Complete mitochondrial genomes of Sinonovacula rivularis and Novaculina chinensis and their phylogenetic relationships within family Pharidae

• Published in: ZooKeys Vol. 1232; no. 5; pp. 249 - 266
• Main Authors: Meng, Yiping, Lv, Liyuan, Lin, Zhihua, Zhang, Demin, Dong, Yinghui
• Format: Journal Article
• Language: English
• Published: Sofia Pensoft Publishers 19.03.2025
• Subjects: Analysis; Anopheles; Clams; Crex; divergent evolution; Domestic relations; family; Fresh water; freshwater; Genes; Genomes; Genomic analysis; Genomics; Identification and classification; Mitochondria; mitochondrial genome; monophyly; Morphology (Animals); Pharidae; Phylogenetics; Phylogeny; Positive selection; Ribosomal RNA; rRNA; salinity; Transfer RNA; Transposition; China
• ISSN: 1313-2989; 1313-2970; 1313-2970
• DOI: 10.3897/zookeys.1232.139844

Pharidae is one of the most ecologically and commercially significant families of marine Bivalvia; however, the taxonomy and phylogeny of Pharidae has been ongoing for quite some time and remains a contentious issue. Here, to resolve some problematical relationships among this family, the complete mitochondrial genomes (mitogenomes) of Sinonovacula rivularis (17,159 bp) and Novaculina chinensis (15,957 bp) were assembled, and a comparative mitochondrial genomic analysis was conducted. Both mitogenomes contain 12 protein-coding genes, 22 transfer RNA genes, and two ribosomal RNA genes. Among the published Pharidae mitogenomes, N. chinensis exhibited the smallest genome size but the highest AT content. The results of the phylogenetic trees confirmed the monophyly of the family Solenoidea, and indicated that N. chinensis and Sinonovacula ( S. constricta and S. rivularis ) were closely related in the family Pharidae. From the CREx analysis, we found that transposition and tandem duplication random losses (TDRLs) might have occurred between Pharidae and Solenidae. Moreover, positive selection was detected in nad5 of the foreground N. chinensis , and divergent evolution occurred at site 144 in the freshwater and marine lineages. Overall, our findings provide new molecular data on the phylogenetic and evolutionary relationships of Pharidae, and contribute to unraveling the salinity adaptations of Pharidae.