Runze He, Benguo Yu, Bingmiao Gao, Shuanghuai Cheng
Research progress on rotifer mitochondrial genomes has been slow, with studies primarily focusing on the genus Brachionus and bdelloid rotifers—primarily due to the considerable challenges associated with rotifer clonal cultivation. Rotifers of the genus Asplanchna are predominantly carnivorous, and sequencing and analyzing of their mitochondrial genomes can offers valuable insights into their taxonomic position while laying a solid foundation for related phylogenetic investigations. In this study, the complete mitochondrial genome sequence of Asplanchna sp. was determined and analyzed using high-throughput sequencing. The mitochondrial genome of this Asplanchna representative consists of two circular chromosomes: mtDNA-I (16,916 bp) contains 4 protein-coding genes (PCGs: cob, atp6, nad2, nad1), 2 rRNA-coding genes (16S rRNA and 12S rRNA), and 18 tRNA-coding genes; mtDNA-II (17,982 bp) includes 8 PCGs (cox1, nad6, nad4l, nad4, nad5, cox2, cox3, nad3) and 9 tRNA-coding genes. Both mtDNA-I and mtDNA-II harbor a ~9.4 kb non-coding region (NCR) downstream of the tRNA-Lys gene, with an identical AT content of 66.85% and complete sequence identity between the two NCRs. Codon usage bias analysis revealed a distinct preference in the mitochondrial genome, with serine codon UCU being the most frequently used. Ka/Ks analysis indicated that mitochondrial PCGs are under purifying selection (negative selection) and highly conserved during evolution, consistent with their role as essential energy metabolic units. A maximum likelihood (ML) phylogenetic tree was reconstructed using 10 shared core PCGs from 26 closer related species. The results showed that Asplanchna is closely related to Brachionus but distantly related to bdelloid rotifers and acanthocephalans, which aligns with its morphological taxonomic status.