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. 2022 Jun 15;7(6):1027–1029. doi: 10.1080/23802359.2022.2080606

The complete mitochondrial genome of Acanthopagrus pacificus (Perciformes, Sparidae) from Iriomotejima Island, Okinawa, Japan

Kentaro Kawai 1,✉, Hiroki Fujita 1, Tetsuya Umino 1
PMCID: PMC9225699  PMID: 35756456

Abstract

The Pacific seabream, Acanthopagrus pacificus, is a commercially valuable resource for fisheries around the West Pacific Ocean countries. Although the phylogenetic position of the A. pacificus within the genus Acanthopagrus changes by the differences in the target gene regions or fish sampling locations, the genetic information of the species is quite limited. In this study, the complete mitochondrial genome of A. pacificus from Iriomotejima Island, Okinawa, Japan was determined. The sequence is 16,640 bp in length and consists of 13 protein-coding genes, 2 rRNA genes (12S rRNA and 16S rRNA), 22 tRNA genes, and one control region. A reconstructed phylogenetic tree showed that A. pacificus has the furthest relationship to other Acanthopagrus species in the genus.

Keywords: Mitochondrial DNA, next generation sequencing, Pacific seabream, phylogeny, Sparid

Mitochondrial genomes have been used for the study of species evolution, phylogenetic relationships, and population structure because of their small genome size, rapid evolutionary rates, and absence of sequence recombination. In phylogenetic analyses, the resolution and support were improved by using the whole mitochondrial genome than using protein-coded regions (Cameron et al. 2007). Recent phylogenetic studies using a complete mitochondrial genome revealed detailed evolutionary history in some taxon (Nardi et al. 2010: Ma et al. 2015; Wang et al. 2016).

Genus Acanthopagrus species are commercially and recreationally important coastal fishes from temperate to the tropical zone (Tseng et al. 2009; Iwatsuki and Heemstra 2011; Kawai et al. 2020). Within the genus, Acanthopagrus schlegelii and Acanthopagrus latus, targeted species for stock enhancement and aquaculture in Asian countries, are studied intensively not only in reproductive biology (Law and Sadovy de Mitcheson 2017; Wang et al. 2020; Kawai et al. 2021) but also in genetic population structure (Song et al. 2021; Yamashita et al. 2021; Hsu et al. 2022). Same as the above two species, the Pacific seabream, Acanthopagrus pacificus Iwatsuki et al. 2010, is a commercially important species in the West Pacific Ocean (Iwatsuki et al. 2010; Tran et al. 2021), although information on the population genetics of the species has not been reported. In addition, although partial sequences analysis of mitochondrial DNA and AFLP (amplified fragment length polymorphism) analysis of nuclear DNA indicated some ideas of the phylogenetic position of the A. pacificus within the genus Acanthopagrus, these results varied with the differences in the target regions or collected locations of fish (Hsu et al. 2011; Wu et al. 2018). Because A. pacificus distributes widely in the West Pacific Ocean (Iriomote Island in Okinawa of Japan, Taiwan, southern China, Viet Nam, Philippines, Thailand, Malaysia, Indonesia, Papua New Guinea, northern Australia) (Iwatsuki et al. 2010), the species have a possibility to include cryptic species, as a similar situation of Acanthopagrus morrisoni separated from A. latus complex (Iwasaki et al. 2013). Here, we determined the complete mitochondrial genome sequence of A. pacificus from Iriomotejima Island, Okinawa Prefecture, Japan. The results of this study will provide reference not only for the resolution of the complexed phylogeny of the genus Acanthopagrus but also for the genetic population research of A. pacificus.

