Skip to main content
NCBI home page
Mitochondrial DNA. Part B, Resources logoLink to Mitochondrial DNA. Part B, Resources
. 2023 Jan 26;8(1):157–160. doi: 10.1080/23802359.2023.2167478

The complete mitochondrial genome of Cuspidaria undata (Bivalvia, Anomalodesmata, Cuspidariidae)

Yating Bao a, Meiling Ge a, Yaoyao Zhao b, Zhou Zheng a,c,✉, Qinzeng Xu a
PMCID: PMC9888449  PMID: 36733275

Abstract

The mitochondrial genome of Cuspidaria undata (Verrill, 1884) was sequenced in full using Illumina HiSeq 2500. The circular mitochondrial DNA (mtDNA) was 16,266 bp in size, encoded 37 genes, and contained 13 protein-coding genes (PCGs), 2 rRNAs and 22 tRNAs. The gene order of the 13 PCGs in this species exhibited extensive rearrangement and differences in comparison to other Cuspidariidae, indicating that gene order is not conserved within this family. Phylogenetic analysis based on 13 PCGs and 2 rRNAs recovered a monophyletic Cuspidariidae.

Keywords: Cuspidaria undata, mitochondrial genome, phylogeny, Cuspidariidae

The family Cuspidariidae Dall, 1886. belongs to the class Bivalvia, within the superorder Anomalodesmata (Worms 2020), and includes 19 genera and 254 species (Morton and Machado 2019). Cuspidariidae species are deep-sea predatory bivalves and are the most diversified group among the septibranch bivalves (Amano and Kurita 2020). Deep water mollusks have been sparsely studied and only one complete mitogenome of Cuspidariidae has previously been sequenced, one which belongs to the genus Tropidomya Dall & Smith, 1886 (Williams et al. 2017). In this study, the complete mitochondrial genome of Cuspidaria undata (Verrill, 1884) was sequenced to understand the genomic structure and phylogenetic relationships within this family (Figure 1).

Figure 1.

Figure 1.

Open in a new tab

The maximum likelihood tree of 10 bivalves based on 13 PCGs and 2 rRNAs. Number at branch represents bootstrap probability. The following sequences were used: KX815961.1 (Williams et al. 2017), KX815958.1 (Williams et al. 2017), KX815962.1 (Williams et al. 2017), KX815963.1 (Williams et al. 2017), KF534717.1 (Park and Ahn 2015), KX815957.1 (Williams et al. 2017), KX815960.1 (Williams et al. 2017), KR873102.1 (Wu et al. 2016), MG385135.1 (Soroka and Burzyński 2017).

A specimen of C. undata was collected from the Southern Indian Ocean (16.95110S, 89.66835E) during the China Ocean 52th voyage. The sample (Accession No. FIO2018015207; Contact person: Zhou Zheng, zhengzhou@fio.org.cn) was stored at −80 °C at the Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources. Total DNA was extracted from muscle tissue using a DNeasy Blood & Tissue DNA kit (QIAGEN) and thereafter sequenced using the Illumina HiSeq 2500 Sequencing Platform (Beijing, China). The mitochondrial genome was assembled using NOVOplasty (Dierckxsens et al. 2017) and annotated using the MITOS Web Server (Bernt et al. 2013). Bandage (Wick et al. 2015) was used to verify the circular structure of the mitochondrial genome. The complete mitogenome of C. undata was submitted to GenBank, registration number ON360998.1.

The mitochondrial genome of C. undata was 16,266 bp in length, and contained 13 PCGs, 2 rRNAs and 22 tRNAs. The mtDNA of C. undata composition was 26.1% A, 10.4% C, 21.4% G, and 42.1% T. The percentage of A + T with the C. undata mtDNA was 68.2%. The 22 tRNA-coding genes ranged in size from 60 bp through to 74 bp. The gene order of the 13 PCGs was COX1, NAD6, COB, NAD4L, COX2, ATP6, NAD2, NAD4, ATP8, NAD1, NAD5, NAD3 and COX3, which exhibited extensive rearrangement in comparison to the gene order previously published Tropidomya abbreviata (Forbes, 1843), also within Cuspidariidae (Williams et al. 2017), indicating that the mitochondrial gene order of this family is not conservative. In addition, we made a table describing the characteristics of C. undata mitochondrial genome (Table 1), and drew the mitochondrial genome map of C. undata (Figure 2) using OrganellarGenomeDRAW (OGDRAW) version 1.3.1 (Greiner et al. 2019).

Table 1.

Mitochondrial genome of C. undata with gene order, positions, lengths, nucleic acid composition, coding strand, start and stop codons, anticodons and amino acid size.

