The complete mitochondrial genome of the giant clam, Tridacna maxima (Tridacnidae Tridacna)

Abstract

In this study, we present the first complete mitochondrial genome sequence of the giant clam Tridacna maxima. The total length of the mitogenome is 18,632 bp. It contains the typical mitochondrial genomic structure, including 13 protein-coding genes, 23 transfer RNA genes, 2 ribosomal RNA genes, and 1 control region (D-loop). Mitogenome base composition is biased toward A + T content, at 61.54%. A phylogenetic tree based on complete mitogenome sequences revealed that, within the genus Tridacna, T. maxima is closely related to T. squamosa and T. derasa.

Keywords:

• Tridacna maxima
• mitochondrial genome
• phylogenetic relationship

Members of the family Tridacnidae (giant clams) have medium to very large bivalves. Among them, Tridacna gigas is the largest externally-shelled living mollusc (Rosewater 1965). Giant clams are not only important to coral reef ecosystems, but also constitute a significant food source in Asia and the South Pacific, and are in demand for the shell and aquarium trade (Keys and Healy 1999). In this study, we sequenced the complete mitochondrial genome of T. maxima to further the study of the taxonomy and phylogenetic relationships of Tridacnidae by increasing the amount of available molecular data.

The specimen was collected from Sanya, Hainan province, China (N109.51, E18.21) by a local fisherman, and stored in the Marine Biodiversity Collection of the South China Sea at the Chinese Academy of Sciences in Guangzhou, China. The total genomic DNA was extracted following the modified CTAB DNA extraction protocol (Attitalla 2011), followed by library preps and pair-end sequencing (2 × 150 bp) with HiSeq (Illumina, San Diego, CA). Approximately 5855 Mb of raw data and 5074 Mb of clean data were obtained, and de novo assembled by the SOAP de novo software (Zhao et al. 2011) with an average of approximately 300× coverage.

The mitogenome of T. maxima is 18,632 bp in length (GenBank accession number MK105973). It is shorter than those of T. derasa (20,760 bp) (Haitao et al. 2018), T. squamosa (20,930 bp) (Gan et al. 2016), and H. hippopus (22,463 bp) (Ma et al. 2018), making it the smallest mitogenome of Tridacnidae reported to date, mainly due to the difference in the length of the control region. It contains 13 protein-coding genes (PCGs), 23 transfer RNA genes (tRNAs), 2 ribosomal RNA (12S rRNA and 16S rRNA) genes, and a non-coding control region (D-loop). The mitogenome base composition of T. maxima is biased toward A + T content at 61.54% (26.49% A, 35.05% T, 15.85% C, 22.60% G), similar to the mitochondrial genomes of T. derasa, T. squamosa, and H. hippopus. The 13 identified PCGs vary in length from 117 to 1656 bp. NAD1, NAD3, NAD4, and NAD5 initiate with ATA as the start codon; while ATP6, COXII, NAD6 and Cytb begin with TTG; ND4L, ND2 and ATP8 begin with ATG; COXIII with ATC; and COXI with GTG. Eleven of the PCGs contain a complete (TAA) stop codon and the remaining two genes end with TAG. The 12S rRNA gene is located between tRNA-Leu and ND6, and is 896 bp long, while the 16S rRNA gene is located between tRNA-Ile and ND1, with a length of 1208 bp. A 1418 bp control region (D-loop) was located between tRNA-Arg and COII, with an A + T content of 61.71%.

A neighbor-joining phylogenetic tree of T. maxima and four other closely related species was constructed with the complete mitochondrial genomes using MEGA6 (Tamura et al. 2013) (Figure 1). As expected, the result showed that, within the genus Tridacna, T. maxima is closely related to T. squamosa and T. derasa.

Figure 1. Neighbor-joining phylogenetic tree of Tridacna maxima and four other closely related species based on the complete mitochondrial genomes. GenBank accession numbers: Cerastoderma edule (MF374632); Hippopus hippopus (MG722975); Tridacna squamosa (KP205428); and Tridacna derasa (MG755811).

Disclosure statement

No potential conflict of interest was reported by the authors.

Additional information

Funding

This work was supported by the National Key R&D Program of China [2018YFC1406505]; the National Science Foundation of China [31702340]; Guangdong Natural Science Foundation [2017A030310442]; the Strategic Pilot Project of the Chinese Academy of Sciences [XDA13020202, XDA13020403]; and the Science and Technology Planning Project of Guangdong Province, China [2017B030314052].