中,叶绿体基因组DNA的PCR产物差异不大,鉴别效果不明显;而线粒体基因DNA的PCR产物差异大,鉴别效果明显.因此以线粒体DNA为模板进行PCR扩增,在不同植物间存在良好的差异性,适合于不同植物间的鉴别,在法庭科学中具有实际应用价值.     

适于基因组测序的高纯度的大豆线粒体基因组DNA提取方法

为满足高通量二代测序要求,本研究采用大豆黄花苗为试材,结合差速离心、蔗糖密度梯度离心及超速离心方法提取高纯度大豆线粒体基因组DNA(mt DNA)。结果表明,差速离心能够有效去除核基因组掺杂;超速离心与蔗糖密度梯度离心结合能够有效去除叶绿体污染。提取的mt DNA经琼脂糖凝胶电泳、紫外光度计检测及叶绿体和细胞核特异性引物检测表明,该方法提取的大豆mt DNA无叶绿体DNA及核DNA污染,且纯度高,可满足测序等对线粒体高纯度的要求,为研究大豆线粒体相关性状的机理奠定了坚实基础。     

Shotgun法测序制备高纯度水稻基因组DNA的方法探讨(英)

在用散弹 (shotgun)法测定水稻 (OryzasativaL .ssp .indica)基因组全序列的过程中 ,叶绿体和线粒体DNA的污染问题非常严峻 .应用脉冲场电泳 (PFGE)技术对水稻基因组DNA进行纯化 ,结果表明它能够有效去除叶绿体和线粒体DNA ,使其污染率从 3%降低到 0 2 % .同时 ,比较了水稻绿苗和黄化苗的DNA得率 ,以及HB法和NIB法制备大分子质量(HMW)DNA的异同 .最后提出一套制备水稻基因组DNA的方法 ,包括黄化苗培养 ;细胞核的分离、包埋和裂解 ;脉冲场电泳纯化、回收聚集在低熔点 (LMP)胶中的水稻HMWDNA .用该方法所得的水稻基因组DNA ,纯度高 (无叶绿体和线粒体DNA污染 )、基因组完整 (机械剪切和降解少 )、回收率高 (操作过程中DNA损失少 ) .另外 ,首次报道在融化的低熔点(LMP)胶中对水稻HMWDNA于 38℃进行超声波处理 ,能够获得用于shotgun文库和梯度文库构建所需要的各种DNA片段(1 5～ 3kb ,3～ 12kb) ,并且效果优于在TE中进行操作     

在玉米线粒体基因组内的叶绿体DNA序列

目前,研究家们发现除了在核基因中具有叶绿体DNA片段外,在许多种高等植物的线粒体基因组中也具有叶绿体DNA序列。采用限制性内切酶进行研究发现,在玉米线粒体基因组内至少存在三个重要的叶绿体DNA序列:(i)1,5-二磷酸核酮糖羧化酶的大亚     

叶绿体的遗传进化

叶绿体是半自主性细胞器,其生长和增殖受核基因组和自身的基因组2套遗传系统的控制、关于叶绿体的起源有2种学说,近年来．大量叶绿体基因组全序列被测定,以及分子生物学的研究结果为内共生起源学说提供了更多证据。相对于线粒体,叶绿体DNA的结构更趋于保守一,叶绿体与核基因组所编码的蛋白质互相协调来维持叶绿体的正常功能。在进化过程中,基因可能从叶绿体大量转移到细胞核中。叶绿体基因组的信息常常表现出“母性遗传”特征．因而,使之更具生物反应器的优势。     