Gene Position
 Length (bp) Nucleic acid
 Coding strand Codon
 Anticodons Amino acid size
Start End AT (%) GC (%) Start Stop
cox1 25 1569 1545 63.49 36.51 + GTT TAA   514aa
trnA 1629 1693 65 70.77 29.23 +     TGC  
trnQ 2519 2592 74 68.92 31.08 +     TTG  
trnS 2594 2663 70 61.43 38.57 +     TGA  
trnE 2667 2734 68 75.00 25.00 +     TTC  
trnL 2741 2804 64 65.62 34.38 +     TAG  
trnV 2805 2872 68 83.82 16.18 +     TAC  
rrn16 2855 4178 1324 73.04 26.96 +        
trnI 4179 4245 67 64.18 35.82 +     GAT  
nad6 4300 4788 489 69.53 30.47 + ATG TAG   162aa
trnR 4787 4853 67 70.15 29.85 +     TCG  
cob 4857 6017 1611 68.48 31.52 + ATA TAA   386aa
trnG 6029 6094 66 66.67 33.33 +     TCC  
trnL 6097 6164 68 67.66 32.84 +     TAA  
trnN 6166 6234 69 75.36 24.64 +     GTT  
trnK 6235 6300 66 57.58 42.42 +     TTT  
trnY 6298 6363 66 60.61 39.39 +     GTA  
nad4l 6366 6647 282 67.73 32.27 + ATG TAA   93aa
trnM 6648 6712 65 63.08 36.92 +     CAT  
cox2 6734 7498 765 63.40 36.60 + ATG TAG   254aa
trnP 7538 7604 67 76.12 23.88 +     TGG  
atp6 7607 8278 672 67.71 32.29 + ATG TAA   223aa
trnS 8285 8352 68 64.71 35.29 +     TCT  
nad2 8385 9392 1008 68.06 31.94 + ATT TAA   335aa
nad4 9433 10788 1356 68.44 31.56 + ATG TAA   451aa
atp8 10852 11013 162 72.84 27.16 + ATG TAA   53aa
rrn12 11029 11927 899 69.86 30.14 +        
nad1 11975 12904 930 69.14 30.86 + ATA TAG   309aa
trnT 12908 12975 68 73.53 26.47 +     TGT  
trnD 12974 13040 67 79.10 20.90 +     GTC  
trnF 13041 13104 64 67.19 32.81 +     GAA  
trnW 13107 13173 67 68.66 31.34 +     TCA  
trnH 13178 13237 60 75.00 25.00 +     GTG  
nad5 13274 14977 1704 69.07 30.93 + ATT TAA   567aa
nad3 14989 15339 351 69.52 30.48 + GTG TAG   116aa
trnC 15339 15402 64 65.63 34.37 +     GCA  
cox3 15408 16199 792 63.38 36.62 + ATG TAG   263aa
Open in a new tab

Figure 2.

Figure 2.

Open in a new tab

Map of the mitochondrial genome of C. undata. The mitochondrial genome of C. undata was 16,266 bp in length, and contained 13 PCGs, 2 rRNAs and 22 tRNAs, marked in different colors in the map.

The maximum likelihood (ML) phylogenetic tree of C. undata was constructed based on the 13 PCGs and 2 rRNAs, containing seven other Anomalodesmata species and two Palaeoheterodonta species as outgroups. Nucleotide sequences from each mitogene were aligned using MAFFT v7.313 (Katoh et al. 2002) and then trimmed with Gblocks 0.9 b (Talavera and Castresana 2007). All of the aligned gene sets were concatenated using SequenceMatrix v1.7.8 (Vaidya et al. 2011). The best fitting nucleotide-substitution model of each partition was evaluated using PartitionFinder2 (Lanfear et al. 2017). ML analysis was analyzed using IQ-TREE v. 1.6.8 (Nguyen et al. 2015) with 1,000 bootstrap replicates. The phylogenetic position of C. undata (ON360998.1) was sister to T. abbreviata and the family Cuspidariodea recovered a monophyletic clade.

Funding Statement

This work was supported by the National Natural Science Foundation of China [42176242], the foundation of China Ocean Mineral Resources R & D Association [DY135-E2-4], and Global Change and Air-Sea Interaction Program [GASI-02-PAC-CJ09].

Ethical approval

In this study, all experimental protocols relating to animal experiments were in accordance with the measures for the Administration of Affairs Concerning Experimental Animal of Shandong Province, China (approved by the Shandong Provincial Government in 1992). All animal experiments in this study were approved by the Ethical Committee of Ministry of Natural Resources of the People’s Republic of China. All studies were conducted in accordance with ethical guidelines and the legal requirements of the study country.

