A distinct mitogenome of peanut worm Sipunculus nudus (Sipuncula, Sipunculidae) from Beibu Gulf

Abstract

Peanut worm, Sipunculus nudus is a cosmopolitan species found in inter-tidal sands. In this article, based on the samples collected from the Beibu Gulf, China, a mitochondrial DNA sequence by Illumina high throughput sequencing, was carried out on muscle and determined the complete mitogenome. This mitogenome of peanut worm is 15,331 base pairs in length (Accession number: MN481531) and comprises of 37 genes as in the typical mitochondrial gene arrangement of Sipunculus. Moreover, the phylogenetic analysis shows that our sample is a novel type in China and has a distantly genetic relationship with the known populations in South China Sea. This mitogenome will serve as the foundation for the molecular genetic studies of peanut worm.

Keywords:

• Peanut worm
• Sipunculus nudus
• mitogenome
• high-throughput sequencing technique
• phylogenetic analysis

Peanut worm Sipunculus nudus (Sipuncula, Sipunculidae) is the most known species in the genus Sipunculus, widely distributed in all oceans (Cutler 1994). At least five distinct branches of S. nudus were revealed by molecular markers (Kawauchi and Giribet 2014), which were partially supported by the reported four mitogenomes for samples from France and China (Mwinyi et al. 2009; Song et al. 2016; Zhong et al. 2018). Moreover, combined with the field survey, the South China Sea (SCS), especially the Beibu Gulf in China could be a hotspot where the peanut worms have a high genetic diversity (Wang et al. 2012; Hsu et al. 2013; Hsueh and Tan 2016).

Here, the mature peanut worms were collected from the inter-tidal sands in Suixi Town close to Beibu Gulf, China (21°11'32.3”N 109°44'27.2”E). The muscle was used to extract DNA using the method of proteinase K digestion. The typical specimen and DNA were deposited in the museum of Guangdong Ocean University (#s.nudus0003). Partial DNA was subjected to high-throughput sequencing (Illumina Hiseq) and successfully acquired the complete mitogenome. This mitogenome contains 37 genes which include 22 transfer RNA genes, 2 ribosomal RNA genes, 13 protein-coding genes. Evolutionary analyses were conducted in MEGA6 with mitogenomic sequences of the other peanut worms by Maximum Likelihood (ML, GTR + G+I), Neighbor Joining (NJ), and Maximum Parsimony (MP) methods (Tamura et al. 2013). Different methods support a similar topology.

As shown in Figure 1, the evolutionary tree is reconstructed with FJ422961 from France as outgroup. Among the 4 taxa from China Sea, the MN481531 is divided early as a distinct SCS branch, while a 100 bootstrap value supports the closest genetic relationship between the two taxa (KJ754934 and MG873457) representing well-known populations in SCS (Hsu et al. 2013).

Figure 1. Maximum-likelihood (ML, GTR + G + I) consensus trees based on mitogenomic DNA sequences. All the bootstrap values are indicated at the nodes. The percentages of replicate trees in which the associated taxa clustered together in the bootstrap test (1000 replicates) are shown above the branches. Initial tree(s) for the heuristic search were obtained automatically by applying Neighbor-Join and BioNJ algorithms to a matrix of pairwise distances estimated using the Maximum Composite Likelihood (MCL) approach, and then selecting the topology with superior log likelihood value. A discrete Gamma distribution was used to model evolutionary rate differences among sites (5 categories (+G, parameter = 0.5832)). The rate variation model allowed for some sites to be evolutionarily invariable ([+I], 42.3774% sites). The analysis involved 5 nucleotide sequences. All positions containing gaps and missing data were eliminated. There were a total of 14806 positions in the final dataset.

Disclosure statement

The authors report no competing of interest.

Additional information

Funding

This work was supported by Science and Technology Planning Project of Guangdong Province, China [2017A030303075, 2016A020209010].