The complete mitochondrial genome of Neoporphyra dentata (Bangiales, Rhodophyta).

Neoporphyra dentata (Kjellman) L.-E. Yang & J. Brodie, 2020 is an economically valuable species in seaweed aquaculture in the southwest coastal regions of Korea. Here, we report the complete mitogenome information of N. dentata using Illumina Miseq platform permitted assembly of a circular mitochondrial genome of 26,807 bp from N. dentata consisting of 29.9% GC contents, 9 protein coding genes (PCGs), 2 ribosomal RNA genes (12S rRNA and 16S rRNA), 23 transfer RNA (tRNA) genes, and a non-coding region. The overall nucleotide composition was A: 38%, T: 32%, C: 14.7%, and G: 15.2%. The mitochondrial genome of N. dentata contributes to revealing the phylogenetic relationships among species of the Bangiaceae family.

Neoporphyra, a genus of red algae in the Bangiaceae family, is one of the most popular seaweeds for the production of sheet-like dried seafood, commonly referred to as dried laver, mostly in East Asian countries such as South Korea (‘Gim’), China (‘Zicai’), and Japan (‘Nori’) (Choi et al. 2014). The production of Neoporphyra as a marine crop has been reported that the annual value of laver in 2017 was almost $950 million (Kim 2013; Kim et al. 2017). Neoporphyra dentata is a native species that is distributed and intensively farmed in the southwest coastal regions of Korea. Although N. dentata production represents 10–20% of the domestic laver production in Korea, this species is increasing in economic importance in Korea as an alternative resource due to its plasticity in response to subtropical climate change (Kim et al. 2017; Kim et al. 2019). Therefore, we characterized the complete mitochondrial genome of N. dentata based on Illumina’s Miseq platform data.

Young blade samples were collected from Songji-myeon (34°33′00.0″N 126°36′'00.0″E), Haenam County, Jeonnam Province, Republic of Korea, and deposited in the Ocean and Fisheries Science Institute Haenam Branch at Haenam, Korea (specimen code JOFP0004562, http://www.jeonnam.go.kr; Sung-Je Choi; csjchoi@korea.kr). Genomic DNA was extracted from young blades using a DNeasy Power Plant Pro Kit (Qiagen, Valencia, CA, USA), in accordance with the manufacturer's protocol. Whole-genome resequencing was performed at Coscience Co. Ltd. (Mokpo, South Korea) using the Illumina Miseq platform (Illumina, Hayward, CA), yielding 7,731,923 paired raw reads. Assembly was conducted with various k-mers using SPAdes (Bankevich et al. 2012) using Pyropia yezoensis (NC_017837) as the reference and a circular contig of the N. dentata mitogenome was obtained. Finally, the resulting contig consensus sequence was annotated using MITOS2 (Bernt et al. 2013) and adjusted manually using DOGMA (Wyman et al. 2004). The annotated mitogenome of N. dentata was submitted to GenBank under accession number LC650807.

The complete mitogenome of N. dentata is a circular molecule that is 26,807 bp in length and contained 9 PCGs, 2 rRNA genes, 23 tRNA genes, one origin of L strand replication, and one control region. The N. dentata genome contains nine protein coding genes (rps11, rps12, ymf16, ymf39, atp8, atp9, nad3, nad4L, and cox3). All protein coding genes and ORFs have a conserved, typical ATG codon as a start signal and the common stop [codon is TAA (7 of 9 genes), whereas TAG is used as translation termination codon of nad3 and rps12 genes. To investigate its phylogenetic position, the mitogenome sequences of 11 complete mitogenomes of Bangiaceae and 3 outgroup species were aligned using Mega 7.0 (Kumar et al. 2016) with 1,000 bootstrap replicates (Figure 1). Phylogenetic analysis based on the complete mitogenomes showed that N. dentata was most closely related to N. haitanensis. The complete mitogenome of N. dentata will serve as a valuable tool for understanding the phylogenetic relationship and evolutionary history Bangiaceae.

Figure 1.

NJ phylogeny based on 11 complete mitogenomes of Bagiaceae species and one Laminaria and two Saccharina species as an outgroup. All the sequences were downloaded from NCBI’s GenBank.