高等植物细胞质雄性不育分子机理的研究进展

从线粒体DNA、叶绿体DNA和线粒体质粒DNA方面较详细地阐述了高等植物细胞质雄性不育的分子机理及最新进展;探讨了细胞核DNA和细胞质DNA之间的相互关系。     

肺囊康定产生菌Glarea lozoyensis线粒体基因组序列的再分析（英文）

【目的】Glarea lozoyensis是抗真菌药物卡泊芬净的产生菌,其突变菌株ATCC 74030的线粒体基因组已被报道。我们此前的研究发现诱变剂能引起该菌某些细胞核基因的突变,但诱变剂是否也能引起线粒体DNA序列的改变并不清楚。【方法】组装野生型菌株ATCC 20868的线粒体基因组,并与发表的突变型菌株ATCC 74030的线粒体基因组进行比较。通过PCR验证野生和突变菌株线粒体基因组间表现差异之处,并利用正确的线粒体基因组序列进行新的分析。【结果】我们成功组装出野生型菌株ATCC20868的线粒体基因组,通过比较其与发表的ATCC 74030的线粒体基因组序列,发现存在6处单核苷酸变异位点和2处具有长度差异的区域。然而,随后的PCR验证和序列比较并没有发现2个菌株间存在这些差异。最初观察到的碱基差异是因为发表的ATCC 74030线粒体基因组存在序列错误。有趣的是,在Glarea lozoyensis的线粒体基因组中,我们发现存在3个具有内含子的t RNA基因和1个rnp B基因。同时,该菌线粒体基因组中存在多种重复序列,在其线粒体和细胞核基因组间也存在明显的DNA片段重复事件。【结论】诱变剂没有引起G.lozoyensis线粒体DNA的任何改变;发表的ATCC 74030的线粒体基因组存在序列错误。我们报道G.lozoyensis正确的线粒体基因组序列,并且发现该菌线粒体和细胞核基因组间频繁的基因交流。     

植物细胞核基因和细胞质基因

植物细胞不同于动物细胞,前者有三大遗传系统,即细胞核、叶绿体和线粒体遗传系统,后者只有细胞核和线粒体遗传系统。所谓细胞质基因,即为叶绿体和线粒体基因。在这三个遗传系统中,各有自己的DNA复制、转录和转译自主性,但叶绿体、线粒体遗传系统又受到核遗传系统的部分控制,所以它们的自主性又不是完全的。当前植物分子遗传学的研究,不仅是分析三个遗传系统基因组的结构和基因表达,而且要研究之间的相互作用和基因的协同表达及其调控机制,才能对生产实践中提出的问题提供理论依据和解决途径。     

蛹虫草线粒体DNA与细胞核DNA进化关系的比较

【目的】分析蛹虫草是否存在核内线粒体DNA片段,比较蛹虫草线粒体DNA与细胞核DNA的碱基变异程度及所反映的菌株间的系统发育关系。【方法】通过本地BLAST或LAST对蛹虫草线粒体基因组和核基因组进行序列相似性搜索;从10个已知线粒体基因组的蛹虫草菌株中分别扩增7个细胞核蛋白编码基因片段,并与其在14个线粒体蛋白编码基因上的碱基变异情况进行比较。【结果】蛹虫草核基因组中存在5处较短的核内线粒体DNA片段,总长只有278bp。蛹虫草核DNA的变异频率整体上高于线粒体DNA。核DNA和线粒体DNA所反映的蛹虫草菌株间的系统发育关系存在显著差异。【结论】蛹虫草线粒体DNA与核DNA间不存在长片段的基因交流,二者变异频率不同,所反映的蛹虫草菌株间的系统发育关系也有差异。本研究增加了对蛹虫草线粒体与细胞核DNA进化关系的认识。     

Cucumber: a model angiosperm for mitochondrial transformation?

