Skip to main content
NCBI home page
Mitochondrial DNA. Part B, Resources logoLink to Mitochondrial DNA. Part B, Resources
. 2021 Jul 22;6(8):2455–2457. doi: 10.1080/23802359.2021.1955771

Complete mitochondrial genome of the commensal scale worm, Arctonoe vittata (Grube, 1855) (Polychaeta: Polynoidae), collected from benthic habitat of the eastern coast of Korea

Jiseon Park a, Jongwoo Jung b, Kwang-Soo Kim c, Taeseo Park d,✉
PMCID: PMC8317944  PMID: 34368445

Abstract

The complete mitogenome sequence of the commensal polynoid scale worm Arctonoe vittata was determined for the first time in the present study. The total length of the newly sequenced mitogenome was 15,125 bp, including 13 protein-coding genes, 2 rRNA genes, and 22 tRNA genes. The phylogenetic position of A. vittata was examined by maximum likelihood analysis using concatenated 13 protein-coding genes with 18 selected polychaete species. Arctonoe vittata was nested within the suborder Aphroditiformia and closely related to Aphrodita australis among the selected species. The newly determined mitogenome sequence will be useful for further phylogenetic and evolutionary studies of this group.

Keywords: Arctonoe vittata, commensal, scale worm, complete mitogenome, Polynoidae

The polynoid scale worm Arctonoe vittata (Grube, 1855) is known to be commensally associated with various invertebrates such as gastropods, asteroids, holothuroids, and even with other tube-dwelling polychaetes (Hanley 1989; Ruff 1995; Park et al. 2016). There are three nominal species in the genus Arctonoe Chanberlin, 1920: A. vittata, Arctonoe fragilis (Baird, 1863), and Arctonoe pulchra (Johnson, 1897). However, A. vittata is the only species known to be distributed in northeastern Asian waters (Okuda 1936; Uschakov 1982; Imajima and Hartman 1964; Imajima 1998, 2001; Park et al. 2016).

Mitochondrial genes have been widely used in phylogenetic and evolutionary studies of metazoans (Zhang et al. 2018). However, despite their high species diversity, only about 90 complete polychaete mitogenomes have been published to date (Aguado et al. 2016; Seixas et al. 2017; Zhang et al. 2018). The aim of the present study was to determine the complete mitochondrial genome sequence of A. vittata for the first time.

A single specimen of A. vittata was extracted from the mantle cavity of the snowy limpet [Niveotectura pallida (Gould, 1859)] collected by SCUBA divers in the subtidal rocky zone (at the depth of 27 m) of the East Sea (38.372315N, 128.523263E, Goseong-gun, Gangwon-do, Korea). The specimen was immediately fixed in pure ethanol for genomic DNA extraction. Species identification was performed under a field stereomicroscope (EZ4 HD, Leica, Germany) based on Park et al. (2016). Genomic DNA was extracted from the small body tissue using the DNeasy Blood & Tissue kit (Qiagen, Hilden, Germany). The REPLI-g Mitochondrial DNA Kit (Qiagen, Hilden, Germany) was used for mitochondrial DNA amplification. Mitochondrial genome sequencing and library construction were conducted using the NovaSeq 6000 sequencing system (Illumina, San Diego, CA, USA) and Truseq DNA PCR-Free kit (Illumina, San Diego, CA, USA). Assembler and annotation tools, GetOrganelle (Jin et al. 2020) and Chlorobox (Tillich et al. 2017), were used, respectively. A voucher specimen was housed at the National Institute of Biological Resources (NIBR, http://www.nibr.go.kr/, Taeseo Park, polychaeta@gmail.com), Korea (NIBRIV0000810302).

The total length of the newly determined complete mitogenome of A. vittata was 15,125 bp (GenBank accession no. MZ131647). The mitogenome consisted of 37 encoded genes (including 13 protein-coding genes, 2 rRNA genes, and 22 tRNA genes). The overall nucleotide composition was 28.6% A, 18.0% C, 13.9% G, and 39.4% T, with a high A + T content (68.1%). Phylogenetic analysis was conducted to examine the phylogenetic position of A. vittata using the MEGA X software (Kumar et al. 2018). The tree was reconstructed by the maximum likelihood method using the GTR + G + I model with a bootstrap of 1000 replicates. Thirteen protein-coding genes were concatenated from 11 Nereidiformia species, one Aphroditiformia species, five Glyceriformia species, and one Eunicida species as an outgroup. As a result, A. vittata was grouped into the suborder Aphroditiformia and found to be closely related to Aphrodita australis Baird, 1865 (Figure 1).

Figure 1.

Figure 1.

Open in a new tab

Maximum-likelihood (ML) tree reconstructed using a concatenated data set of 13 protein-coding genes based on 19 mitogenome sequences including Arctonoe vittata from the present study. Bootstrap replicates were performed 1000 times. The GenBank accession number of each species is shown in parentheses after the species name.

