The complete mitochondrial genome of Parasesarma pictum (Brachyura: Grapsoidea: Sesarmidae) and comparison with other Brachyuran crabs

Abstract

Mitochondrial DNA (mtDNA) is an extrachromosomal genome which can provide important information for evolution and phylogenetic analysis. In this study, we assembled a complete mitogenome of a crab Parasesarma pictum (Brachyura: Grapsoidea: Sesarmidae) from next generation sequencing reads at the first time. P. pictum is a mudflat crab, belonging to the Sesarmidae family (subfamily Sesarminae), which is perched on East Asia. The 15,716 bp mitogenome covers 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), 2 ribosomal RNA genes (rRNAs), and one control region (CR). The control region spanns 420 bp. The genome composition was highly A+T biased 75.60% and showed negative AT-skew (-0.03) and negative GC-skew (-0.47). Compared with the ancestor of Brachyura, the gene order of Sesarmidae has several differences and the gene order of P. pictum is typical for mitogenomes of Sesarmidae. Phylogenetic tree based on nucleotide sequences of mitochondrial 13 PCGs using BI and ML determined that P. pictum has a sister group relationship with Parasesarma tripectinis and belongs to Sesarmidae.

Gene Arrangement and Adaptive Evolution in the Mitochondrial Genomes of Terrestrial Sesarmid Crabs Geosesarma faustum and Geosesarma penangensis

“…This result confirmed that Geosesarma belongs to Grapsoidea, Sesarmidae, congruent with the morphological assignments (Ng et al, 2008;Ng, 2017;Ng and Wowor, 2019;Shy and Ng, 2019). All Sesarmidae species cluster into a clade consisting of two sister groups, which was consistent with previous findings (Wang et al, 2019;Li et al, 2020;Lu et al, 2020; Sesarmidae species are most closely related to Gecacinidae, constituting part of the Grapsoidea group, which is in accordance with the results of the studies by Chen et al (2019), Wang et al (2019), Lu et al (2020), and. The mitochondrial phylogenomic analyses including our dataset have shown the divergent phylogenetic status of Grapsidae and Dotilidae (Wang et al, 2019;Li et al, 2020;.…”

“…While cox1, cox2, atp8, cox3, nad4, and nad4L initiated by the standard ATG codon, atp6, nad3, nad5, nad6, cob, and nad1 (G. penangensis) used ATA, and nad6 (G. faustum) used GTG. Most PCGs, i.e., atp8, atp6, cox3, nad3, nad5, nad4, nad6, nad1, and cox1 (G. penangensis), were terminated by TAA, whereas nad2 used TAG as stop codon, and cox2, cob, and cox1 (G. faustum) terminated by a single T. These incomplete stop codons have been observed in many brachyuran mitogenomes (Wang et al, 2019; and are thought to be completed by posttranscriptional polyadenylation (Ojala et al, 1981).…”

Complete mitochondrial genome and phylogenetic analysis of Uca Borealis

“…From the phylogenetic tree, we found U. borealis and Tubuca arcuata are clustered in one branch with high nodal support value (BI posterior probabilities [PP] ¼ 100, Figure 1). In addition, the relationship among Sesarmidae, Xenograpsidae, Grapsidae, Ocypodidae, Varunidae, Potamidae, and Bythograeidae is also identified and is largely consistent with previous researches (Shen et al 2013;Wang et al 2018aWang et al , 2018b.…”

Evidence of Extensive Intraspecific Noncoding Reshuffling in a 169-kb Mitochondrial Genome of a Basidiomycetous Fungus

“…The overlapping start and stop codons of nad genes have been observed in not only fungi but also animals (Franco et al. 2017; Wang et al. 2019), presumably because of the mRNA transcription of these genes has remained coupled across independent lineages.…”