Brachyuran crabs comprise the most species-rich clades among extant Decapoda and are divided into several major superfamilies. However, the phylogeny of Brachyuran remains controversial, comprehensive analysis of the overall phylogeny is still lacking. Complete mitochondrial genome (mitogenome) can indicate phylogenetic relationships, as well as useful information for gene rearrangement mechanisms and molecular evolution. In this study, we firstly sequenced and annotated the complete mitogenome of Macrophthalmus abbreviatus (Brachyura; Macrophthalmidae). The mitogenome length of M. abbreviatus is 16,322 bp, containing the entire set of 37 genes and a control region typically observed in Brachyuran mitogenomes. The genome composition of M. abbreviatus was highly A+T biased 76.3% showing positive AT-skew (0.033) and negative GC-skew (− 0.351). In M. abbreviatus mitogenome, most tRNA genes were folded into the clover-leaf secondary structure except trnH, trnS1 and trnC, which was similar to the other species in Macrophthalmidae. Phylogenetic analysis showed that all families form a monophyletic, and Varunidae and Macrophthalmidae clustered into a monophyletic clade as sister groups. Comparative analyses of rearrangement among Brachyura revealed that Varunidae (Grapsoidea) and Macrophthalmidae (Ocypodoidea) had the same gene order, which reinforced the result of phylogeny. The combined results of two aspects revealed that the polyphyly of Ocypodoidea and Grapsoidea were well supported. In general, the results obtained in this research will contribute to further studies on molecular based for the classification and gene rearrangements of Macrophthalmidae or even Brachyura.

Brachyuran 蟹是现存十足目中物种最丰富的进化枝，分为几个主要的超科。然而，Brachyuran的系统发育仍然存在争议，仍然缺乏对整体系统发育的综合分析。完整的线粒体基因组 (mitogenome) 可以指示系统发育关系，以及基因重排机制和分子进化的有用信息。在这项研究中，我们首先对Macrophthalmus abbreviatus (Brachyura; Macrophthalmidae)的完整丝裂原组进行了测序和注释。M. abbreviatus的有丝分裂基因组长度为 16,322 bp，包含整套 37 个基因和一个通常在 Brachyuran 有丝分裂基因组中观察到的控制区域。M. abbreviatus的基因组组成高度 A+T 偏差为 76.3%，显示正 AT 偏斜 (0.033) 和负 GC 偏斜 (− 0.351)。在M. abbreviatus mitogenome 中，除trnH、trnS1和trnC外，大多数 tRNA 基因都折叠到三叶草二级结构中, 这与 Macrophthalmidae 中的其他物种相似。系统发育分析表明，所有科都形成一个单系群，而疣猴科和巨眼蜥科作为姐妹群聚成一个单系进化枝。Brachyura 之间重排的比较分析表明，Varunidae (Grapsoidea) 和 Macrophthalmidae (Ocypodoidea) 具有相同的基因顺序，这加强了系统发育的结果。两方面的综合结果表明，Ocypodoidea 和 Grapsoidea 的多系得到了很好的支持。总的来说，本研究获得的结果将有助于进一步基于分子的研究，用于大眼科甚至短尾目的分类和基因重排。