The complete mitochondrial genome of Chaenostoma orientale (Brachyura, Macrophthalmidae) and its phylogenetic position

Abstract The systematics of thoracotreme crabs, particularly the superfamily Ocypodoidea, remain highly contentious because of profound incongruences between molecular phylogenies and traditional morphology. Within this group the family Macrophthalmidae is of special interest: its internal relationships are poorly resolved and its monophyly is questionable, with some taxa unexpectedly nesting within Varunidae. Resolving these uncertainties is severely hindered by a scarcity of genomic data. Here we address this gap by sequencing and characterising the first complete mitochondrial genome of Chaenostoma orientale Stimpson, 1858, a representative intertidal macrophthalmid. The 15 640-bp circular mitogenome encodes the typical 37 genes (13 PCGs, 22 tRNAs, 2 rRNAs) and exhibits a pronounced AT bias (65.6%; A 34.7%, T 30.9%, C 23.2%, G 11.2%), with positive AT-skew (0.0577) and negative GC-skew (−0.3507). Phylogenetic analyses incorporating 152 representative species across 147 genera and 51 families of Brachyura available on NCBI firmly place C. orientale within Macrophthalmidae and recover Macrophthalmidae + Varunidae as a strongly supported clade. All examined mitogenomes of these two families share an identical gene order (except a single trnL1 translocation in the symbiotic Asthenognathus inaequipes Stimpson, 1858), providing independent structural corroboration of their sister-group relationship. Relative to the ancestral crustacean arrangement, the C. orientale gene order matches that of confamilial taxa and arose via two consecutive tandem duplication-random loss events, a pathway conserved across most Macrophthalmidae and Varunidae. The shared synteny, together with accelerated rearrangements in symbiotic lineages, advances understanding of gene-order evolution and the molecular systematics of thoracotreme crabs.