The newly determined mitogenome sequence of A. vittata will be useful for understanding the phylogenetic position of polynoid polychaetes.

Funding Statement

This research was supported by grants from the National Institute of Biological Resources [NIBR202006101, NIBR202130202].

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 available in National Center for Biotechnology Information (NCBI) GenBank (https://www.ncbi.nlm.nih.gov) under the accession no. MZ131647. The associated BioProject, SRA, and BioSample numbers are PRJNA727905, SRR14565548, and SAMN19229861, respectively. The data that support the findings of this study are openly available in Mendeley Data (http://dx.doi.org/10.17632/67d3×6yyff.1).

References

  1. Aguado MT, Richter S, Sontowski R, Golombek A, Struck TH, Bleidorn C.. 2016. Syllidae mitochondrial gene order is unusually variable for Annelida. Gene. 594(1):89–96. [DOI] [PubMed] [Google Scholar]
  2. Hanley JR. 1989. Revision of the scaleworm genera Arctonoe Chamberlin and Gastrolepidia Schmarda (Polychaeta, Polynoidae) with the erection of a new subfamily, Arctonoinae. The Beagle, Records of the Northern Territory Museum of Arts and Sciences. 6:1–34. [Google Scholar]
  3. Imajima M. 1998. Polychaetous worms in the Ishikari Bay. Memoirs of the National Science Museum. 21:123–129. in Japanese) [Google Scholar]
  4. Imajima M. 2001. Annelida, Polychaeta II. Tokyo (Japan): Seibutsu kenkyujo Publishing Co.; p. 1–542. [Google Scholar]
  5. Imajima M, Hartman O.. 1964. The polychaetous annelids of Japan. Los Angeles (CA): University of California Press; 1–452. [Google Scholar]
  6. Jin JJ, Yu WB, Yang JB, Song Y, Depamphilis CW, Yi TS, Li DZ.. 2020. GetOrganelle: a fast and versatile toolkit for accurate de novo assembly of organelle genomes. Genome Biol. 21(1):1–31. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. 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]
  8. Okuda S. 1936. Japanese commensal polynoids. Annotationes Zoologicae Japonenses. 15(4):561–571. [Google Scholar]
  9. Park T, Lee S-k, Kim W.. 2016. New record of commensal scale worms, Arctonoe vittata (Grube, 1855) and Hyperhalosydna striata (Kinberg, 1856) (Polychaeta: Polynoidae) from Korean waters. J Species Res. 5(3):517–529. [Google Scholar]
  10. Ruff RE. 1995. Family Polynoidae Malmgren, 1867. In: Blake JA, Hilbig B, Scott PH, editors. Taxonomic atlas of the benthic fauna of the Santa Maria Basin and Western Santa Barbara Channel. Volume 5. The Annelida Part 2. Polychaeta: Phyllodocida (Syllidae and scale-bearing families), Amphinomida and Eunicida. Santa Barbara (CA): Santa Barbara Museum of Natural History; p. 1–378. [Google Scholar]
  11. Seixas VC, Russo CA, Paiva PC.. 2017. Mitochondrial genome of the Christmas tree worm Spirobranchus giganteus (Annelida: Serpulidae) reveals a high substitution rate among annelids. Gene. 605:43–53. [DOI] [PubMed] [Google Scholar]
  12. Tillich M, Lehwark P, Pellizzer T, Ulbricht-Jones ES, Fischer A, Bock R, Greiner S.. 2017. GeSeq - versatile and accurate annotation of organelle genomes. Nucleic Acids Res. 45(W1):W6–W11. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Uschakov PV. 1982. Polychaetes of the suborder Aphroditiformia of the Arctic Ocean and the northwestern part of the pacific, families Aphroditidae and Polynoidae. Fauna SSSR, Mnogoshchetinkovyye chervi (fauna of the USSR, Polychaeta), Academiya Nauk SSSR, Moscow. 1–272. [Google Scholar]
  14. Zhang Y, Sun J, Rouse GW, Wiklund H, Pleijel F, Watanabe HK, Chen C, Qian PY, Qiu JW.. 2018. Phylogeny, evolution and mitochondrial gene order rearrangement in scale worms (Aphroditiformia, Annelida). Mol Phylogenet Evol. 125:220–231. [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 available in National Center for Biotechnology Information (NCBI) GenBank (https://www.ncbi.nlm.nih.gov) under the accession no. MZ131647. The associated BioProject, SRA, and BioSample numbers are PRJNA727905, SRR14565548, and SAMN19229861, respectively. The data that support the findings of this study are openly available in Mendeley Data (http://dx.doi.org/10.17632/67d3×6yyff.1).

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

RESOURCES