Complete Mitochondrial Genomes of Two Water Mite Species in the Family Sperchontidae (Acari: Hydrachnidiae): Characterization and Phylogenetic Implications

TL;DR

This study sequenced the first complete mitochondrial genomes of two water mite species, revealing insights into their genetic structure and evolutionary relationships.

Contribution

The first complete mitogenomes of Sperchontidae water mites are reported, offering new data on gene rearrangements and phylogenetic relationships.

Findings

Both mitogenomes contain 37 genes with strong A+T bias and show purifying selection in protein-coding genes.

Gene rearrangements in Sperchontidae involve both tRNAs and PCGs, differing from patterns in other water mite families.

Phylogenetic analyses confirm close relationships within Hydrachnidiae and Trombidiae but leave higher-level relationships unresolved.

Abstract

Background: The family Sperchontidae Thor, 1900 is proposed as a transitional group between the “lower” and “higher” water mites (Subcohort Hydrachnidiae), and is important for understanding the evolutionary history of Hydrachnidiae. However, mitogenomic data are lacking. Methods: The first complete mitogenomes of Sperchontidae were sequenced from two species, Sperchon plumifer and Sperchon sp. Structural features were analyzed, gene rearrangements were compared with five published water mite mitogenomes, and phylogenetic relationships among 31 species within the order Trombidiformes were reconstructed. Results: Both mitogenomes contained the typical 37 genes and exhibited a strong A+T bias (73.1–73.6%), positive AT-skew, and negative GC-skew. Protein-coding genes (PCGs) were generally initiated with ATN/TTG codons and terminated with TAA/TAG or incomplete T–, with codon usage biased toward T/U-ending codons; all PCGs were under purifying selection (Ka/Ks < 1). Most tRNAs lacked canonical cloverleaf structures due to D- or T-arm loss. Gene rearrangements occurred in all examined water mite mitogenomes, with intrageneric rearrangements restricted to tRNAs in Hygrobatidae and Unionicolidae but involving both tRNAs and PCGs in Sperchontidae. Phylogenetic analyses using ML and BI (13 PCGs + 2 rRNAs) strongly supported a close relationship between Hydrachnidiae and Trombidiae (BS = 100%, PP = 1.00) and confirmed the three supercohorts in Trombidiformes (Eleutherengonides, Anystides, Eupodides), though relationships among them remained unresolved. Conclusions: This study reports the first two complete mitogenomes of Sperchontidae, providing preliminary insights into gene rearrangement patterns in water mites. The phylogenetic analyses based on mitochondrial genomes provide additional support for the consistency with traditional morphology at lower taxonomic levels, such as within genera and families, whereas relationships among supercohort-level taxa remain unstable and require additional data for further clarification.

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