软体动物线粒体基因组学及分子系统发生研究

IOCAS-IR > 海洋环流与波动重点实验室

	软体动物线粒体基因组学及分子系统发生研究
其他题名	Researches on Molluscan Mitogenomics and Molecular Phylogenetics
	任建峰
学位类型	博士
	2008-06-06
学位授予单位	中国科学院海洋研究所
学位授予地点	海洋研究所
关键词	扇贝超科栉孔扇贝海湾扇贝巨蛎属帘蛤科紫斑文蛤线粒体基因组基因排列系统树分子系统发生
摘要	本研究以双壳纲、翼形亚纲、珍珠贝目、扇贝超科的栉孔扇贝(Chlamys farreri )、海湾扇贝(Argopecten irradians)和牡蛎超科巨蛎属(Crassostrea)的长牡蛎(C. gigas)、葡萄牙牡蛎(C. angulata)、熊本牡蛎(C. sikamea)、香港巨牡蛎(C. hongkongensis)和近江牡蛎(C. ariakensis)5种牡蛎及异齿亚纲、帘蛤目、帘蛤科的紫斑文蛤(Meretrix pethechialis)为研究对象，系统的研究了以上物种的线粒体基因组全序列的特点。并以线粒体12个蛋白质编码基因的序列，在氨基酸和核苷酸水平上构建了软体动物的分子系统发生树。本研究旨在为利用线粒体基因组全序列全面构建软体动物分子系统发生树，为软体动物的系统发生和进化研究提供一种新的思路和前期基础工作，本研究主要内容分为以下三个部分：一、栉孔扇贝和海湾扇贝线粒体基因组序列分析及分子系统发生研究采用Long-PCR技术扩增了栉孔扇贝和海湾扇贝线粒体全基因组，利用步移法结合文库构建的测序策略获得了线粒体基因组的序列。海湾扇贝线粒体全基因组长度为16,211 bp，栉孔扇贝接近全序列长度为20,789 bp。两个基因组都编码35个基因，包括12个蛋白质编码基因，2个rRNA和21个tRNA。与典型的动物线粒体基因组相比，两个基因组都缺少一个蛋白质编码基因atp8和2个trnS, 在海湾扇贝基因组中有1个trnF的重复，而在栉孔扇贝基因组中有1个trnM的重复。基因排列比较显示，尽管海湾扇贝、栉孔扇贝和巨扇贝分类学上属于同一扇贝科，但是它们的线粒体基因排列非常不同。在四种扇贝中，虾夷扇贝与栉孔扇贝的基因排列顺序非常相似；即使排除tRNA的比较，栉孔扇贝和海湾扇贝基因组仅仅共享三个小的基因块；而海湾扇贝与巨扇贝仅有一个相同的基因块。在所有的系统发生分析中，四种扇贝稳定的系统发生关系得到强有力的支持，海湾扇贝较其他三种扇贝较早的分化出来；栉孔扇贝比其他两种扇贝与虾夷扇贝亲缘关系更近。贝叶斯法和最大似然法分析都支持扇贝超科的单系发生。二、巨蛎属牡蛎线粒体基因组全序列分析及分子系统发生研究采用Long-PCR扩增技术和步移法结合文库构建的技术策略获得了巨蛎属C. gigas、C. angulata、C. sikamea、C. hongkongensis和C. ariakensis 5种牡蛎线粒体全基因组序列，并于GenBank已公布的美洲牡蛎C.virginica序列进行比较研究。C. gigas、C. angulata、C. sikamea、C. hongkongensis和C. ariakensis线粒体全基因组长度分别为18,225 bp、18,225 bp、18,243 bp、18,622 bp和18,414 bp，都长于C. virginica基因组17,244 bp的长度。本研究的5种牡蛎线粒体基因组都编码39个基因，包括12个蛋白质编码基因，2个rRNA和25个tRNA。与典型的线粒体基因组相比，都缺少一个蛋白质编码基因atp8，有trnM、trnK和trnQ 3个tRNA基因的重复，更特别的是基因组中的rrnL分为两段，这在其它线粒体基因组中未见报道，有一个重复的rrnS；而C. virginica基因组编码37个基因，与其他牡蛎相比，没有trnK和trnQ重复，只有一个rrnS。基因排列比较显示，巨蛎属的5种牡蛎C. gigas、C. angulata、C. sikamea、C. hongkongensis和C. ariakensis基因排列完全一致，而与C. virginica的基因排列相比仍然有较大的差别，有多个tRNA发生易位。系统发生分析显示，C. gigas和C. angulata首先聚在一起，然后与C. sikamea聚为一支。C. hongkongensis和C. ariakensis聚成一支。C. virginica为单独的一支。系统树清楚的显示出C. gigas和C. angulata以及C. hongkongensis和C. ariakensis非常近的亲缘关系，这也是长期以来，牡蛎分类学上的经典问题，有学者认为C. gigas和C. angulata为同一物种，线粒体基因组的数据显示C. gigas和C. angulata可能达到不同物种的差异。传统分类上的“近江牡蛎”的“白蚝”和“赤蚝”，线粒体序列差别明显，完全支持两种牡蛎新种名的制定。三、紫斑文蛤线粒体基因组全序列分析及分子系统发生研究采用Long-PCR扩增技术和步移法结合文库构建的技术策略获得了紫斑文蛤线粒体基因组全序列。该基因组全长19,567 bp，编码36个基因，包括12个蛋白质编码基因，2个rRNA和22个tRNA。与典型的线粒体基因组相比，缺少一个蛋白质编码基因atp8和1个trnS, 有1个trnQ基因的重复。基因排列比较显示，双壳类的基因排列在低的分类阶元时相对保守。在帘蛤科中，紫斑文蛤M. petechialis和菲律宾蛤仔V. philippinarum共享四个完全一致的基因块，两个大的基因块是cox1-L1-nad1-nad2-nad4L-I 和 cox2-P-cob-rrnL-nad4-H-E-S2-atp6-nad3-nad5，另两个小基因块只包括tRNA基因。在以氨基酸序列构建的分子系统树中，帘蛤科紫斑文蛤与菲律宾蛤仔首先聚在一起，然后，它们与A. tuberculata形成一个进化枝。这一枝与H. arctica结合起来，支持异齿亚纲单系发生。
