The complete mitochondrial genome of Ophiura kinbergi (Ophiuroidea, Ophiurina): genome structure and phylogenetics

Abstract

The length of the complete mitochondrial genome was 16,626 bp for Ophiura kinbergi, containing 35 genes similar to other known ophiuroids. The GC content was 33.35%. The gene structure was identical to known mitochondrial genomes from the species of genus Ophiura. Phylogenetic results indicated conserved relationships between O. kinbergi and three other Ophiura species. These results could provide detailed information for better understanding the evolution patterns of brittle stars, especially for the genus Ophiura.

Keywords:

• Mitochondrial genome
• Ophiuroid
• phylogeny

Ophiura kinbergi, belonging to Ophiurida, Ophiuroidea, is a common species widely distributed from the Red Sea to the West Pacific Ocean (Liao 2004). Marine bioactive substances could be produced by this species, such as Ophiurasaponin and some anti-oxidants (Zhen et al. 2015). The sample was collected from the Yellow Sea (35°N, 123°E) and was stored in Key Laboratory of Science and Engineering for Marine Ecology and Environment, First Institute of Oceanography, MNR (No. FIO-ECH-YSJ01).

The whole genome of O. kinbergi was sequenced on the Illumina HiSeq 2500 Sequencing Platform (Illumina, Hayward, CA) by Novogene Corporation (Beijing, China). It was assembled using SPAdes 3.6.1(Bankevich et al. 2012). BLAST algorithm-based search against other available Ophiuroidea mitogenomes in GenBank was used to query mitochondrial genomic fragments. Price (Ruby et al. 2013) and MITObim v1.8 (Hahn et al. 2013) were used to fill the gaps. The mitochondrial reads were collected by bowtie2 (Langmead and Salzberg 2012) and reassembled. The circular structure of the mitochondrial genome was verified using Bandage (Wick et al. 2015). The complete mitochondrial genome of O. kinbergi was submitted to Genbank and the accession number was MH910618.

The gene structure of O. kinbergi contains 35 genes, including 13 coding genes, 2 ribosomal RNA genes, and 22 transfer RNA genes. Lengths of the whole mitochondrial genomes and protein-coding genes were 16,626 and 11,535 bp, respectively. The GC content of this mitochondrial genome was 33.35%. The gene order within the genus Ophiura was identical, which illustrated the conserved gene structure in this genus.

Phylogenetic relationships among O. kinbergi and 22 brittle stars were analyzed using the maximum-likelihood method by IQTREE (Nguyen et al., 2015). The nucleotide models of each gene were selected by ModelFinder (Kalyaanamoorthy et al. 2017). This phylogenetic tree was divided into four orders, which were consistent with O’Hara et al. (2018) (Figure 1). The relationship between O. kinbergi and other ophiuroids showed it closest to Ophiura albida. This study provided additional details for the phylogenetic studies of Ophiuroidea and genus Ophiura.

Figure 1. The maximum-likelihood tree of 13 protein-coding mitochondrial genes in 23 ophiuroids. Number at each branch represents the bootstrap probability.

Disclosure statement

No potential conflict of interest was reported by the author(s).

Additional information

Funding

This study was supported by the Basic Scientific Fund for National Public Research Institutes of China [2018Q09], National Natural Science Foundation of China [41706190, 4181101341], and the Key Laboratory for Ecological Environment in Coastal Areas, State Oceanic Administration [201609].