The experiments in this study complied with the fundamental guidelines for the proper conduct of animal experiments and related activities in academic research institutions under the jurisdiction of the Ministry of Education, Culture, Sports, Science, and Technology (Notice No. 71, 1 June 2006). The A. pacificus specimen was collected by line fishing at Urauchi River (24.400783 N, 123.782696 E) in Iriomotejima Island, Okinawa, Japan, on 7 March 2022. The specimen was deposited at Hiroshima University Museum (Deposit No. HUM-I-02335: Norio Shimizu, museum@hiroshima-u.ac.jp). The specimen was identified based on the description of key characteristics of the Acanthopagrus species (Iwatsuki 2013). Total genomic DNA was extracted from the pectoral fin by the phenol-chloroform Isoamyl alcohol extraction method. The high-throughput DNA sequencing was performed by Bioengineering Lab. Co., Ltd. (Sagamihara, Japan) using DNBSEQ-G400 system (MGI Tech Co., Ltd.: Shenzhen, China) with a paired-end 200 bp sequencing. The obtained raw reads (5,916,726 reads, 2,366,690,400 bp) were trimmed using fastp (Chen et al. 2018) to remove adapters and low-quality reads. After filtering, the paired-end reads were assembled to a complete mitochondrial genome using NOVOplasty (Dierckxsens et al. 2017), with A. pacificus (LC458140) as the seed reference. Mitochondrial genes were annotated using MitoAnnotator (Iwasaki et al. 2013).

The complete mitogenome of A. pacificus was 16,640 bp in length (GenBank accession no. LC707238) and consisted of 13 protein-coding genes, 2 rRNA genes (12S rRNA and 16S rRNA), 22 tRNA genes, and one control region. The gene arrangement was identical to that observed in A. schlegelii (Shi et al. 2012; Ma et al. 2016) and A. latus (Xia et al. 2008; Pan et al. 2021).

Phylogenetic analysis of genus Acanthopagrus was conducted with the complete mitochondrial genome sequences of A. schlegelii (accession no. JQ746035, KT805958 and LC680889) and A. latus (accession no. EF506764 and MN909968) obtained from NCBI (Xia et al. 2008; Shi et al. 2012; Ma et al. 2016; Pan et al. 2021). The Complete mitochondrial genome of Rhabdosargus sarba (accession no. KM272585) (Li et al. 2016) from NCBI served as an outgroup. These sequences were aligned using MUSCLE (Edgar 2004). The phylogenetic tree was reconstructed using MEGA X (Kumar et al. 2018) with the maximum likelihood method (K2P + G + I model). Bootstrap analyses for the phylogenetic tree were conducted with 1000 replications (Figure 1).

Figure 1.

Figure 1.

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A phylogenetic tree reconstructed with complete mitochondrial genome sequences of Acanthopagrus pacificus and other species.

The phylogenetic tree showed that A. pacificus has the furthest relationship to the A. latus and A. schlegelii, which supports the previous studies on phylogenetic relationships of Acanthopagurus species using partial mitochondrial genome sequences and nuclear DNA AFLP analysis (Hsu et al. 2011).

Acknowledgments

We thank Umi Suzuki, the fishing guide in Iriomotejima Island, Okinawa for assisting the A. pacificus specimen collection. We wish to thank Norio Shimizu at Hiroshima University Museum for registering the specimen.

Funding Statement

Encouragement Award to K. K. [020920] from Graduate School of Integrated Sciences for Life, Hiroshima University.

Author contributions

K. K. conceived and designed the experiments, prepared the funding, performed the experiments, analyzed the data, authored drafts of the paper, and approved the final draft. H. F. analyzed the data, prepared the figure, revised drafts, and approved the final draft. T. U. conceived and designed the experiments, authored or reviewed drafts of the paper, and approved the final draft. All authors agreed to be accountable for all aspects of this work.

Disclosure statement

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

Data availability statement

The mitochondrion genome sequence data that support the findings of this study are openly available in GenBank with the accession no. LC707238 (https://www.ncbi.nlm.nih.gov/nuccore/LC707238). The associated BioProject, DRA, and BioSample numbers are PRJDB13470, DRA013995, and SAMD00468474 respectively.