其他摘要	The mitochondrial genomes of two scallops Chlamys farreri and Argopecten irradians in Pectinoidea, and five oysters C. gigas, C. angulata, C. sikamea, C. hongkongensis and C. ariakensis in Ostreoidea, Pteriomorphia were sequenced and analysed. In additional, the mitochondrial genome of Meretrix pethechialis in Veneridae was also sequenced and analysed. Based on the sequences of protein-coding genes, molluscan molecular phylogenetic trees were constructed at amino acid and nucleotide levels. The aim of the research is to provide a new method and basic reference to studying molluscan phylogenetics based on complete mitochondrial genomes. The main contents consist of the following three parts. 1 The analysis of mitochondrial genomes of two scallops C. farreri and A. irradians, and their molecular phylogenetics The complete mitochondrial genomes of two scallops C. farreri and A. irradians were amplified with Long-PCR techniques. The sequences were obtained with primer-walking and cloning strategies. The complete mitochondrial genome of A. irradians is 16,211 bp in length and the nearly complete mitochondrial genome of C. farreri is 20,789 bp. Both of the genomes contain 35 genes including 12 protein-coding genes, 2 ribosomal RNAs and 21 transfer RNAs. In contrast to the typical animal mitochondrial genome, both of them are lack of one protein-coding gene atp8 and two trnSs, and with an additional copy of trnF in A. irradians and trnM in C. farreri, respectively. Gene order and genome content were compared among four scallops. Gene arrangement of C. farreri closely resembles that of Mizuhopecten yessoensis. Two genomes of C. farreri and A. irradians show only three small identical gene blocks while two genomes of A. irradians and Placopecten magellanicus share only two gene blocks. Comparison of the gene arrangement demonstrated that four scallops have few identical gene junctions although they belong to the same family. The stable relationships among four scallops are robustly supported in all analyses. A. irradians diverged earlier than other three scallops. C. farreri is closer to M. Yessoensis than to other two scallops. Both Bayesian and ML analyses supported the monophyly of the superfamilies Pectinoidea. 2 The analysis of mitochondrial genomes of genus Crassostrea and their molecular phylogenetics The complete mitochondrial genomes of five oysters C. gigas, C. angulata, C. sikamea, C. hongkongensis and C. ariakensis were amplified with Long-PCR techniques and sequenced with primer-walking and cloning strategies. The sequence comparisions among the five oysters and the C. virginica were conducted. The complete mitochondrial genomes of five oysters are 18,225 bp, 18,225 bp, 18,243 bp, 18,622 bp and 18,414 bp in length. They are longer than the genome of C. virginica of 17,244 bp. The five genomes sequenced in this