The complete mitochondrial genome of Chinese endemic specie Phascolosoma esculenta (Sipuncula, Phascolosomatidae) from Beibu Bay

Abstract

Phascolosoma esculenta is economic important species in the fishery and aquaculture in southeast China. However, whether P. esculenta is conservative endemic specie or a complex of cryptic forms had not been verified yet. Here, we report the complete mitochondrial genome sequence of P. esculenta from Beibu Bay. The mitogenome has 15,494 base pairs and made up of total of 38 genes (13 protein-coding, 23 transfer RNAs, and 2 ribosomal RNAs), and a putative control region. There were only 56 mutations sites within Chinese populations. This study adds second mitogenome of P. esculenta, and will provide useful genetic information for future conservation and exploitation of this economic valuable marine benthic invertebrate.

Keywords:

• Mitochondrial genome
• Phascolosoma esculenta
• Sipuncula

Sipuncula (known as peanut worms) is a clade of unsegmented, coelomate marine worms, which inhabit a diversity of benthic substrates in all major oceans(Lemer et al. 2015). Phascolosoma currently includes 17 valid species, in which many species has been considered as cosmopolitan taxon (Johnson et al. 2016). However, due to limited set of external morphological and internal anatomical characters, recent research has revealed the occurrence of cryptic species in this putatively cosmopolitan species (Kawauchi and Giribet 2010; Johnson et al. 2016). Phascolosoma esculenta, a species restricted to the coastal zone of southeast China, has a free-swimming larvae phase last for approximately 15 days (Gao et al. 2018), However, the cryptic speciation of this species has not yet been verified. Mitochondrial genome is useful molecular techniques for species delimitation, especially when there is small number of unambiguous taxonomic characters available for species delimiting. In this study, we report the complete mitochondrial genome sequence of Chinese endemic specie P. esculenta from Beibu Bay, which will be an important genetic resource to assist in species delimitation and resource management of P. esculenta.

The tissue samples of P. esculenta from 5 individuals were collected from Beibu Bay, China (Qinzhou, 21.66066 N, 108.678115 E), and the whole body specimens (#GG0185) were deposited at Marine biological Herbarium, Guangxi Institute of Oceanology, Beihai, China. The total genomic DNA was extracted from the muscle of the specimens using an SQ Tissue DNA Kit (OMEGA, Guangzhou, China) following the manufacturer’s protocol. DNA libraries (350bp insert) were constructed with the TruSeq NanoTM kit (Illumina, San Diego, CA) and were sequenced (2 × 150bp paired-end) using HiSeq platform at Novogene Company, China. Mitogenome assembly was performed by MITObim (Hahn et al. 2013). The complete mitogenome of P. esculenta from Zhejiang, China (GenBank accession number: NC_012618.1) was chosen as the initial reference sequence for MITObim assembly. Gene annotation was performed by MITOS (Bernt et al. 2013).

The complete mitogenome of P. esculenta from Beibu Bay was found to be 15,494 bp in length (GenBank accession number: MG873458), including the usual set of gene for mitogenome except for extra threonine tRNA which consisting of 13 protein-coding, 23 tRNA and 2 rRNA genes, and a putative control region. The overall base composition of the mitogenome was estimated to be A 32.2%, T 33.4%, C 21.4% and G 12.9%, with a high A + T content of 65.6%, which is similar, but slightly higher than Wenzhou population (65.5%) (Shen et al. 2009). Compared with the high polymorphism within cosmopolitan sipunculan species (Sipunculus nudus, 37.0%) (Zhong et al. 2018), the mitogenome of Chinese endemic specie P. esculenta shared only 0.5% (56 mutations) polymorphism within Chinese populations, which indicated the relatively weak genetic divergence within P. esculenta. Phylogenetic analysis also showed the weak genetic divergence of P. esculenta (Figure 1), which consistent with genetic diversity study of P. esculenta based on mitochondrial cytochrome b gene. Our study suggested P. esculenta is conservative endemic specie without cryptic form, which will contribute to further conservation and exploitation of this economic valuable marine benthic invertebrate.

Figure 1. Phylogenetic tree in Sipuncula. The complete mitogenomes are downloaded from GenBank, and the phylogenic tree is constructed by maximum-likelihood method with 100 bootstrap replicates. The bootstrap values were labeled at each branch nodes. The gene's accession number for tree construction is listed as follows: Phascolosoma pacificum (NC_031412), Phascolosoma esculenta From Wenzhou(NC_012618), Sipunculus nudus from France (NC_011826), Sipunculus nudus from Yanta (KP751904), Sipunculus nudus from Gulei (KJ754934), and Sipunculus nudus from Beibu Bay (MG873457).

Disclosure statement

No potential conflict of interest was reported by the authors.

Additional information

Funding

This work was financially supported by Scientific Research and Technology Development Program of Guangxi (Grant No. AB16380105), Science and Technology Major Project of Guangxi (Grant No. AA17204069 & AA17204044), and the Fundamental Research Funds for Guangxi Academy of Sciences (Grant No. 2017YJJ23001).