The complete mitochondrial genome of Anneissia pinguis (Crinoidea, Articulata, Comatulidae), from South Korea.

In this study, the complete mitochondrial genome sequence of Anneissia pinguis was examined by next-generation sequencing analysis. The complete mitogenome of A. pinguis has 15,912 bp in length and 37 genomes consist of 13 protein-coding genes (PCGs), 22 tRNAs, 2 rRNAs, and 1 control region (D-loop). Both gene orders and characteristics were in accordance with other species belonging to the phylum Echinodermata. Phylogenetic analysis revealed the establishment of molecular taxonomic relationship in class Crinoidea based on complete mitogenome.

Genus Anneissia belonging to the order Comatulida of the subclass Articulata has been accepted within the nine species of genus Oxycomanthus Hoggett, Birtles & Vail, 1986 by Summers et al. (2014). For now, the genus Anneissia consists of nine species. Among them, in Korea, only three species had been reported, and Anneissia pinguis (AH Clark 1909) was not recorded yet. We provide the complete mitogenome of A. pinguis (MW008594) for contributing to the establishment of the evolutionary relationship of crinoids.

The specimen was collected in Jeju Island, Korea (33°41′05.0′′N, 127°28′02.0′′E) by trawling, at a depth of 89 m on 31 October 2017, and identified based on the morphological studies (Clark 1909; Gislén 1922). Voucher specimens (MERBK-C-20203247) and mitochondrial DNA (mt-DNA) samples were deposited in storage and freezer (−80 °C) of Marine Echinoderm Resources Bank of Korea (Philjae Kim, swubio@naver.com, Seoul, Korea), respectively. For isolating the mitochondria, gonad was used as a tissue sample. The mitochondria isolation method and whole experiment steps were conformed to the description by Song et al. (2016). The mitochondria were isolated using Mitochondria Isolations Kit (Qiagen, Germany), and mitochondria DNA (mt-DNA) was extracted by DNeasy Blood and Tissue Kit (Qiagen, Germany). For NGS, mt-DNA was amplified with REPLI-g Mitochondrial DNA Kit (Qiagen, Germany) and Exonuclease-Resistant Random Primer (Thermo Fisher Scientific, USA). The NGS analysis was conducted by Illumina Hiseq 4000 (platform (Illumina Inc., USA). The complete mitogenome was reconstructed by Geneious prime 2019.0.4. The phylogenetic analysis was conducted with the mitogenomes dataset of nine Echinodermata, including A. pinguis. The best-fit substitution model was estimated using jModelTest 2.1.1 (Guindon and Gascuel 2003) .

The complete mitogenome of A. pinguis (MW008594) is composed 15,912 bp of nucleotide. The genome is consists of 13 PCGs, 22 tRNA genes, 2 rRNA genes, and 1 control region (D-loop). The gene arrangement was in accord with other crinoids, except Antedon mediterranea (NC_010692). In all PCGs, the most common initiation codon is ‘ATG,’ except for ND4L, and ND5 started with ‘GTG.’ The most common termination codon is ‘TAA’ (ND4L, COX2, ATP8, ATP6, COX3, ND3, ND6, ND2), then is ‘TAG’ (COX1, ND5, ND1). Rest of the four PCGs (ND4, CytB) have incomplete terminal codon ‘T—.’ The mitochondrial base composition is 24.8% A, 46.6% T, 11.6% C, and 17% G.

The dataset for phylogenetic analysis included 13 PCGs of eight crinoids, and one asteroid (Asterias amurensis, AB183559) was used as an outgroup. The maximum-likelihood (ML) analysis was conducted using PhyML 3.1 with GTR + I + G model with 1000 replication of bootstrap assembling (Guindon et al. 2010). In the ML tree, A. pinguis formed a monophyletic clade in the crinoid group (Figure 1). In the molecular analysis based on complete mitogenome information, all crinoids that we compared were well distinguished at the species-level. The newly obtained mitogenome in this study will be used as a genomic resource, and be contributed to further evolutionary studies of Echinodermata based on molecular evidence.

Figure 1.

Phylogenetic tree inferred by maximum-likelihood using of 13 protein coding genes of nine echinodermata mitochondrial genomes, including A. pinguis (MW008594). Bootstrap support values based on 1000 replicates are displayed on each node as >70.