The complete mitochondrial genome of sponge Halichondria sp. (Demospongiae, Suberitida, Halichondriidae) from Dok-do

Abstract

The mitogenome sequence of Halichondria sp. was determined for the first time in this study. Specimens were identified as a new species belonging to genus Halichondria and more detailed taxonomic study is ongoing. Circular complete mitogenome is 19,687 bp in length, containing 14 protein-coding genes (PCGs), 2 ribosomal RNAs (rRNAs), and 25 transfer RNAs (tRNAs). Nucleotide composition of mitogenome consists of 28.9% A, 15.1% C, 21.9% G, 34.1% T, revealing high content of A + T similar to the other Suberitid sponges. Results will be useful for inferring phylogenetic relationships among the members of Halichondriid.

Keywords:

• Mitochondrial genome
• Halichondria
• Halichondriidae
• Demosponge

The genus Halichondria Fleming, 1828 is characterized by a tangential ectosomal skeleton (Kang and Sim 2008). Hailchondria sp. collected from Dok-do island is similar to H. okadai (Kadota, 1992) in shape, ectosomal skeletal, and growth form, but it differs in spicule size and choanosomal skeleton. Specimens were identified as a new species belonging to genus Halichondria and more detailed taxonomic study based on specimens collected from Dok-do island is ongoing by Dr. DW Kang and Dr. HJ Kim, National Marine Biodiversity Institute of Korea. Until now, the only two species (Halichondria okadai, Hymeniacidon sinapium) of Halichondriid have been reported for their complete mitochondrial genomes (Jun et al. 2015; Kim et al. 2017). We report the complete mitochondrial genome (mitogenome) of H. sp. for the first time and it will be valuable information for further study on molecular taxonomy and phylogeny of Halichondria species.

Specimens of Halichondria sp. were collected from the subtidal zone of Dok-do island in the East Sea (Sea of Japan) of Korea using SCUBA diving. Voucher specimens were deposited in the National Marine Biodiversity Institute of Korea (MABIK IV00166751). Genomic DNA was extracted from the tissue and mitogenome sequences were analyzed by application of Illumina Hiseq2000 sequencing platform (Macrogen, Seoul, Korea). Sequences were assembled and annotated, in comparison with the previously reported mitogenome sequences of Halichondriid species (Jun et al. 2015; Kim et al. 2017) using Geneious v9.1.8 (Kearse et al. 2012). In addition, we used the mitochondrial genome annotation (MITOS) server (Bernt et al. 2013), and tRNAscan-SE server (Lowe and Chan 2016) for annotation. Maximum-likelihood (ML) tree was constructed to investigate the molecular taxonomic position of these species using GTR + G model in MEGA6 (Tamura et al. 2013) and the dataset was used as nucleotide sequences of 14 protein-coding genes (PCGs) from mitogenomes of the other 12 species in the order Halichondrida.

The complete mitogenome of Halichondria sp. (GeneBank accession number MK105765) is 19,687 bp in length, containing 14 protein-coding genes (PCGs), 2 ribosomal RNAs (rRNAs), and 25 transfer RNAs (tRNAs). Overall, nucleotide base composition of H. sp. is 28.9% A, 15.1% C, 21.9% G, 34.1% T, revealing high A + T bias (63%) similar to the other Halichondriid sponges. All PCGs use typical ATG as a start codon. Thirteen PCGs (cox2, atp8, atp6, cox3, cytb, atp9, nad4, nad6, nad3, nad4l, cox1, nad1 and nad4) use TAA as the stop codon, while one (nad2) gene has TAG. The length of tRNA genes range from 69–84 bp and all tRNAs have the typical cloverleaf structure.

In ML tree (Figure 1), H. sp. was clustered with Halichondriid sponges previously announced from GenBank, with high bootstrap values of 99%. Halichondriid sponges indicate the polyphyly and are a sister-group relationship with the family Suberitidae, as well as support for previously published 28S rRNA and COI gene trees (Erpenbeck et al. 2005, 2007, 2012).

Figure 1. Maximum-likelihood (ML) tree based on the protein-coding genes (PCGs) of Halichondria with family Halichondriidae and other sponges under order Suberitida. Three species derived from Tetractinellida was used as outgroup for tree rooting. Numbers above the branches indicate ML bootstrap values from 1,000 replications.

Disclosure statement

The authors declare that they do not have any conflict of interest. The authors alone are responsible for the content and writing of the paper.

Additional information

Funding

This work was supported by the grants of National Marine Biodiversity Institute of Korea [2019M00100].