Complete mitochondrial genome of Henricia pachyderma (Asteroidea, Spinulosida, Echinasteridae) and phylogenetic analysis

Abstract

Next-generation sequencing was used to obtain the complete mitogenome of Henricia pachyderma (Hayashi, 1940). The mitogenome form was found to be a circular molecule 16,192 bp long with a 57.1% AT bias. Gene arrangement and composition of H. pachyderma were exactly the same as those of previously reported mitogenomes from other species of the family Echinasteridae, including H. leviuscula and Echinaster (Othilia) brasiliensis. Phylogenetic analysis with maximum likelihood and Bayesian inference revealed that H. pachyderma formed a monophyletic clade with H. leviuscula and E. (O.) brasiliensis belonging the same taxon, family Echinasteridae.

Keywords:

• Echinodermata
• Asteroidea
• Henricia
• phylogeny
• mitogenome

The genus Henricia is a major taxon of sea stars along the coast of the North Pacific and has high species diversity (Wakita et al. 2019). Therefore, some studies have attempted analysis of species identification and phylogenetic relationships using molecular phylogenetic methods (Chichvarkhin 2017; Knott et al. 2018; Wakita et al. 2019). However, it is difficult to define species boundaries in the genus Henricia, and this remains an issue in the phylogeny of the genus (Clark and Downey 1992; Mah and Blake 2012; Chichvarkhin 2017). For the above-mentioned reasons, mitogenomic studies of the genus Henricia have not addressed numerous cases. In this study, we carefully identified Henricia specimens based on morphological comparisons with previous morphological studies showing clearly elucidated results (Hayashi 1940; Djakonov 1961). The complete mitochondrial genome sequence of H. pachyderma was characterized and a phylogenetic analysis within the class Asteroidea with data from GenBank was performed.

A specimen was collected from waters adjacent to Pohang in the East Sea, Korea (36°11′58″N, 129°24′47″E) at a depth of 15 m, by scuba diving. Voucher specimens and mitochondrial DNA samples were deposited in the Marine Echinoderm Resources Bank of Korea (Seoul, Korea) and granted a voucher number: MERBK-A-1261. Mitochondrial DNA analyses conformed to the method described by Lee and Shin (2018). Phylogenetic analysis was performed with 32 complete mitogenomes of echinoderms (16 asteroids, including H. pachyderma, four crinoids, four ophiuroids, four echinoids, and four holothuroids) and two hemichordates (Balanoglossus carnosus and B. clavigerus), which were used as outgroups for this analysis. Phylogenetic analysis of the mitogenome nucleotide sequence dataset was performed using the maximum likelihood (ML) method with RAxML 8.2 (Stamatakis 2014) and Bayesian inference (BI) with MrBayes 3.2 (Ronquist et al. 2012).

The mitogenome sequence of H. pachyderma was 16,192 bp long and was submitted to GenBank under the accession number MK947912. The gene arrangement of H. pachyderma was exactly the same as that of previously reported mitogenomes for other species of the family Echinasteridae, such as H. leviuscula and Echinaster (Othilia) brasiliensis. The overall nucleotide composition of H. pachyderma was 29.2% A, 24.8% C, 18.1% G, and 27.9% T with a 57.1% AT bias. The 11 protein-coding gene sequences (PCGs) were initiated with the start codon (methionine), but ND3 and ND4L initiated with the isoleucine, ATT and ATC, respectively. The 12 PCGs terminated with a termination codon (TAA or TAG); however, CytB did not have a termination codon, and the 3′ end terminated with phenylalanine (TTC)+T. To reveal the phylogenetic analysis of H. pachyderma within the class Asteroidea, a phylogenetic tree was constructed based on the concatenated sequences of 13 PCGs identified using the ML and BI methods. Henricia pachyderma was closely clustered with H. leviuscula and Echinaster (Othilia) brasiliensis belonging to the same taxon, family Echinasteridae (Figure 1). The mitogenome newly obtained in this study expanded the genomic resources available for further evolutionary studies of the class Asteroidea among others and will play a significant role in conservation genetics.

Figure 1. Phylogenetic analysis of Henricia pachyderma and an additional 31 echinoderms performed with the maximum likelihood and Bayesian inference methods based on the nucleotide sequences of 13 protein-coding gene sequences. Two hemichordates (Balanoglossus carnosus and B. clavigerus) were used as outgroups. The bootstrap support and posterior properties values are indicated on each node as >70 and 0.7.

Disclosure statement

The authors report no conflicts of interest. The authors alone are responsible for the content and writing of this article.

Additional information

Funding

This research was a part of the project titled “Improvement of management strategies on marine disturbing and harmful organisms” funded by the Ministry of Oceans and Fisheries, Korea [No. 20190518].