软甲纲动物和星虫动物线粒体基因组特征及分子进化研究

IOCAS-IR > 海洋环流与波动重点实验室

	软甲纲动物和星虫动物线粒体基因组特征及分子进化研究
其他题名	Mitochondrial genomic characters of malacostracans and sipunculans and the molecular evolutionary research based on mitochondrial genomes
	申欣
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	软甲纲星虫动物线粒体基因组系统发育基因组学
摘要	在过去的几十年间，利用线粒体基因组序列探讨后生动物深层次的系统发育关系已取得初步进展。这主要得益于，线粒体基因组与其它分子标记相比具备诸多优势。迄今为止，超过1,200个后生动物的线粒体基因组已被测定，然而所获得的数据分布极不均衡。软甲纲历来是甲壳动物分类学和系统发育学研究的重要类群，在形态学特征和分子生物学各方面取得广泛的发展。尽管软甲纲本身作为单系群已得到大多数甲壳动物学家认可，但是软甲纲内部各个类群之间的系统发育关系迄今仍颇有争议。本文报道了凡纳滨对虾Litopenaeus vannamei、中国明对虾Fenneropenaeus chinensis、脊尾白虾Exopalaemon carinicauda、太平洋磷虾Euphausia pacifica和采自南极普里兹湾南极磷虾Euphausia superba的线粒体基因组，其长度分别为15,989 bp、16,004 bp、15,730 bp、16,898 bp和15,498 bp以上（部分非编码区没有测定）。本研究发现凡纳滨对虾、中国明对虾、脊尾白虾和太平洋磷虾的线粒体基因组包含后生动物线粒体基因组典型的基因组成（13个蛋白质编码基因、22个转运RNA、2个核糖体RNA和一个非编码的AT富含区）；然而，南极磷虾与后生动物线粒体基因组典型的基因组成相比，存在1个trnN基因的重复。与泛甲壳动物线粒体基因组的原始排列相比，凡纳滨对虾和中国明对虾线粒体基因组的基因排列完全一致；脊尾白虾的线粒体基因组发生罕见的trnP和trnH易位，从而说明在真虾下目中线粒体基因组的基因排列并不保守；太平洋磷虾线粒体基因组的基因排列出现3个转运RNA的重排（trnL1、trnL2和trnW）；南极磷虾线粒体基因组的基因排列除了出现太平洋磷虾具有的这3个转运RNA重排之外，还有1个trnN的重复和1个trnI基因的重排。另外，在太平洋磷虾线粒体基因组最大的非编码区中存在一个154 bp×4.7的串连重复区域，如此大片段的串联重复区域（>150 bp）在软甲纲动物线粒体基因组中是首次报道。目前所获得的线粒体基因组数据强有力地支持口足目、对虾科、真虾下目和短尾下目为单系群。通过比较基因排列及蛋白质编码基因核苷酸和氨基酸序列的系统发育分析得知真虾类和龙虾类为腹胚亚目的原始类群，并支持“（（Penaeus＋Fenneropenaeus）＋Litopenaeus）＋Marsupenaeus”的系统发育关系。此外，线粒体基因组的数据也强有力地支持磷虾目为单系群。但对于磷虾目在软甲纲中的分类地位及与其它类群的系统发育关系存在一些分歧：基于蛋白质编码基因核苷酸和氨基酸数据的贝叶斯分析强有力地支持磷虾目和十足目近缘，这个结果和传统的分类系统完全一致；然而，基于核苷酸序列的邻接法、氨基酸序列的邻接法和最大似然法均强有力地支持磷虾类和对虾类亲缘关系较近，从而破坏了十足目的单系性，与传统的认识并不一致，但由于自展值的支持率非常高，所以深层次的分析需要进一步加强。星虫动物属于海洋生物中的一个小门类，自1555年被记载以来，其在后生动物中的分类地位就备受争议。本研究测定了星虫动物门的第一条线粒体基因组：革囊星虫Phascolosoma esculenta的线粒体基因组，全长为15,494 bp，包含13个蛋白质编码基因、22个转运RNA、2个核糖体RNA和1个非编码的AT富含区，所有37个基因在同一条链上编码。与后生动物线粒体基因组的典型组成相比，存在一个trnR基因的缺失和一个trnM基因的重复。比较星虫动物和其它后生动物的线粒体基因组，可以得到以下结论：1）星虫动物和环节动物（包括螠虫动物）的线粒体基因组有相近的基因排列，而且所有基因都在同一链上编码；2）基于蛋白质编码基因的系统发育分析强有力地支持星虫动物和环节动物（包括螠虫动物）组成一个单系群，而将软体动物排除在外。因此，本研究认为以前许多星虫动物和软体动物“共享”的特征，包括发育特征和缺乏分节等，需要重新考虑。
其他摘要	Over the past decades, inference of a deeper phylogenetic relationship of metazoan with whole mitochondrial genome sequences has gained popularity. This resulted from many advantages offered over other molecular markers for phylogenetic analysis. Although more than one thousand and two hundreds mitochondrial genome sequences have been determined to date, the taxonomic sampling is still highly biased. Malacostracans have been the subject of a huge number of classificatory and phylogenetic studies employing morphological characters and molecular characters. Though Malacostraca itself is widely regarded as a monophyletic grouping, the relationships among the various groups of the Malacostraca are still controversial. In this paper, we report the mitochondrial genomes from the Litopenaeus vannamei Boone 1931, Fenneropenaeus chinensis Osbeck 1765, Exopalaemon carinicauda Holthuis 1950, Euphausia pacifica Hansen 1911 and Euphausia superba Dana 1852 (sampling from Prydz Bay, Antarctic). The mitochondrial genomes of them is 15, 989 bp, 16, 004 bp, 15, 730 bp, 16, 898 bp and more than 15, 498 bp in length (partial non-coding region was not determined), respectively. As seen in other metazoans, the genomes of L. vannamei, F. chinensis, Exopalaemon carinicauda and Euphausia pacifica contain a standard set of 13 protein-coding genes (PCGs), 22 transfer RNA genes, two ribosomal RNA genes and an AT-rich non-coding region. However, the mitochondrial genome of Euphausia superba has an extra trnN gene compared with standard set of metazoan mitochondrial genomes. The gene arrangements of