Complete mitochondrial genome of Parasesarma affine (Brachyura: Sesarmidae): Gene rearrangements in Sesarmidae and phylogenetic analysis of the Brachyura

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Abstract

In this study, the complete mitochondrial DNA (mtDNA) sequence of the crab Parasesarma affine is determined, characterized and compared with other decapod crustaceans. The P. affine mitochondrial genome (mitogenome) is 15,638 bp in size, and contains 13 protein-coding genes (PCGs), 2 ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA) genes and a control region (CR). Then, 23 of the 37 genes are encoded by the heavy (+) strand while 14 are encoded by the light (−) strand. All PCGs are initiated by ATN codons and 4 of the 13 PCGs harbored the incomplete termination codon by T or TA. The CR with a high A + T% (82.33%) spans 678 bp. The nucleotide composition of the P. affine mitogenome is also biased toward A + T nucleotides (74.83%). The gene order of P. affine has a difference that trnI-trnQ turns into trnQ-trnI when compared with ancestor of Brachyura, which can also been seen in other Sesarmidae species. Phylogenetic tree based on nucleotide sequences of mitochondrial 13 PCGs from 49 decapod crustaceans and one outgroup using Bayesian inference (BI) and Maximum Likelihood (ML), which determined that P. affine belongs to Sesarmidae and Parasesarma is monophyletic.

Introduction

The mtDNA molecule of crabs generally ranges from 14 to 19 kilobases (Kb) in length and is a circular molecule with 37 genes. These genes include 13 PCGs: ATPase subunits 6 and 8 (atp6 and atp8), cytochrome coxidase [subunits1–3 (cox13), cytochrome b (cob)], NADH dehydrogenase subunits 1–6 and 4L (nad1nad6 and nad4L), rRNAs L and S (rrnL and rrnS), 22 tRNAs and a variable control region (CR) which contains some initiation sites for transcription and replication of the genome [[1], [2], [3]]. mtDNA forms an independent unit of genetic information which evolves separately from the nuclear genome. It is characterized by maternal inheritance, simple structure, a small genome size, conserved gene content and organization, high mutation rate, and accelerated rate of nucleotide substitution [[4], [5], [6]]. Thus, mtDNA has been widely used as an informative molecular marker for diverse evolutionary studies among species, including molecular evolution, phylogenetics, population genetics, and comparative and evolutionary genomics [1, [6], [7], [8], [9]]. Moreover, because of their rapid evolutionary rate and lack of genetic recombination, mtDNA can also provide important information on rearrangement laws and phylogenetic analysis [1].

Sesarmid crabs are considered as the key initial processors of the leaves of mangrove in the Indo-West-Pacific region which play an important ecological role in mangrove ecosystems [10, 11]. According to the previous research reports, the family of Sesarmidae has 34 genera in total [[12], [13], [14], [15]]. P. affine (Brachyura: Grapsoidea: Sesarmidae) is one of the most important mangrove sesarmid crabs [16]. P. affine typically inhabits mangrove swamps, preferring the upper intertidal region of estuaries, and living in small crevices and abandoned holes which made by other species [7]. However, to date, research about this species is very poor not only in morphology but also in molecular.

In this study, we successfully determined the complete mitochondrial genome sequence of P. affine, which can help us to understand the features of mtDNA of P. affine. Further, the available complete mitogenomes are used to provide a deeper understanding about the phylogenetic relationship of P. affine and related species. This information may provide insights into phylogenetic rearrangement and enable phylogenetic analysis within Brachyura.

Section snippets

DNA extraction

An individual specimen of P. affine was collected from Shanghai, China (121°54′38″E, 30°51′28″N). Total genomic DNA was extracted from the muscle tissue using the Aidlab Genomic DNA Extraction Kit following the manufacturer's instructions (Aidlab Biotech, Beijing, China). Specimen was incubated at 55 °C for 5 h to lyse completely and the total genomic DNA was eluted in 50 mL double-distill water (ddH2O). The quality of separated DNA was detected by electrophoresis and then the DNA was stored

Genome structure, organization and composition

The mitogenome of P. affine is a closed circular molecule 15,638 bp in size. The gene content is typical of other Decapoda mitochondrial genomes, including 13 PCGs (cox13, nad16, nad4L, cob, atp6 and atp8), 2 rRNA genes (rrnS and rrnL), 22 tRNA genes (one for each amino acid, two for Leucine and Serine), and a major non-coding region known as the CR (Fig. 1 & Table 1). Most genes (23 of 37) are encoded on the heavy (+) strand while the remaining 14 genes (4 of the 13 PCGs, 8 tRNAs and 2

Conclusion

In this study, we firstly sequenced the complete 15,638 bp mitogenome of P. affine, in which 37 genes (13 PCGs, 2 rRNA genes and 22 tRNA genes) and one control region are located as a typical of Brachyura mitogenome. With all PCGs are initiated by ATN codon, the cox1, cox2 and cob genes have incomplete stop codons consisting of just a T, and the other 10 PCGs stop with the canonical TAN or TA. The AT-skew (−0.022) and the GC-skew (−0.200) are both negative in the mitogenomes of P. affine which

Acknowledgements

This study was funded by the National Natural Science Foundation of China (grant number 31702014), and Doctoral Scientific Research Fund of Yancheng Teachers University to ZFW, and Open Fund of Jiangsu Key Laboratory for Bioresources of Saline Soils (grant number JKLBS2016007).

Conflict of interest

The authors declare there are no competing interests.

Ethical approval

All applicable international, national, and/or institutional guidelines for the care and use of animals were followed.

Authors' contributions

ZFW, HYG, XJS, QW and ZQW designed and conceived the experiment. YTT, ZFW, YZB and CYJ performed the data analysis and draft the manuscript. All authors read and approved the final manuscript.

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