References

  1. Cameron SL, Lambkin CL, Barker SC, Whiting MF.. 2007. A mitochondrial genome phylogeny of Diptera: whole genome sequence data accurately resolve relationships over broad timescales with high precision. Systemat Entomol. 32(1):1027–59. [Google Scholar]
  2. Chen S, Zhou Y, Chen Y, Gu J.. 2018. fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics. 34(17):i884–i890. [DOI] [PMC free article] [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–e18. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Edgar RC. 2004. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32(5):1792–1797. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Hsu TH, Guillén Madrid AG, Burridge CP, Cheng HY, Gwo JC.. 2011. Resolution of the Acanthopagrus black seabream complex based on mitochondrial and amplified fragment‐length polymorphism analyses. J Fish Biol. 79(5):1182–1192. [DOI] [PubMed] [Google Scholar]
  6. Hsu TH, Lee HT, Lu HJ, Liao CH, Gong HY, Huang CW.. 2022. Maintenance of genetic diversity of Black Sea Bream despite unmonitored and large-scale hatchery releases. Biology. 11(4):554. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Iwasaki W, Fukunaga T, Isagozawa R, Yamada K, Maeda Y, Satoh TP, Sado T, Mabuchi K, Takeshima H, Miya M, et al. 2013. MitoFish and MitoAnnotator: a mitochondrial genome database of fish with an accurate and automatic annotation pipeline. Mol Biol Evol. 30(11):2531–2540. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Iwatsuki Y. 2013. Review of the Acanthopagrus latus complex (Perciformes: Sparidae) with descriptions of three new species from the Indo-West Pacific Ocean. J Fish Biol. 83(1):64–95. [DOI] [PubMed] [Google Scholar]
  9. Iwatsuki Y, Heemstra PC.. 2011. A review of the Acanthopagrus bifasciatus species complex (Pisces: Sparidae) from the Indian Ocean, with redescriptions of A. bifasciatus (Forsskål 1775) and A. catenula (Lacepède 1801) YUKIO IWATSUKI (Japan) & PHILLIP C. HEEMSTRA (South Africa). Zootaxa. 3025(1):38–50. [Google Scholar]
  10. Iwatsuki Y, Kume M, Yoshino T.. 2010. A new species, Acanthopagrus pacificus from the Western Pacific (Pisces, Sparidae). Bullet Natl Museum Nature Sci Series A. 36(4):115–130. [Google Scholar]
  11. Kawai K, Fujita H, Sanchez G, Furusawa S, Umino T.. 2020. Estimating the spawning season of black sea bream Acanthopagrus schlegelii in Hiroshima Bay, Japan, from temporal variation in egg density. Fish Sci. 86(4):645–653. [Google Scholar]
  12. Kawai K, Fujita H, Sanchez G, Umino T.. 2021. Oyster farms are the main spawning grounds of the black sea bream Acanthopagrus schlegelii in Hiroshima Bay, Japan. PeerJ. 9:e11475. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Kumar S, Stecher G, Li M, Knyaz C, Tamura K.. 2018. MEGA X: molecular evolutionary genetics analysis across computing platforms. Mol Biol Evol. 35(6):1547–1549. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Law CSW, Sadovy de Mitcheson Y.. 2017. Reproductive biology of black seabream Acanthopagrus schlegelii, threadfin porgy Evynnis cardinalis and red pargo Pagrus major in the northern South China Sea with consideration of fishery status and management needs. J Fish Biol. 91(1):101–125. [DOI] [PubMed] [Google Scholar]
  15. Li J, Yang H, Xie Z, Yang X, Xiao L, Wang X, Li S, Chen M, Zhao H, Zhang Y.. 2016. The complete mitochondrial genome of the Rhabdosargus sarba (Perciformes: Sparidae). Mitochondr DNA Part A. 27(3):1606–1607. [DOI] [PubMed] [Google Scholar]
