Mitochondrial genomes have become a powerful tool in exploring the molecular genetics and phylogenetic relationships of mollusks. At present, the taxonomic position and phylogenetic relationships of Modiolidae species remain poorly elucidated, particularly in the case of subfamilies. In this study, the mitochondrial genomes of two Modiolidae species, i.e., Modiolatus flavidus (Dunker, 1857) from Modiolinae and Botula cinnamomea (Gmelin, 1791) from Botulinae, were assembled and characterized for the first time, and their phylogenetic relationships and gene arrangements were analyzed. The mitochondrial genome of B. cinnamomea was 36,850 bp in length and composed of 36 functional genes, including 12 protein-coding genes (PCGs), 22 transfer RNAs (tRNAs), and 2 ribosomal RNAs (rRNAs). By contrast, the mitochondrial genome of M. flavidus was 18,013 bp in length and consisted of 37 functional genes, with an additional tRNAM compared to B. cinnamomea. All PCGs showed an A + T bias (50.0%–63.4%), positive GC skews (0.255–0.555), and negative AT skews (− 0.422– − 0.108) in nucleotide composition in both mitochondrial genomes. Phylogenetic analysis based on either mitochondrial genomes or gene markers (cox1 and 16S rRNA) revealed that M. flavidus did not cluster directly with other Modiolinae members but instead with representatives of Limnoperninae and Botulinae. The variations in functional gene arrangement further corroborated the relatively distant relationship between M. flavidus, which exhibited a unique PCGS order of cox1-nad3-cox3-atp6-nad4-nad6-nad2-cytb-nad4l-nad5-cox2-nad1, and other Modiolinae species which shared a conserved PCG arrangement: cox1-nad3-atp6-nad4-cox3-nad6-nad2-cytb-nad4l-nad5-cox2-nad1 (excluding atp8). Similarly, our results revealed that Leiosolenus failed to form a direct clade with Botula (the type genus of Botulinae), further suggesting ambiguous subfamilial placement of Leiosolenus. We therefore suggested that M. flavidus and the genus Leiosolenus have incorrect subfamilial placements, which warranted further taxonomic revision. Furthermore, we tentatively propose a new subfamilial classification scheme: M. flavidus is placed within another new subfamily designated Modiolatinae. This study supplements and enriches molecular genetic data to advance taxonomic revision and phylogenetic reconstruction in Mytilidae.

Comparative mitochondrial genome analysis undermine the established taxonomic status of Modiolatus flavidus

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发表日期：

2026年7月28日

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Xiaoyu Qin,
Chenxia Zuo,
Fei Teng,
Xiaoran Qiu,
Zhen Zhang

摘要

Mitochondrial genomes have become a powerful tool in exploring the molecular genetics and phylogenetic relationships of mollusks. At present, the taxonomic position and phylogenetic relationships of Modiolidae species remain poorly elucidated, particularly in the case of subfamilies. In this study, the mitochondrial genomes of two Modiolidae species, i.e., Modiolatus flavidus (Dunker, 1857) from Modiolinae and Botula cinnamomea (Gmelin, 1791) from Botulinae, were assembled and characterized for the first time, and their phylogenetic relationships and gene arrangements were analyzed. The mitochondrial genome of B. cinnamomea was 36,850 bp in length and composed of 36 functional genes, including 12 protein-coding genes (PCGs), 22 transfer RNAs (tRNAs), and 2 ribosomal RNAs (rRNAs). By contrast, the mitochondrial genome of M. flavidus was 18,013 bp in length and consisted of 37 functional genes, with an additional tRNA^M compared to B. cinnamomea. All PCGs showed an A + T bias (50.0%–63.4%), positive GC skews (0.255–0.555), and negative AT skews (− 0.422– − 0.108) in nucleotide composition in both mitochondrial genomes. Phylogenetic analysis based on either mitochondrial genomes or gene markers (cox1 and 16S rRNA) revealed that M. flavidus did not cluster directly with other Modiolinae members but instead with representatives of Limnoperninae and Botulinae. The variations in functional gene arrangement further corroborated the relatively distant relationship between M. flavidus, which exhibited a unique PCGS order of cox1-nad3-cox3-atp6-nad4-nad6-nad2-cytb-nad4l-nad5-cox2-nad1, and other Modiolinae species which shared a conserved PCG arrangement: cox1-nad3-atp6-nad4-cox3-nad6-nad2-cytb-nad4l-nad5-cox2-nad1 (excluding atp8). Similarly, our results revealed that Leiosolenus failed to form a direct clade with Botula (the type genus of Botulinae), further suggesting ambiguous subfamilial placement of Leiosolenus. We therefore suggested that M. flavidus and the genus Leiosolenus have incorrect subfamilial placements, which warranted further taxonomic revision. Furthermore, we tentatively propose a new subfamilial classification scheme: M. flavidus is placed within another new subfamily designated Modiolatinae. This study supplements and enriches molecular genetic data to advance taxonomic revision and phylogenetic reconstruction in Mytilidae.