| Owing to abundance of mitochondria in cells, lack of recombination, maternal inheritance, absence of introns, and higher evolutionary rates, mitochondrial genome are extensively used for comparative and evolutionary genomics, molecular evolution, population genetics, species identification, and phylogenetic relationships at various taxonomic levels. Gene arrangement has been shown to be a very powerful tool for reconstructing evolutionary relationships. In recent studies, phylogenetic analysis based on complete mt sequence data have proved to enhance resolution and statistical confidence of inferred phylogenetic trees when compared with analyses based only on small portions of the mtDNA. Taxonomy and phylogeny of Heterodonta, which is by far the most diverse major group of Bivalvia, are long-debated issues and a complete agreement has not been reached yet. In particular, the morphologically-inferred phylogenies of subclass Heterodonta were challenged by recent phylogenetic studies based on molecular data. With technological and methodological advances, and associated decreasing costs of DNA sequencing, the amplification and sequencing of whole mitochondrial genomes has become routine. To date, only10complete mitochondrial genomes of Heterodonta have been determined. In this study,12complete mitochondrial genomes including4mitochondrial genomes of Coelomactra antiquate, belonging to9species of subclass Heterodonta were newly determined. We not only compared the mitochondrial genome organization and gene arrangements, but also reconstructed the phylogenetic relationships of subclass Heterodonta. The main results were listed as follows:1. Comparative study on complete mitochondrial genomes of two Solen speciesSolen grandis and Solen strictus are important economic shellfish in China. In recent years, the wild stocks of two Solen species have decreased dramatically due to over-exploitation. However, to date, little molecular information is known about the two commercial species. The complete mitochondrial genomes of S. grandis and S. strictus were determined and compared in this study. The two Solen species had the similar composition, AT content, size of each genes and the same gene order. However, some start and stop codon of two Solen species were different. Analysis of the ratios of Ka/Ks of protein-coding genes between S. grandis and S. strictus showed that cox1, cox2and cox3are under the strongest selective pressure while nad2, nad3and nad6are under the least selective pressure. The largest non-coding regions of both Solen species with some hairpin structures and (TA)12microsatellite-like elements, were not conservative. Besides, there was another tandem repeat sequence in the largest non-coding region of mitochondrial genome of S. strictus. The results indicated that there were obviously differences between two Solen mitochondrial genomes which could be as important molecular marker to distinguish S. grandis and S. strictus.2. Study on complete mitochondrial genomes of six Tellinoidea speciesTaxonomy and phylogeny of subclass Heterodonta including Tellinoidea are long-debated issues and a complete agreement has not been reached yet. Mitochondrial (mt) genomes have been proved to be a powerful tool in resolving phylogenetic relationship. In this study, we newly sequenced the complete mitochondrial genomes of six species belonging to superfamily Tellinoidea in traditional classification. The complete mt genomes of six species vary in size from16,352bp to18,182bp. In addition, the hairpin-like secondary structures are found in the largest non-coding regions of six freshly sequenced mt genomes, five of which also contain tandem repeats. It is noteworthy that two species belonging to the same genus show different gene arrangements. Twelve mt protein coding genes of newly determined mt genomes, as well as those of all other heterodont bivalves, were used to illustrate the phylogenetic relationship of Heterodonta. Our analysis indicates that Sinonovacula constricta, distant from the Solecurtidae belonging to Tellinoidea, is as a sister group with two Solen species of family Solenidae. Besides, the results show that all five species of Tellinoidea cluster together, while Sanguinolaria diphos has closer relationship with Solecurtus divaricates, Moerella iridescens and Semele scaba rather than with Sanguinolaria olivacea. By comparative study of the gene order rearrangements and phylogenetic relationships of the five species belonging to Tellinoidea, our results support that comparisons of mt gene order rearrangements, to some extent, are a useful tool for phylogenetic studies. Based on phylogenetic analyses of multiple protein-coding genes, we prefer classifying the genus Sinonovacula within the superfamily Solenoidea and not the superfamily Tellinoidea. Besides, both gene order and sequence data agree that Sanguinolaria (Psammobiidae) is not monophyletic.3. Study on complete mitochondrial genomes of Coelontactra antiquafeCryptic species which improve our understanding of species diversity and evolutionary histories within marine animals have been increasingly revealed in the marine realm. Coelomactraantiquate is an important commercial bivalve species, but has been suffering from severe population decline due to over-exploitation and deterioration of environmental conditions. To test the hypothesis that cryptic species might exist in C. antiquate presented, four complete mitogenomes of C. antiquate from northern and southern China were determined in this study. Comprehensive comparative analysis of the mitochondrial genomes of C. antiquatebetween northern and southern population reveals significant differences in genome composition, protein coding genes, tRNA genes, non-coding regions, genetic divergence and phylogenetic analysis. The results provide strong mitogenome evidence for the existence of cryptic species in C. antiquate. Besides, our results also support that comprehensive comparative analysis of mtDNA represents an accessible and powerful tool to identify cryptic species. |
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