Sequencing and analysis of the complete mitochondrial genome of Hippopus porcellanus

Abstract

In this study, the complete mitochondrial genome of Hippopus porcellanus was reported. The whole mitochondrial genome was 21,565bp in length with a 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 was biased toward A + T content, at 60.3%. A phylogenetic tree based on complete mitogenome sequences revealed that, H. porcellanus is closely related to H. hippopus, both of which belong to the genus Hippopus.

Keywords:

• Hippopus porcellanus
• Mitochondrial genome
• phylogenetic relationship

Giant clams (Bivalvia: Tridacnidae), the largest bivalve mollusks in the world, inhabit the shallow coral reefs of the Indo-Pacific region. 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). These clams belong to the subfamily Tridacninae, which has two genera namely: Hippopus and Tridacna (Othman et al. 2010). Two species belong to Genus Hippopus: Hippopus hippopus Linnaeus 1758 and Hippopus porcellanus Rosewater 1982. In this study, we sequenced the complete mitochondrial genome of H. porcellanus to further investigate 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 Tropical Marine Biodiversity Collections of South China Sea (TMBC), Chinese Academy of Sciences, Guangzhou, China (specimen accession number: TMBC030713). The total genomic DNA was extracted following the modified CTAB DNA extraction protocol (Attitalla 2011), and followed by library preps and pair-end sequenced (2 × 150 bp) with HiSeq (Illumina, San Diego, CA). Approximately 5,987 Mb of raw data and 5,216 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 310× coverage.

The mitogenome of H. porcellanus was 21,565bp in length (GenBank accession number MT755622), containing 13 protein-coding genes (PCGs), 23 transfer RNA genes (tRNAs), two ribosomal RNA (12S rRNA and 16S rRNA) genes and a non-coding control region (D-loop). The mitogenome base composition of H. porcellanus was biased toward A + T content at 60.3% (26.4% A, 33.9% T, 15.0% C, 24.6% G). The 13 identified PCGs vary in length from 114 to 1,677 bp. COI, ATP8, ND5, ND2, ND4L, ND1 and ATP6 initiated with ATG as the start codon, while ND3 and COIII begin with TTG, ND4 begin with ATT, COII with ATA, ND6 with GTG and Cytb with ATC. Three types of stop codons were TAA (ND4, COII, COIII, ND4L, ND6, Cytb), TAG (COI, ATP8, ND5, ATP6, ND3, ND1) and TAT (ND2). The lengths of the 23 tRNA genes ranged from 58 to 74 bp, and all of the tRNA genes contained typical secondary structure. The 12S rRNA gene was located between tRNA-Leu and tRNA-Second Leu, and was 922 bp long, while the 16S rRNA gene was located between tRNA-Ile and ND1, with a length of 1,269 bp. A 2,605 bp control region (D-loop) was located between tRNA-Met and COII, with an A + T content of 54.7%.

A neighbor-joining phylogenetic tree of H. porcellanus with five other closely related species was constructed with the complete mitochondrial genomes using MEGA6 (Tamura et al. 2013) (Figure 1). The result suggested that, H. porcellanus is closely related to H. hippopus, both of which belong to the genus Hippopus.

Figure 1. Neighbor-joining phylogenetic tree of Hippopus porcellanus and five other closely related species based on the complete mitochondrial genomes.

Disclosure statement

No potential conflict of interest was reported by the author(s).

Data availability statement

The genome sequence data that support the findings of this study are openly available in GenBank of NCBI at (https://www.ncbi.nlm.nih.gov/) under the accession no. MT755622. The associated BioProject, SRA, and Bio-Sample numbers are PRJNA704757, SRR13827840, and SAMN18054235, respectively.

Additional information

Funding

This work was supported by the National Science Foundation of China [31702340; 31872566]; Strategic Pilot Project of the Chinese Academy of Sciences [XDA13020202; XDA13020403]; Key Special Project for Introduced Talents Team of Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou) [GML2019ZD0404]; National Key R&D Program of China [2018YFC1406505; 2020YFD0901100]; Science and Technology Program of Guangzhou, China [No.201804020073]; the Network Service Local Plan STS of the Chinese Academy of Sciences [KFJ-STS-QYZD-158]; Institution of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences [ISEE2018PY01; ISEE2018ZD02; ISEE2018PY03]; the Open Foundation of the State Key Laboratory of Loess and Quaternary Geology [SKLLQG1813; SKLLQG1918]; the China Agricultural Shellfish Industry Technology System Project [CARS-49] and the Science and Technology Planning Project of Guangdong Province, China [2017B030314052].