Plants possess three major genomes, carried in the chloroplast, mitochondrion, and nucleus. The chloroplast genomes of higher plants tend to be of similar sizes and structure. In contrast both the nuclear and mitochondrial genomes show great size differences, even among closely related species. The largest plant mitochondrial genomes exist in the genus Cucumis at 1500 to 2300 kilobases, over 100 times the sizes of the yeast or human mitochondrial genomes. Biochemical and molecular analyses have established that the huge Cucumis mitochondrial genomes are due to extensive duplication of short repetitive DNA motifs. The organellar genomes of almost all organisms are maternally transmitted and few methods exist to manipulate these important genomes. Although chloroplast transformation has been achieved, no routine method exists to transform the mitochondrial genome of higher plants. A mitochondrial-transformation system for a higher plant would allow geneticists to use reverse genetics to study mitochondrial gene expression and to establish the efficacy of engineered mitochondrial genes for the genetic improvement of the mitochondrial genome. Cucumber possesses three unique attributes that make it a potential model system for mitochondrial transformation of a higher plant. Firstly, its mitochondria show paternal transmission. Secondly, microspores possess relatively few, huge mitochondria. Finally, there exists in cucumber unique mitochondrial mutations conditioning strongly mosaic (msc) phenotypes. The msc phenotypes appear after regeneration of plants from cell culture and sort with specific rearranged and deleted regions in the mitochondrial genome. These mitochondrial deletions may be a useful genetic tool to develop selectable markers for mitochondrial transformation of higher plants.     

The Mitochondrial Genome of Soybean Reveals Complex Genome Structures and Gene Evolution at Intercellular and Phylogenetic Levels

Determining mitochondrial genomes is important for elucidating vital activities of seed plants. Mitochondrial genomes are specific to each plant species because of their variable size, complex structures and patterns of gene losses and gains during evolution. This complexity has made research on the soybean mitochondrial genome difficult compared with its nuclear and chloroplast genomes. The present study helps to solve a 30-year mystery regarding the most complex mitochondrial genome structure, showing that pairwise rearrangements among the many large repeats may produce an enriched molecular pool of 760 circles in seed plants. The soybean mitochondrial genome harbors 58 genes of known function in addition to 52 predicted open reading frames of unknown function. The genome contains sequences of multiple identifiable origins, including 6.8 kb and 7.1 kb DNA fragments that have been transferred from the nuclear and chloroplast genomes, respectively, and some horizontal DNA transfers. The soybean mitochondrial genome has lost 16 genes, including nine protein-coding genes and seven tRNA genes; however, it has acquired five chloroplast-derived genes during evolution. Four tRNA genes, common among the three genomes, are derived from the chloroplast. Sizeable DNA transfers to the nucleus, with pericentromeric regions as hotspots, are observed, including DNA transfers of 125.0 kb and 151.6 kb identified unambiguously from the soybean mitochondrial and chloroplast genomes, respectively. The soybean nuclear genome has acquired five genes from its mitochondrial genome. These results provide biological insights into the mitochondrial genome of seed plants, and are especially helpful for deciphering vital activities in soybean.     

Molecular evolution of chloroplast DNA sequences

Comparative data on the evolution of chloroplast genes are reviewed. The chloroplast genome has maintained a similar structural organization over most plant taxa so far examined. Comparisons of nucleotide sequence divergence among chloroplast genes reveals marked similarity across the plant kingdom and beyond to the cyanobacteria (blue-green algae). Estimates of rates of nucleotide substitution indicate a synonymous rate of 1.1 x 10(-9) substitutions per site per year. Noncoding regions also appear to be constrained in their evolution, although addition/deletion events are common. There have also been evolutionary changes in the distribution of introns in chloroplast encoded genes. Relative to mammalian mitochondrial DNA, the chloroplast genome evolves at a conservative rate.      

植物线粒体DNA质料研究进展

本文列出了已发现的高等植物中的线粒体ＤＮＡ质粒,按分子形状分为线粒体环状ＤＮＡ质粒和线粒体线状ＤＮＡ质粒,环状线粒体ＤＮＡ质粒的特征是分子较小,序列中有正向／反向重复序列,ＯＲＦ一般较小。线状线粒体ＤＮＡ质粒的特征是分子较大,末端有重复序列,５’端与蛋白质共价结合,有较长的ＯＲＦ。还分别介绍了它们的复制机制、转录和起源。质粒间及质粒及核基因组、线粒体基因组、叶绿体基因组的同源性也作了介绍。最后,综     

