ArticleBiochemical genetics2026
Complete Mitochondrial Genome Analysis of Atypopenaeus stenodactylus and Its Phylogenetic Significance Within Penaeidae.
Article in Biochemical genetics, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.
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Abstract
Phylogenetic relationships within Penaeoidea, particularly among taxa of Penaeidae, have long remained controversial. To expand mitogenomic resources for Penaeidae and evaluate the phylogenetic position of Atypopenaeus stenodactylus (Stimpson, 1860), we sequenced and annotated its complete mitochondrial genome and analyzed gene composition, codon usage, tRNA secondary structure, selective pressure, intraspecific mitogenomic variation and phylogenetic relationships. The mitogenome of A. stenodactylus is a typical closed circular double-stranded DNA molecule of 15,933 bp, containing 13 protein-coding genes (PCGs), 22 tRNA genes, two rRNA genes and one D-loop region, with a pronounced A + T bias. Among the 22 tRNAs, all except trnS1, which lacks the DHU arm, formed typical cloverleaf structures, although some showed limited local variation. All 13 PCGs had Ka/Ks values below 1, indicating overall purifying selection; nad6 showed the highest Ka/Ks value, whereas cox1 had the lowest. Comparative analysis of the three available A. stenodactylus mitogenomes, PV007824, PX672768 and PV434778, revealed conserved gene order and low sequence divergence, with variation mainly concentrated in the non-coding D-loop region. Phylogenetic analysis based on 13 PCGs placed A. stenodactylus within Penaeidae and showed close relationships with Metapenaeus, Alcockpenaeopsis, Batepenaeopsis and Trachypenaeus, although traditional Penaeidae monophyly was not recovered. After inclusion of the three conspecific mitogenomes, PV007824, PX672768 and PV434778 clustered together, further supporting the stability of the inferred phylogenetic position. Overall, this study enriches mitogenomic resources for Penaeidae and provides new molecular evidence for resolving phylogenetic relationships within Penaeoidea.
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