Department of Marine Organism Taxonomy & Phylogeny, Qingdao Key Laboratory of Marine Biodiversity and Conservation, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China.
Department of Marine Organism Taxonomy & Phylogeny, Qingdao Key Laboratory of Marine Biodiversity and Conservation, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; College of Life Sciences, Qingdao Agricultural University, Qingdao 266109, China.
Int J Biol Macromol. 2023 Sep 30;249:126081. doi: 10.1016/j.ijbiomac.2023.126081. Epub 2023 Aug 1.
Taxonomy and phylogenetic relationships within the family Mactridae have remained debatable because of the plasticity of morphological characteristics and the lack of accurate molecular data, thereby resulting in abundant synonyms and taxa rearrangements. Mitochondrial genomes (mitogenomes) have been widely used as powerful tools to reconstruct phylogenies of various groups of mollusks; however, they have not been used for studying the phylogeny of mactrids specifically. In the present study, mitogenomes of seven Mactridae species, namely Mactra chinensis, Mactra cygnus, Mactra quadrangularis, Mactra cumingii, Mactrinula dolabrata, Raeta pulchella, and Raeta sp., were sequenced by Illumina high-throughput sequencing, and a comparative mitochondrial genomic analysis was conducted. The newly sequenced mitogenomes were double-stranded circular molecules, with all functional genes encoded on the heavy strand. All the new mactrid mitogenomes had two rRNA genes (12S and 16S), 13 protein-coding genes (PCGs) (atp6, cox1, cox2, cox3, cytb, nad1, nad2, nad3, nad4, nad4l, nad5, nad6, and atp8), and 22 tRNAs. The mitogenomes showed considerable variation in AT content, GC skew, and AT skew. The results of the phylogenetic analysis confirmed monophyly of the family Mactridae and suggested that genera Mactrinula, Spisula, Rangia, and Mulinia should not be placed under subfamily Mactrinae. Our results supported that potential cryptic species existed in Mactra antiquata. We also proposed subfamily Kymatoxinae should belong to the family Mactridae rather than Anatinellidae and Mactra alta in China should be Mactra cygnus. Additionally, conservation in functional gene arrangement was found in genera Mactra, Raeta, and Lutraria. But gene orders in S. sachalinensis and S. solida were quite different, questioning their congeneric relationship. Our results further suggested that the taxonomy within the family Mactridae requires an integrative revision.
在中国，科贝类的分类和系统发育关系一直存在争议，因为形态特征的可塑性和缺乏准确的分子数据，导致了大量的同义词和分类群的重新排列。线粒体基因组（mitogenomes）已被广泛用作重建各种软体动物群体系统发育的有力工具；然而，它们尚未被用于专门研究马珂贝类的系统发育。在本研究中，通过 Illumina 高通量测序对 7 种马珂贝类物种（中华马珂蛤、缢蛏、四角蛤蜊、长足马珂蛤、秀丽巴非蛤、美丽凹线蛤和未定种）的线粒体基因组进行了测序，并进行了比较线粒体基因组分析。新测序的线粒体基因组为双链环状分子，所有功能基因均编码在重链上。所有新的马珂贝类线粒体基因组都有两个 rRNA 基因（12S 和 16S）、13 个蛋白质编码基因（PCGs）（atp6、cox1、cox2、cox3、cytb、nad1、nad2、nad3、nad4、nad4l、nad5、nad6 和 atp8）和 22 个 tRNA。线粒体基因组在 AT 含量、GC 倾斜和 AT 倾斜方面表现出相当大的变异。系统发育分析的结果证实了马珂贝类科的单系性，并表明 Mactrinula、Spisula、Rangia 和 Mulinia 属不应归入 Mactrinae 亚科。我们的研究结果支持 Mactra antiquata 中存在潜在的隐种。我们还提出，Kymatoxinae 亚科应属于马珂贝类科，而中国的 Mactra alta 应为 Mactra cygnus。此外，在 Mactra、Raeta 和 Lutraria 属中发现了功能基因排列的保守性。但 S. sachalinensis 和 S. solida 的基因顺序差异很大，质疑它们的同属关系。我们的研究结果进一步表明，马珂贝类科的分类需要综合修订。