Mitochondrial DNA of Vitis vinifera and the issue of rampant horizontal gene transfer

The mitochondrial genome of grape (Vitis vinifera), the largestorganelle genome sequenced so far, is presented. The genomeis 773,279 nt long and has the highest coding capacity amongknown angiosperm mitochondrial DNAs (mtDNAs). The proportionof promiscuous DNA of plastid origin in the genome is also thelargest ever reported for an angiosperm mtDNA, both in absoluteand relative terms. In all, 42.4% of chloroplast genome of Vitishas been incorporated into its mitochondrial genome. In orderto test if horizontal gene transfer (HGT) has also contributedto the gene content of the grape mtDNA, we built phylogenetictrees with the coding sequences of mitochondrial genes of grapeand their homologs from plant mitochondrial genomes. Many incongruentgene tree topologies were obtained. However, the extent of incongruencebetween these gene trees is not significantly greater than thatobserved among optimal trees for chloroplast genes, the commonancestry of which has never been in doubt. In both cases, weattribute this incongruence to artifacts of tree reconstruction,insufficient numbers of characters, and gene paralogy. Thisfinding leads us to question the recent phylogenetic interpretationof Bergthorsson et al. (2003, 2004) and Richardson and Palmer(2007) that rampant HGT into the mtDNA of Amborella best explainsphylogenetic incongruence between mitochondrial gene trees forangiosperms. The only evidence for HGT into the Vitis mtDNAfound involves fragments of two coding sequences stemming fromtwo closteroviruses that cause the leaf roll disease of thisplant. We also report that analysis of sequences shared by bothchloroplast and mitochondrial genomes provides evidence fora previously unknown gene transfer route from the mitochondrionto the chloroplast.     

植物线粒体DNA质粒研究进展

本文列出了已发现的高等植物中的线粒体DNA质粒,按分子形状分为线粒体环状DNA质粒和线粒体线状DNA质粒,环状线粒体DNA质粒的特征是分子较小, 序列中有正向/反向重复序列,ORF一般较小。线状线粒体DNA质粒的特征是分子较大,末端有重复序列,5'端与蛋白质共价结合,有较长的ORF。还分别介绍了它们的复制机制、转录和起源。质粒间及质粒与核基因组、线粒体基因组、叶绿体基因组的同源性也作了介绍。最后,综述了植物线粒体DNA质粒与植物的细胞质雄性不育（CMS）之间的关系。     

Evidence for new nuclear and mitochondrial genome organizations among high-frequency somatic embryogenesis-derived plants of allotetraploid Coffea arabica L. (Rubiaceae)

 The most important commercial species of coffee, Coffea arabica, which produces 73% of the world's coffee crop and almost all of the coffee in Latin America, is the only tetraploid (allotetraploid, 2n=4x=44) species known in the genus. High-frequency somatic embryogenesis, plant regeneration and plant recovery were achieved from leaf explants of a mature, elite plant of C. arabica cv. Cauvery (S-4347) using a two-step culture method. To assess the genetic integrity of the nuclear, mitochondrial and chloroplast genomes among the hardened regenerants, we employed multiple DNA markers (RFLP, RAPD, ISSR) for sampling various regions of the genome. Although the nuclear and mitochondrial genomes of the mother plant and five ramets derived from the mother ortet were similar in organization, this was not so in the somatic embryo-derived plants where both nuclear and mitochondrial genomes changed in different, characteristic ways and produced novel genome organizations. A total of 480 genetic loci, based on the data obtained from a total of 16 nuclear, mitochondrial and chloroplast gene probes, in combination with nine restriction enzyme digests, 38 RAPD and 17 SSR primers, were scored in 27 somatic embryo-derived plants and the single control. Among these, 44 loci were observed to be polymorphic. A relatively low level of polymorphism (4.36%) was found in the nuclear genome, while polymorphism in the mitochondrial genome (41%) was much higher. No polymorphism was detected in the chloroplast genome. The polymorphism in the mitochondrial genome was found in only 4 plants. Such selective polymorphism was not true for the nuclear genome. Thus, this in-depth and comprehensive study demonstrates, for the first time, the presence of subtle genetic variability and novel genome organizations in the commercially well-established somatic embryogenesis-derived plants of this important coffee species. Received: 2 July 1999 / Revision received: 1 February 2000 / Accepted: 17 February 2000     

