The complete mitochondrial genome and phylogenetic analysis of Amusium pleuronectes

Abstract

Amusium pleuronectes, commonly known as the Asian moon scallop, is widely distributed in Indo-Pacific coasts. In this study, the complete mitogenome sequence of A. pleuronectes (18,044 bp) is reported, which represents the first mitogenome from the Amusium genus. This mitogenome contains 13 protein-coding genes, 2 rRNAs, and 22 tRNA genes, showing similar mitogenome features for most marine bivalves. Phylogenetic analysis reveals that within the family Pectinidae, the genus Amusium is closely related to the genus Argopecten. The mitogenome of A. pleuronectes provides a valuable resource for further advancing the understanding of bivalve phylogeny and evolution.

Keywords:

• Amusium pleuronectes
• mitochondrial genome
• phylogenetic analysis

Amusium pleuronectes, commonly known as the Asian moon scallop, is widely distributed in Indo-Pacific coastal areas (Minchin 2003) and characterized by beautiful two-colored shells. Except for high economic value, the Asian moon scallop is often used as a biological monitor to evaluate the impact of human activities on the marine environment (Siriprom and Limsuwan 2009). However, genetic information for this species remains scarce. Recently, complete mitogenome has been considered as an effective tool for phylogeny and phylogeography studies (Curole and Kocher 1999; Saccone et al. 1999). In this study, we report the sequencing and assembly of the complete mitogenome of A. pleuronectes, which is the first mitogenome of the genus Amusium.

The example of A. pleuronectes was derived from Tung Ping Chau Bay near Tung Chung village (Guangdong province, China, 22.4907°N, 114.5801°E) at a depth of 7–8 m. All soft tissues were preserved in liquid nitrogen after sampling. Total DNA was extracted using the phenol/chloroform/isoamyl alcohol method (Sambrook et al. 1989). The DNA sample was deposited at the Key Laboratory of Marine Genetics and Breeding (Ministry of Education), Ocean University of China (Specimen code: OUC-MGB-2018-AP-08). Whole genomic sequencing of the individual sample was performed using the Illumina NovaSeq 6000 sequencing platform. The mitogenome of A. pleuronectes was de novo assembled using NOVOPlasty (Dierckxsens et al. 2017), gene information of which was retrieved by the MITOS software (Bernt et al. 2013).

The complete circular mitogenome of A. pleuronectes was 18,044 bp in length. Thirteen protein-coding genes (PCGs), 2 ribosomal RNA genes, and 21 transfer RNA genes were annotated. The 13 conserved PCGs were cytochrome oxidase subunit (I, II, and III), NADH dehydrogenase subunit (1, 2, 3, 4, 5, 6, and 4 L), and ATP synthase subunit (6, and 8), which was similar to the reported mitochondrial genomes of most marine bivalve mollusks (Liu et al. 2019; Ma et al. 2019; Liu et al. 2020). The base composition of A. pleuronectes was A = 22.22%, T = 38.60%, G = 25.55%, and C = 13.63%. The overall AT content (60.82%) was higher than the GC content (39.18%). The small subunit ribosomal RNA (12S rRNA) and large subunit ribosomal RNA (16S rRNA) were annotated with sizes of 968 bp and 1,420 bp, respectively. The length of 22 tRNAs ranged from 63 bp to 72 bp. The whole mitogenome sequence has been deposited in GenBank under the accession number of MT419374.

Previous studies of the phylogeny of the family Pectinidae were mostly based on the sequence information of few genes (Serb 2016; Smedley et al. 2019). In this study, a mitogenome-level phylogenetic tree was constructed based on all the available scallop mitogenomes, including A. pleuronectes and 11 other scallop species (from six genera of Pectinidae), as well as two outgroup species (Figure 1). The phylogenetic tree was constructed using the neighbor-joining (NJ) algorithm with 1000 bootstrap trials. The phylogeny tree indicated that the genus Amusium represented by A. pleuronectes was closely related to the genus Argopecten as reported by previous studies (Serb 2016; Smedley et al. 2019). The A. pleuronectes mitogenome provides a valuable resource for further advancing our understanding of bivalve phylogeny and evolution.

Figure 1. The phylogenetic tree of A. pleuronectes and 13 other bivalves based on complete mitochondrial genomes. The accession numbers of downloaded sequences are as follows: Argopecten irradians concentricus (KT161259.1), Argopecten irradians irradians (NC_012977.1), Argopecten irradians (NC_009687.1), Argopecten venteicosus (KT161261.1), Argopecten purpuratus (NC_027943.1), Crassadoma gigantea (MH016739.1), Azumapecten farreri (NC_012138.1), Mizuhopecten yessoensis (NC_009081.1), Mimachlamys nobilis (NC_011608.1), Mimachlamys senatoria (NC_022416.1), Placopecten magellanicus (NC_007234.1), Crassostrea gigas (NC_001276.1), and Limnoperna fortunei (NC_028706.1).

Disclosure statement

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

Data availability statement

The data that support the findings of this study are openly available in GeneBank at [https://www.ncbi.nlm.nih.gov/nuccore/MT419374.1/], reference number [Accession number: MT419374].

Additional information

Funding

We acknowledge the grant support from National Natural Science Foundation of China [U1706203] and Fundamental Research Funds for the Central Universities [201841001].