  16. Ma H, Ma C, Li C, Lu J, Zou X, Gong Y, Wang W, Chen W, Ma L, Xia L.. 2015. First mitochondrial genome for the red crab (Charybdis feriata) with implication of phylogenomics and population genetics. Sci Rep. 5(1):1–14. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Ma X, Xie Z, Zhou L, Chen Y.. 2016. The complete mitochondrial genome of Acanthopagrus schlegelii (Perciformes: Sparidae) with phylogenetic consideration. Mitochondr DNA B Resour. 1(1):348–349. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Nardi F, Carapelli A, Boore JL, Roderick GK, Dallai R, Frati F.. 2010. Domestication of olive fly through a multi-regional host shift to cultivated olives: comparative dating using complete mitochondrial genomes. Mol Phylogenet Evol. 57(2):678–686. [DOI] [PubMed] [Google Scholar]
  19. Pan C, Gao C, Chen T, Chen X, Yang C, Zeng D, Feng P, Jiang W, Peng M.. 2021. The complete mitochondrial genome of yellowfin seabream, Acanthopagrus latus (Percoiformes, Sparidae) from Beibu Bay. Mitochondr DNA B Resour. 6(4):1313–1314. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Shi X, Su Y, Wang J, Ding S, Mao Y.. 2012. Complete mitochondrial genome of black porgy Acanthopagrus schlegelii (Perciformes, Sparidae). Mitochondr DNA. 23(4):310–312. [DOI] [PubMed] [Google Scholar]
  21. Song P, Liu C, Cai Z, Liu S, Xiang J, Shan B, Ji D, Li Y, Lin L.. 2021. Genetic characteristics of yellow seabream Acanthopagrus latus (Houttuyn, 1782) (Teleostei: Sparidae) after stock enhancement in southeastern China coastal waters. Region Studies Marine Sci. 48:102065. [Google Scholar]
  22. Tran TT, Tran HD, Nguyen NT.. 2021. Notes on morphology and spatio-temporal distribution of early-stage juveniles of Acanthopagrus pacificus (Sparidae) in the estuary of northern Vietnam. Sustain Water Resour Manag. 7(5):1–5. [Google Scholar]
  23. Tseng MC, Jean CT, Tsai WL, Chen NC.. 2009. Distinguishing between two sympatric Acanthopagrus species from Dapeng Bay, Taiwan, using morphometric and genetic characters. J Fish Biol. 74(2):357–376. [DOI] [PubMed] [Google Scholar]
  24. Wang K, Li X, Ding S, Wang N, Mao M, Wang M, Yang D.. 2016. The complete mitochondrial genome of the Atylotus miser (Diptera: Tabanomorpha: Tabanidae), with mitochondrial genome phylogeny of lower Brachycera (Orthorrhapha). Gene. 586(1):184–196. [DOI] [PubMed] [Google Scholar]
  25. Wang SB, Lau KY, Liu KM, Joung SJ, Liu CH.. 2020. Reproductive characteristics of the hermaphroditic yellowfin seabream Acanthopagrus latus in the waters off western Taiwan. Aquac Res. 51(12):5015–5028. [Google Scholar]
  26. Wu R, Zhang H, Liu J, Niu S, Xiao Y, Chen Y.. 2018. DNA barcoding of the family Sparidae along the coast of China and revelation of potential cryptic diversity in the Indo-West Pacific oceans based on COI and 16S rRNA genes. J Ocean Limnol. 36(5):1753–1770. [Google Scholar]
  27. Xia J, Xia K, Jiang S.. 2008. Complete mitochondrial DNA sequence of the yellowfin seabream Acanthopagrus latus and a genomic comparison among closely related Sparid species. DNA Sequence. 19(4):385–393. [PubMed] [Google Scholar]
  28. Yamashita Y, Sanchez G, Kawai K, Tomano S, Fujita H, Umino T.. 2021. The role of the isolation of the marginal seas during the Pleistocene in the genetic structure of black sea bream Acanthopagrus schlegelii (Bleeker, 1854) in the coastal waters of Japan. PeerJ. 9:e11001. [DOI] [PMC free article] [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 mitochondrion genome sequence data that support the findings of this study are openly available in GenBank with the accession no. LC707238 (https://www.ncbi.nlm.nih.gov/nuccore/LC707238). The associated BioProject, DRA, and BioSample numbers are PRJDB13470, DRA013995, and SAMD00468474 respectively.

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