Author contributions

Yating Bao, Meiling Ge and Yaoyao Zhao were involved in the conception and design, analysis and interpretation of the data. Yating Bao and Meiling Ge drafted the paper. Qinzeng Xu participated in the formal analysis and data curation of the project, and revised it critically for intellectual content. Zhou Zheng provided the funds and resource for this research and gave final approval of the version to be published. All authors agree to be accountable for all aspects of the work.

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 (https://www.ncbi.nlm.nih.gov/nuccore/ON360998) (GeneBank Number: ON360998.1). The associated BioProject, SRA, and Bio-Sample numbers are PRJNA848421, SRR19647706, and SAMN29005581, respectively.

References

  1. Amano K, Kurita H.. 2020. A new Paleocene species of Myonera (Bivalvia: Cuspidariidae) from eastern Hokkaido, Northern Japan. Nautilus Greenville Then Sanibel. 134(1):51–56. [Google Scholar]
  2. 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]
  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. Greiner S, Lehwark P, Bock R.. 2019. OrganellarGenomeDRAW (OGDRAW) version 1.3.1: expanded toolkit for the graphical visualization of organellar genomes. Nucleic Acids Res. 47(W1):W59–W64. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Katoh K, Misawa K, Kuma K, Miyata T.. 2002. MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res. 30(14):3059–3066. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Lanfear R, Frandsen PB, Wright AM, Senfeld T, Calcott B.. 2017. PartitionFinder 2: new methods for selecting partitioned models of evolution for molecular and morphological phylogenetic analyses. Mol Biol Evol. 34(3):772–773. [DOI] [PubMed] [Google Scholar]
  7. Morton B, Machado FM.. 2019. Predatory marine bivalves: a review. Adv Mar Biol. 84:1–98. [DOI] [PubMed] [Google Scholar]
  8. Nguyen LT, Schmidt HA, von Haeseler A, Minh BQ.. 2015. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol Biol Evol. 32(1):268–274. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Park H, Ahn DH.. 2015. Complete mitochondrial genome of the Antarctic soft-shelled clam, Laternula elliptica (Bivalvia; Laternulidae). Mitochondrial DNA. 26(4):642–643. [DOI] [PubMed] [Google Scholar]
  10. Soroka M, Burzyński A.. 2017. Hermaphroditic freshwater mussel Anodonta cygnea does not have supranumerary open reading frames in the mitogenome. Mitochondrial DNA B Resour. 2(2):862–864. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Talavera G, Castresana J.. 2007. Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments. Syst Biol. 56(4):564–577. [DOI] [PubMed] [Google Scholar]
  12. Vaidya G, Lohman DJ, Meier R.. 2011. SequenceMatrix: concatenation software for the fast assembly of multi-gene datasets with character set and codon information. Cladistics. 27(2):171–180. [DOI] [PubMed] [Google Scholar]
  13. Williams ST, Foster PG, Hughes C, Harper EM, Taylor JD, Littlewood DTJ, Dyal P, Hopkins KP, Briscoe AG.. 2017. Curious bivalves: systematic utility and unusual properties of anomalodesmatan mitochondrial genomes. Mol Phylogenet Evol. 110:60–72. [DOI] [PubMed] [Google Scholar]
  14. Wick RR, Schultz MB, Zobel J, Holt KE.. 2015. Bandage: interactive visualization of de novo genome assemblies. Bioinformatics. 31(20):3350–3352. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Worms. 2020. World register of marine species. http://www.marinespecies.org/aphia.php?p=taxdetails&id=1788.
  16. Wu RW, An CT, Wu XP, Zhou CH, Ouyang S.. 2016. Complete maternal mitochondrial genome of freshwater mussel Aculamprotula tientsinensis (Bivalvia: unionidae: unioninae). Mitochondrial DNA A DNA Mapp Seq Anal. 27(6):4520–4521. [DOI] [PubMed] [Google Scholar]

Associated Data

This section collects any data citations, data availability statements, or supplementary materials included in this article.

Data Availability Statement

The genome sequence data that support the findings of this study are openly available in GenBank of NCBI (https://www.ncbi.nlm.nih.gov/nuccore/ON360998) (GeneBank Number: ON360998.1). The associated BioProject, SRA, and Bio-Sample numbers are PRJNA848421, SRR19647706, and SAMN29005581, respectively.

Articles from Mitochondrial DNA. Part B, Resources are provided here courtesy of Taylor & Francis

RESOURCES