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A Distinct Mitogenome of Peanut Worm Sipunculus Nudus (Sipuncula, Sipunculidae) from Beibu Gulf

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A Distinct Mitogenome of Peanut Worm Sipunculus Nudus (Sipuncula, Sipunculidae) from Beibu Gulf Mitochondrial DNA Part B Resources ISSN: (Print) 2380-2359 (Online) Journal homepage: https://www.tandfonline.com/loi/tmdn20 A distinct mitogenome of peanut worm Sipunculus nudus (Sipuncula, Sipunculidae) from Beibu Gulf Yusong Guo, Chun Wang, Jiawei Zhang, Qingheng Wang, Gyamfua Afriyie & Zhongduo Wang To cite this article: Yusong Guo, Chun Wang, Jiawei Zhang, Qingheng Wang, Gyamfua Afriyie & Zhongduo Wang (2020) A distinct mitogenome of peanut worm Sipunculusnudus (Sipuncula, Sipunculidae) from Beibu Gulf, Mitochondrial DNA Part B, 5:2, 1839-1840, DOI: 10.1080/23802359.2019.1689195 To link to this article: https://doi.org/10.1080/23802359.2019.1689195 © 2019 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group. Published online: 15 Apr 2020. Submit your article to this journal View related articles View Crossmark data Full Terms & Conditions of access and use can be found at https://www.tandfonline.com/action/journalInformation?journalCode=tmdn20 MITOCHONDRIAL DNA PART B 2019, VOL. 5, NO. 2, 1839–1840 https://doi.org/10.1080/23802359.2019.1689195 MITOGENOME ANNOUNCEMENT A distinct mitogenome of peanut worm Sipunculus nudus (Sipuncula, Sipunculidae) from Beibu Gulf Yusong Guo, Chun Wang, Jiawei Zhang, Qingheng Wang, Gyamfua Afriyie and Zhongduo Wang Key Laboratory of Aquaculture in South China Sea for Aquatic Economic Animal of Guangdong Higher Education Institutes, Fisheries College, Guangdong Ocean University, Zhanjiang, China ABSTRACT ARTICLE HISTORY Peanut worm, Sipunculus nudus is a cosmopolitan species found in inter-tidal sands. In this article, Received 4 October 2019 based on the samples collected from the Beibu Gulf, China, a mitochondrial DNA sequence by Illumina Accepted 27 October 2019 high throughput sequencing, was carried out on muscle and determined the complete mitogenome. KEYWORDS This mitogenome of peanut worm is 15,331 base pairs in length (Accession number: MN481531) and Sipunculus Peanut worm; Sipunculus comprises of 37 genes as in the typical mitochondrial gene arrangement of . Moreover, the nudus; mitogenome; high- phylogenetic analysis shows that our sample is a novel type in China and has a distantly genetic rela- throughput sequencing tionship with the known populations in South China Sea. This mitogenome will serve as the foundation technique; phylogen- for the molecular genetic studies of peanut worm. etic analysis Peanut worm Sipunculus nudus (Sipuncula, Sipunculidae) is Guangdong Ocean University (#s.nudus0003). Partial DNA the most known species in the genus Sipunculus, widely dis- was subjected to high-throughput sequencing (Illumina tributed in all oceans (Cutler 1994). At least five distinct Hiseq) and successfully acquired the complete mitogenome. branches of S. nudus were revealed by molecular markers This mitogenome contains 37 genes which include 22 trans- (Kawauchi and Giribet 2014), which were partially supported fer RNA genes, 2 ribosomal RNA genes, 13 protein-coding by the reported four mitogenomes for samples from France genes. Evolutionary analyses were conducted in MEGA6 with and China (Mwinyi et al. 2009; Song et al. 2016; Zhong et al. mitogenomic sequences of the other peanut worms by 2018). Moreover, combined with the field survey, the South Maximum Likelihood (ML, GTR þ GþI), Neighbor Joining (NJ), China Sea (SCS), especially the Beibu Gulf in China could be a and Maximum Parsimony (MP) methods (Tamura et al. 2013). hotspot where the peanut worms have a high genetic diversity Different methods support a similar topology. (Wang et al. 2012; Hsu et al. 2013; Hsueh and Tan 2016). As shown in Figure 1, the evolutionary tree is reconstructed Here, the mature peanut worms were collected from the with FJ422961 from France as outgroup. Among the 4 taxa from inter-tidal sands in Suixi Town close to Beibu Gulf, China China Sea, the MN481531 is divided early as a distinct SCS (2111’32.3”N 10944’27.2”E). The muscle was used to extract branch, while a 100 bootstrap value supports the closest genetic DNA using the method of proteinase K digestion. The typical relationship between the two taxa (KJ754934 and MG873457) specimen and DNA were deposited in the museum of representing well-known populations in SCS (Hsu et al. 2013). Figure 1. Maximum-likelihood (ML, GTR þ G þ 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 evolu- tionary rate differences among sites (5 categories (þG, parameter ¼ 0.5832)). The rate variation model allowed for some sites to be evolutionarily invariable ([þI], 42.3774% sites). The analysis involved 5 nucleotide sequences. All positions containing gaps and missing data were eliminated. There were a total of 14806 posi- tions in the final dataset. CONTACT Zhongduo Wang [email protected] Key Laboratory of Aquaculture in South China Sea for Aquatic Economic Animal of Guangdong Higher Education Institutes, Fisheries College, Guangdong Ocean University, Zhanjiang 524025, China ß 2019 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. 1840 Y. GUO ET AL. Disclosure statement Hsueh P, Tan KS. 2016. New records of peanut worms (Sipuncula) from Singapore. Raffles B Zool. 34:235–240. The authors report no competing of interest. Kawauchi GY, Giribet G. 2014. Sipunculus nudus Linnaeus, 1766 (Sipuncula): cosmopolitan or a group of pseudo-cryptic species? An integrated molecular and morphological approach. Mar Ecol. 35(4): Funding 478–491. Mwinyi A, Meyer A, Bleidorn C, Lieb B, Bartolomaeus T, Podsiadlowski L. This work was supported by Science and Technology Planning Project of 2009. Mitochondrial genome sequence and gene order of Sipunculus Guangdong Province, China [2017A030303075, 2016A020209010]. nudus give additional support for an inclusion of Sipuncula into Annelida. BMC Genomics. 10(1):27. Song S, Ding S, Yan Q, Qin Y. 2016. Complete mitochondrial genome of ORCID Sipunculus nudus (Sipuncula, Sipunculidae). Mitochondrial DNA. 27(2): – Zhongduo Wang http://orcid.org/0000-0003-0835-4463 1022 1023. Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. 2013. MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol. – References 30(12):2725 2729. Wang QH, Guo YS, Wang ZD, Du XD, Deng YW. 2012. Isolation and char- Cutler EB. 1994. The Sipuncula: their systematics, biology, and evolution. acterization of microsatellite DNA loci from the peanut worm, Cornell University Press. Ithaca and London. Sipunculus nudus. Genet Mol Res. 11(2):1662–1665. Hsu TH, Ning Y, Gwo JC, Zeng ZN. 2013. DNA barcoding reveals cryptic Zhong S, Zhao Y, Zhang Q, Chen X. 2018. The complete mitochondrial diversity in the peanut worm Sipunculus nudus. Mol Ecol Resour. 13(4): genome of the cryptic species in peanut worm Sipunculus nudus 596–606. (Sipuncula, Sipunculidae) from Beibu Bay. Mitochondrial DNA Part B. 3(2):484–485..
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