L. vannamei and F. chinensis mitochondrial genoms are consistent with the pancrustacean ground pattern. Unusual translocation of trnP and trnH was found when comparing with the pancrustacean ground pattern, which indicating gene order is not conserved among Caridea. Translocation of three tRNAs (trnL1, trnL2 and trnW) was found in the mitochondrial genome of Euphausia pacifica when comparing with the pancrustacean ground pattern. Besides the translocation of above three tRNAs, the duplication of trnN and translocation of trnI were founded in the mitochondrial genome of Euphausia superba. The largest non-coding region in the mitochondrial genome of Euphausia pacifica contains one section with tandem repeats (4.7×154 bp), which is the first report of largest tandem repeats (>150 bp) founded in the malacostracan mitochondrial genomes. All analyses based on nucleotide and amino acid data strongly support the monophyly of Stomatopoda, Penaeidae, Caridea and Brachyura. Both the pattern of gene rearrangements and phylogenomic analyses using concatenated nucleic acid and amino acid sequences of the 13 mitochondrial PCGs strengthened the support that Caridea and Palinura are primitive members of Pleocyemata and that (((Penaeus+Fenneropenaeus)+Litopenaeus)+Marsupenaeus). The Euphausiacea clade was also recovered as monophyletic with strong statistical support. However, the taxonomic position and phylogenetic relationship of Euphausiacea within Malacostraca is unstable. The Bayesian analysis based on nucleotide and amino acid data strongly support the close relationship between Euphausiacea and Decapoda, which is coincidence with traditional views. The Neighbor-Joining approach based on nucleotide and amino acid data and Maximum-Likelihood analysis based on amino acid data strongly support the close relationship between Euphausiacea and Penaeidae, which destroy the monophyly of Decapoda and not coincidence with traditional classification. Nevertheless, the bootstrap value is very high, so the deeper analyses are needed. Sipunculans form a minor phylum of marine animals. Although the group was first documented in 1555, their taxonomic position within Metazoan is controversial. In this paper, we present here the sequence of Phascolosoma esculenta mitochondrial genome, the first one from phylum Sipuncula. The mitochondrial genome of the P. esculenta is 15, 494 bp in length and contains 13 PCGs, 22 transfer RNA genes, 2 ribosomal RNA genes and a non-coding AT-rich region. All of the 37 identified genes are transcribed from the same DNA strand. In comparison to typical metazoan mitochondrial genomes, sipunculid mitochondrial genome lacks trnR but has an extra trnM. From the analyses of mitochondrial genome of P. esculenta and other metazoan, we make the following conclusion: First, sipunculans and annelids (including echiurans) share similar gene order in the mitochondrial genome, with all 37 genes located on the same strand; Second, phylogenetic analyses based on concatenated protein sequences also provide strong evidence that Sipuncula and Annelida (including echiurans) form a monophyletic clade to the exclusion of the Mollusca. Thus, many characteristics that have been hypothesized to link sipunculans with molluscs, including their developmental pattern and lack of segmentation, should be reevaluated.
页数	167
语种	中文
文献类型	学位论文
条目标识符	http://ir.qdio.ac.cn/handle/337002/1219
专题	海洋环流与波动重点实验室
推荐引用方式 GB/T 7714	申欣. 软甲纲动物和星虫动物线粒体基因组特征及分子进化研究[D]. 海洋研究所. 中国科学院海洋研究所,2008.

条目包含的文件
文件名称/大小	文献类型	版本类型	开放类型	使用许可
10001_20051800681204（7897KB）			限制开放	--	浏览