The complete mitochondrial genome of Thalamita sima (Decapoda: Portunidae)

Abstract

Thalamita is one of most important genera of Portunidae. However, the systemically classification and taxonomic studies have so far been limited. In this study, we report the complete mitochondrial genome sequence of T. sima. The mitogenome has 15,831 base pairs (71.7% A + T content) and made up of total of 37 genes (13 protein-coding, 22 transfer RNAs and 2 ribosomal RNAs), and a putative control region. This study was the second available complete mitogenomes of Thalamita and will provide useful genetic information for future phylogenetic and taxonomic classification of Thalamita.

Keywords:

• Mitochondrial genome
• Thalamita sima
• Decapoda

Thalamita is one of the most important genera of Portunidae, which contains the most diverse species after Portunus among the swimming crabs (Portunidae) (Tan et al. 2016). There are about 90 species belonging to Thalamita, however, systemically classifications on them have not been done and misidentifications have been occasionally reported (Spiridonov 2017). In spite of its economic and ecological significance, adequate genetic information about the genus is still missing (Tan et al. 2016; Saher et al. 2018). Here, we report the second complete mitochondrial genome sequence of genus Thalamita, which will provide a better insight into phylogenetic assessment and taxonomic classification.

A tissue sample of T. sima was collected from GuangXi province, China (Beihai, 21.445126N, 109.250713 E), and the whole body specimen (#GQ0264) were deposited at Marine biological Herbarium, Guangxi Institute of Oceanology, Beihai, China. The total genomic DNA was extracted from the muscle of the specimens using an SQ Tissue DNA Kit (OMEGA, Guangzhou, China) following the manufacturer’s protocol. DNA libraries (350 bp insert) were constructed with the TruSeq NanoTM kit (Illumina, San Diego, CA, USA) and were sequenced (2 × 150 bp paired-end) using HiSeq platform at Novogene Company, China. Mitogenome assembly was performed by MITObim (Hahn et al. 2013). The complete mitogenome of T. crenata (GenBank accession number: NC_024438) was chosen as the initial reference sequence for MITObim assembly. Gene annotation was performed by MITOS (Bernt et al. 2013).

The complete mitogenome of T. sima was 15,831 bp in length (GenBank accession number: MG840650), and containing the typical set of 13 protein-coding, 22 tRNA and 2 rRNA genes, and a putative control region. The overall base composition of the mitogenome was estimated to be A 35.3%, T 36.4%, C 17.6% and G 10.7%, with a high A + T content of 71.7%, which is similar, but slightly higher than Orithyia sinica (69.5%) (Zhong et al. 2018). The gene order in T. sima is highly similar to that found in T. crenata, which indicated close relationship between T. sima and T. crenata. The result of phylogenetic tree of 11 species (including other 10 species from family Portunidae in NCBI) also supported the close relationship between T. sima and T. crenata (Figure 1), as they shared the same clade with the highest bootstrap value. The complete mitochondrial genome sequence of T. sima was the second sequenced mitogenomes within the genus Thalamita, which will contribute to further comparative and evolutionary mitogenome studies of the genus Thalamita, and related genera.

Figure 1. Phylogenetic tree of 11 species in family Portunidae. The complete mitogenomes are downloaded from GenBank and the phylogenic tree is constructed by maximum-likelihood method with 100 bootstrap replicates. The bootstrap values were labelled at each branch nodes. The gene's accession number for tree construction is listed as follows: Portunus sanguinolentus (NC_028225), Portunus pelagicus (NC_026209), Portunus trituberculatus (NC_005037), Callinectes sapidus (NC_006281), Monomia gladiator (NC_037173), Scylla olivacea (NC_012569), Scylla serrata (NC_012565), Scylla tranquebarica (NC_012567), Scylla paramamosain (NC_012572) and Thalamita crenata (NC_024438).

Disclosure statement

The authors declare that they have no conflict of interest.

Additional information

Funding

This work was financially supported by Scientific Research and Technology Development Program of Guangxi [Grant No. AB16380105], Science and Technology Major Project of Guangxi [Grant No. AA17204069 & AA17204044] and the Fundamental Research Funds for Guangxi Academy of Sciences [Grant No. 2017YJJ23001].