Decoding the Mitochondrial Genome of the Tiger Shrimp: Comparative Genomics and Phylogenetic Placement Within...

Freshwater shrimps of the family Atyidae, particularly the hyperdiverse genus Caridina, are keystone decomposers in tropical aquatic ecosystems and valuable aquaculture resources. However, their evolutionary relationships remain unresolved due to conflicting morphological and molecular evidence. Here, we sequenced and characterized the complete mitochondrial genome of Caridina mariae (Tiger Shrimp), aiming to (1) elucidate its genomic architecture, and (2) reconstruct a robust phylogeny of Caridea using 155 decapod species to address long-standing taxonomic uncertainties.

Muscle tissue from wild-caught C. mariae (voucher ID: KIZ-2023-001, Guangdong, China) was subjected to Illumina NovaSeq 6000 sequencing (150 bp paired-end). The mitogenome was assembled using MITObim v1.9, annotated via MITOS2, and validated by PCR. Phylogenetic analyses employed 13 protein-coding genes under Bayesian inference (MrBayes v3.2.7; 10⁶ generations, ESS > 200) and maximum likelihood (RAxML v8.2.12; 1000 bootstraps), with Harpiosquilla harpax as the outgroup. The best-fit substitution model (MtZoa + F + I + G4) was selected via jModelTest v2.1.10.

The 15,581 bp circular mitogenome encodes 37 genes (13 PCGs, 22 tRNAs, and 2 rRNAs) and an A + T-rich control region (86.7%). Notably, trnS1 lacks the dihydrouracil arm-a rare structural deviation in Decapoda. The 13 PCGs exhibit moderate nucleotide skew (AT = 0.030; GC = -0.214), while nad5, nad4, and nad6 show significant GC-skew. Phylogenomic analyses strongly support (PP = 1.0; BS = 95) a novel sister-group relationship between Halocaridinidae and Typhlatyinae, contradicting prior morphology-based classifications. The monophyly of Penaeoidea, Astacidea, and Caridea was confirmed, but Eryonoidea and Crangonoidea formed an unexpected clade.

This study provides the first mitogenomic framework for C. mariae, revealing both conserved features (e.g., PCG content) and lineage-specific innovations (e.g., tRNA truncation). The resolved phylogeny challenges traditional Caridea classifications and highlights convergent adaptation in freshwater lineages. These findings offer molecular tools for the conservation prioritization of threatened Caridina species and underscore the utility of mitogenomics in decapod systematics.