study contain 39 genes including 12 protein-coding genes, 2 ribosomal RNAs and 25 transfer RNAs. In contrast to the typical animal mitochondrial genome, they are lack of one protein-coding gene atp8 and with an additional copy of trnM, trnK, trnQ and rrnS. It is a special characterastic that rrnL is splited into two parts in the genomes which is never reported in other mitochondrial genomes. C. virginica genome contains 37 genes，in contrasts to the five oysters; it is lack of the duplication of trnK, trnQ and rrnS. Comparison of gene arrangement demonstrated that gene order of five oysters is completely identical. In contrast to these five oysters, translocations of several tRNAs were occurred in genome of C. virginica. In the phylogenetic trees, C. gigas and C. angulata was clustered firstly, and then they were united with C. sikamea. C. hongkongensis and C. ariakensis formed a clade. C. virginica formed a clade alone. The phylogenetic tree implied that there are much closed relationship between C. gigas and C. angulata, and C. hongkongensis and C. ariakensis. Some researchers present a view that C. gigas and C. angulata are the same species, while the mitochondrial genome sequences demonstrated that the two species have diverged and should be considered as two different species. The new species names for the “white meat” and “brown meat” for the traditional taxonomic Jinjiang oyster are fully supported by the mitochondrial genome data. 3 The analysis of mitochondrial genomes of M. petechialis and its molecular phylogenetics The complete mitochondrial genomes of M. petechialis was amplified with Long-PCR techniques and sequenced with primer-walking and cloning strategies. The genome is 19,567 bp in length and contains 36 genes, including 12 protein-coding genes, 2 ribosomal RNAs and 22 transfer RNAs. In contrast to the typical animal mitochondrial genome, it lacks one protein-coding gene atp8 and one trnS with a duplication of trnQ. The comparison of gene order demonstrated that gene arrangement is relatively conservative in the lower taxonomic units. M. petechialis and V. philippinarum shared four identical gene blocks, two big blocks cox1-L1-nad1-nad2-nad4L-I and cox2-P-cob-rrnL-nad4-H-E-S2-atp6-nad3-nad5, and two small blocks contained tRNAs only. In all phylogenetic analysis, veneridas M. petechialis and V. philippinarum clustered together and then, they formed a clade with A. tuberculata. This clade united with H. arctica recovered the robust monophyly of heterodonta.
页数	127
语种	中文
文献类型	学位论文
条目标识符	http://ir.qdio.ac.cn/handle/337002/1503
专题	海洋环流与波动重点实验室
推荐引用方式 GB/T 7714	任建峰. 软体动物线粒体基因组学及分子系统发生研究[D]. 海洋研究所. 中国科学院海洋研究所,2008.

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