The evolutionary changes in the amino acid sequences and properties of the ATP-synthase in chloroplasts, mitochondria and bacteria]

Studies have been made on ATPase from chloroplasts, cyanobacteria and mitochondria of higher plants and animals. No intraspecies and interspecies variability of chloroplast and mitochondrial ATPase was found with respect to pH optimum of the activity, to specificity to cations as substrate components, to sensitivity to stimulating and inhibiting anions and ethanol, to optimal stimulating ethanol concentration. Intergenus variation of these properties of ATPase from chloroplasts, plant mitochondria, and cyanobacteria was revealed. Analysis of homology of the amino acid sequence in ATP-synthase subunits showed that ATP-synthase genes in chloroplast DNA originate from cyanobacterial genome, whereas ATP-synthase genes in plant and animal mitochondria-from genome of Rhodospirillum rubrum or closely related species. It was established that no recombination between the genetic material of chloroplasts and mitochondria took place during evolution.     

Discovery of the rpl10 Gene in Diverse Plant Mitochondrial Genomes and Its Probable Replacement by the Nuclear Gene for Chloroplast RPL10 in Two Lineages of Angiosperms

Mitochondrial genomes of plants are much larger than those of mammals and often contain conserved open reading frames (ORFs) of unknown function. Here, we show that one of these conserved ORFs is actually the gene for ribosomal protein L10 (rpl10) in plant. No rpl10 gene has heretofore been reported in any mitochondrial genome other than the exceptionally gene-rich genome of the protist Reclinomonas americana. Conserved ORFs corresponding to rpl10 are present in a wide diversity of land plant and green algal mitochondrial genomes. The mitochondrial rpl10 genes are transcribed in all nine land plants examined, with five seed plant genes subject to RNA editing. In addition, mitochondrial-rpl10-like cDNAs were identified in EST libraries from numerous land plants. In three lineages of angiosperms, rpl10 is either lost from the mitochondrial genome or a pseudogene. In two of them (Brassicaceae and monocots), no nuclear copy of mitochondrial rpl10 is identifiably present, and instead a second copy of nuclear-encoded chloroplast rpl10 is present. Transient assays using green fluorescent protein indicate that this duplicate gene is dual targeted to mitochondria and chloroplasts. We infer that mitochondrial rpl10 has been functionally replaced by duplicated chloroplast counterparts in Brassicaceae and monocots.     

Constancy of organellar genome copy numbers during leaf development and senescence in higher plants

In higher plants, plastid and mitochondrial genomes occur at high copy numbers per cell. Several recent publications have suggested that, in higher plants like Arabidopsis and maize, chloroplast DNA is virtually absent in mature and old leaves. This conclusion was mainly based on DAPI staining of isolated chloroplasts. If correct, the finding that chloroplasts in mature leaves lack DNA would change dramatically our understanding of gene expression, mRNA stability and protein stability in chloroplasts. In view of the wide implications that the disposal of chloroplast DNA during leaf development would have, we have reinvestigated the age dependency of genome copy numbers in chloroplasts and, in addition, tested for possible changes in mitochondrial genome copy number during plant development. Analyzing chloroplast and mitochondrial DNA amounts in Arabidopsis and tobacco plants, we find that organellar genome copy numbers remain remarkably constant during leaf development and are present in essentially unchanged numbers even in the senescing leaves. We conclude that, during leaf development, organellar gene expression in higher plants is not significantly regulated at the level of genome copy number and we discuss possible explanations for the failure to detect DNA in isolated chloroplasts stained with DAPI.