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. 2019 Dec 12;5(1):140–141. doi: 10.1080/23802359.2019.1698352

The complete mitochondrial genome and phylogenetic analysis of the dwarf surf clam Mulinia lateralis

Jing Liu a,*, Qifan Zeng a,b,*, Hao Wang a, Mingxuan Teng a, Ximing Guo c, Zhenmin Bao a,d, Shi Wang a,b,✉
PMCID: PMC7748403  PMID: 33366458

Abstract

Mulinia lateralis (Say, 1822) is a species of the bivalve family Mactridae and represents a promising model species for molluscan research. In this study, the complete mitochondrial genome (mitogenome) of M. lateralis was sequenced and assembled for the first time. The 21,668 bp mitogenome contained 13 protein-coding genes, 2 rRNAs, 22 tRNA genes, and an AT-rich region. The overall AT content (69.56%) was higher than GC content (30.44%). Phylogenetic analysis supported that M. lateralis belongs to the family Mactridae. The mitochondrial genome of M. lateralis provides a valuable resource for further understanding the phylogeny of the family Mactridae and for functional studies of molluscan mitochondrial genes.

Keywords: Mulinia lateralis, Bivalvia, mitochondrial genome, phylogenetic analysis

Mulinia lateralis, commonly known as the dwarf surf clam or coot clam, is a small bivalve mollusk that naturally distributes along the coast of Western Atlantic (Walker and Tenore 1984). Due to its small body size (10–20 mm), short generation time (2–3 months) and ease of culture and maintenance, M. lateralis has long been considered as a promising model organism for genetic and transgenic studies in mollusks (Calabrese 1969; Guo and Allen 1994; Lu et al. 1996). Despite its value in molluscan research, omics-scale resources are still limited for this species (Rice et al. 1993; Park and Foighil 2000). In this study, the complete mitogenome of M. lateralis was sequenced and assembled, which represents the first mitogenome for the genus Mulinia of the bivalve family Mactridae.

An adult male M. lateralis derived from a wild population collected from Delaware Bay, New Jersey, United States, was used for this study. All soft tissues without the hepatopancreas were dissected and frozen in liquid nitrogen immediately after sampling. Total DNA was extracted using 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-ML-08). Whole-genome sequencing was performed by Frasergen (Wuhan, China). The mitogenome of M. lateralis was de novo assembled using NOVOPlasty (Dierckxsens et al. 2017).

The complete circular mitochondrial genome of M. lateralis is 21,668 bp in length with high AT nucleotide content (30.87% A, 38.69% T, 18.94% G, and 11.50% C). Thirteen protein-coding genes, two ribosomal RNA genes, and twenty-two transfer RNA genes were annotated by MITOS (Bernt et al. 2013). The 13 conserved protein-coding genes were cox (I, II, and III), nad (1, 2, 3, 4, 5, 6, and 4L), atp (6, and 8), and cob as in Venerida (Xu et al. 2012; Dong et al. 2016; Fernandez-Perez et al. 2017; Zhong et al. 2017). The sequence has been deposited in GenBank under accession number MN326303.

The phylogenetic analysis was carried out using maximum-likelihood (ML) method based on the concatenated amino acid sequences of mitochondrial protein-coding genes. As indicated by the tree, M. lateralis formed a clade with other species of the bivalve family Mactridae (Figure 1), which provides strong evidence that M. lateralis belongs to the Mactridae family.

Figure 1.

Figure 1.

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Maximum-likelihood tree of M. lateralis and 16 other mollusks based on the protein sequences of 12 protein coding genes. Numbers at each node indicate the bootstrap supporting values. The accession numbers for all species are as follows: Donax trunculus (NC_035985.1), Semele scabra (NC_018374.1), Sinonovacula constricta (EU880278.1), Solen grandis (HQ703012.1), Dreissena polymorpha (KY091877.1), Mya arenaria (NC_024738.1), Coelomactra antiquata (JN692486.1), Mactra chinensis (NC_025510.1), Cyclina sinensis (KU097333.1), Meretrix petechialis (NC_012767.1), Venerupis philippinarum (AB065374.1), Paphia amabilis (NC_016889.1), Paphia euglypta (GU269271.1), Lutraria maxima (MF784266), Lutraria rhynchaena (HG799089), Pseudocardium sachalinense (MG431821).

Disclosure statement

The authors report no conflict of interest.

References

  1. Bernt M, Donath A, Jühling F, Externbrink F, Florentz C, Fritzsch G, Pütz J, Middendorf M, Stadler PF. 2013. MITOS: improved de novo metazoan mitochondrial genome annotation. Mol Phylogenet Evol. 69(2):313–319. [DOI] [PubMed] [Google Scholar]
  2. Calabrese A. 1969. Mulinia lateralis: molluscan fruit fly? Proc Natl Shellfisheries Assoc. 59:65–66. [Google Scholar]
  3. Dierckxsens N, Mardulyn P, Smits G. 2017. NOVOPlasty: de novo assembly of organelle genomes from whole genome data. Nucleic Acids Res. 45(4):e18. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Dong PZ, Ma GY, Chang LY, Zhu Y, Tian XX. 2016. The complete mitochondrial genome of Cyclina sinensis (Veneroida: Veneridae). Mitochondrial DNA. 1(1):173–174. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Fernandez-Perez J, Nanton A, Ruiz-Ruano FJ, Camacho JPM, Mendez J. 2017. First complete female mitochondrial genome in four bivalve species genus Donax and their phylogenetic relationships within the Veneroida order. PLoS One. 12(9):e0184464. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Guo XM, Allen SK. 1994. Sex determination and polyploid gigantism in the dwarf surfclam (Mulinia lateralis Say). Genetics. 138(4):1199–1206. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Lu J, Chen TT, Allen SK, Matsubara T, Burns JC. 1996. Production of transgenic dwarf surfclams, Mulinia lateralis, with pantropic retroviral vectors. Proc Natl Acad Sci USA. 93(8):3482–3486. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Park J, Foighil DO. 2000. Sphaeriid and corbiculid clams represent separate heterodont bivalve radiations into freshwater environments. Mol Phylogenet Evol. 14(1):75–88. [DOI] [PubMed] [Google Scholar]
  9. Rice EL, Roddick D, Singh RK. 1993. A comparison of molluscan (Bivalvia) phylogenies based on palaeontological and molecular data. Mol Marine Biol Biotechnol. 2(3):137–146. [PubMed] [Google Scholar]
  10. Sambrook J, Fritsch EF, Maniatis T. 1989. Molecular cloning: a laboratory manual. New York (NY): Cold Spring Harbor Lab Press. [Google Scholar]
  11. Walker RL, Tenore KR. 1984. Growth and production of the dwarf surf clam Mulinia lateralis (Say 1822) in a Georgia estuary. Gulf and Caribbean Res. 7(4):357–363. [Google Scholar]
  12. Xu XD, Wu XY, Yu ZN. 2012. Comparative studies of the complete mitochondrial genomes of four Paphia clams and reconsideration of subgenus Neotapes (Bivalvia: Veneridae). Gene. 494(1):17–23. [DOI] [PubMed] [Google Scholar]
  13. Zhong SP, Zhao YF, Wang XF, Song ZF, Zhang Q. 2017. The complete mitochondrial genome of Lutraria maxima Jonas (Veneroida: Mactridae). Mitochondrial DNA. 2(2):709–710. [DOI] [PMC free article] [PubMed] [Google Scholar]

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