中文摘要：

线粒体基因组已被广泛应用于后生动物分子系统发育和群体遗传的研究。文昌鱼（Amphioxus）作为研究脊椎动物起源和进化的模式动物，在脊椎动物起源和进化研究中占据极为重要的位置。作者综合分析文昌鱼2科7个种的51条线粒体基因组全序列，全面揭示了文昌鱼线粒体基因组的基本特征。文昌鱼线粒体基因组均编码后生动物标准的37个基因，文昌鱼线粒体基因组共有3种基因排列方式，其中文昌鱼属和侧殖丈昌鱼属共有的基因排列与脊椎动物线粒体基因组的典型排列相比最为接近。因此，文昌鱼属和侧殖文昌鱼属线粒体基因组的基因排列方式代表了文昌鱼原始的基因排列方式。与此相比，偏文昌鱼属的3个物种发生了基因重排。文昌鱼线粒体基因组13个蛋白编码基因的Ka／Ks值均远远低于1（0～0．3363），显示出较强的纯化（负）选择。文昌鱼线粒体基因组种问和种内基因变异分析表明，在文昌鱼群体遗传的研究中，nad5、nad4和nad2基因是理想的分子标记，可以作为coxl基因辅助的分子标记，用于分析丈昌鱼不同群体之间的遗传多样性，为其生物多样性的保护及合理利用其生物资源提供更多基础资料。

英文摘要：

Mitochondrial genomes have been widely used in metazoan molecular phylogeny and genetic research. Amphioxus, as research model animals, occupies an important position in the origin and evolution of vertebrates. The basic characteristics of amphioxus mitochondrial genomes were fully revealed by our comprehensive analysis of 51 mitochondrial genome sequences from seven species. Amphioxus mitochondrial genomes contain 37 standard metazoan genes. Three types of gene arrangements were found in amphioxus mitochondrial genomes. Gene arrangements of Branchiostoma and Epigonichthys are most similar to those of typical vertebrate mitochondrial genomes. Therefore, gene arrangement shared by Branchiostoma and Epigonichthys represents the ancestral amphioxus gene order. In contrast, gene rearrangements were found in three species of the genus Asymmetron. The Ka/Ks ratios of the 13 amphioxus mitochondrial protein-coding genes were much lower than one （range between 0 and 0.3363）, indicating a strong purifying selection （negative selection）. The genetic variation analysis of main genes （13 protein coding genes and two ribosomal RNA genes） among and within amphioxus species shows that genes had5, had4 and had2 are ideal molecular markers supplementary to the coxl gene, and will provide useful information on conservation of amphioxus biological diversity and the utilization of biological resources.