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A Mitogenomic Phylogeny and Genetic History of Amphioctopus Fangsiao (D’Orbigny 1839-1841) from China

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A Mitogenomic Phylogeny and Genetic History of Amphioctopus Fangsiao (D’Orbigny 1839-1841) from China Journal of Survey in Fisheries Sciences 6(2) 1-16 2020 A mitogenomic phylogeny and genetic history of Amphioctopus fangsiao (d’Orbigny 1839-1841) from China Lashari P.1,3; Wei Ch.; Gong L.1; Liu L.1; Jiang L.1; Liu B.1; Muhammad F.2; Laghari M.Y.3; Lashari Kh.H.3; Waryani B.3; Hlaing N.N.S.4; Yingying Ye1; Lü Z.1* Received: March 2019 Accepted: November 2019 Abstract Phylogeny and genetic diversity of Amphioctopus fangsiao were assessed by sequence analysis of complete mitochondrial genomes, sequenced from 15 individuals of nine populations. The whole mtDNA genomes size were ranging from 15977 to 15990 bp. Data revealed 1642 polymorphic sites and 1023 parsimony informative sites. The phylogenetic analysis based on neighbor joining tree disclosed two clades. It consisted of four (Dalian, Yantai, Qingdao and Nantong) and five populations (Shanghai, Zhoushan, Xiamen, Dongshan and Zhanjiang). Genetic differentiation coefficient (FST) was recorded higher i.e 0.61476. While, the AMOVA analysis showed that 61.48% of the genetic variation existed between the two clades. However, only 38.52% of the genetic variation existed within each clade. In further, the net genetic distance between the two groups was 0.030. The possible reason of differentiation is quaternary glacial period and Yangtze River. Keywords: Amphioctopus fangsiao, mtDNA, genetic differentiation, phylogeny, populations. 1-National Engineering Research Center of Marine Facilities Aquaculture, College of Marine Downloaded from sifisheriessciences.com at 17:05 +0330 on Thursday September 23rd 2021 [ DOI: 10.18331/SFS2020.6.2.1 ] Sciences and Technology, Zhejiang Ocean University, No.1, Haida South Road, Lincheng Changzhi Island, Zhoushan, Zhejiang, 316022 P.R. China 2-Center of Excellence in Marine Biology, University of Karachi, Main University Road Karachi 75270. Sindh, Pakistan 3-Department Fresh Water Biology & Fisheries, Allama I.I.Kazi Campus, University of Sindh, Jamshoro-76080, Sindh, Pakistan. 4-Biotechnology Research Departments, Ministry of Education, Tazoe Gate, Kyaukse, Union of Myanmar Corresponding author’s Emial: [email protected] 2 Lashari et al., A mitogenomic phylogeny and genetic history of Amphioctopus fangsiao … Introduction (Maltagliati et al., 2002, Hellberg et al., Amphioctopus fangsiao belongs to 2002, Fernandez et al., 2011). Unlike family Octopodidae. It distributes other marine organisms, having high widely in west Pacific Ocean, range of dispersal capacity, large especially in Yellow Sea and Bohai Sea population sizes, high fecundity and (Dong, 1988; Lu et al., 2012). A. planktonic mood of dispersal which fangsiao considered as a potential helps in extensive gene flow (Bohonak species for aquaculture (Wang et al., 1999, Zid et al., 2012), the Octopus 2015), due to its rapid growth rate and species like Octopus minor, O. vulgaris high nutritional value. Tons of its and A. fangsiao show limited dispersal fisheries have annually been harvested capacity both at larval and adult stages alone in Shandong province. However, (Oosthuizen et al., 2004; Kim et al., it has been reported that its natural 2009; Kang et al., 2012; Lü et al., 2013, population is decreasing because of De Luca et al., 2016, 2015, Melis et over-exploitation (Zhang et al., 2009). al., 2018). A. fangsiao adults are either Therefore, it is intuitive to have its slow mover or like sessile, crawling resource management and conservation. away on the sea bed or burrowing deep Until now, few studies are available to in mud. It has benthos-attached eggs, elucidate A. fangsiao genetic aspects spent only a few days as planktonic (Gao et al., 2002; Zhang et al., 2009, larval stage. Therefore, it has weak and Lü et al., 2010, Muhammad et al, dispersal and limited gene flow, 2019). Gao et al. (2002) and Zhang et resulting in the genetic differentiation al. (2009) used allozyme and amplified among populations. fragment length polymorphism (AFLP). Assessment of genetic diversity Lü et al. (2011, 2010) examined several within and among populations has A. fangsiao populations using immense importance, which deliver a mitochondrial 16S rRNA and the COI possible genetic source for future gene and Muhammad et al. (2019), adaptation (Xu, 2012) and in area of investigated using three mtDNA genes evolutionary biology (Hao et al., 2015, (ATPase 6, ND2 and ND5). All the Ortego et al., 2015). In natural earlier studies showed certain level of population its level is determined by the differentiation. The whole mtDNA interplay of mutation, migration, drift genome approach of investigation was and selection (Harrison, 1991, Vellend not carried earlier. and Geber 2005, Wethington et al., Downloaded from sifisheriessciences.com at 17:05 +0330 on Thursday September 23rd 2021 [ DOI: 10.18331/SFS2020.6.2.1 ] A. fangsiao is one of the marine 2007). The role of each of these forces species that spawn life time in marine depends on the life history of the ecosystem. The fluctuating physical species. It’s mating system and properties of marine ecosystem dispersal abilities, as well as extrinsic influence organisms which restrict gene factors such as the landscape matrix, its flow over large geographic distances history and anthropogenic actions (Gow, Journal of Survey in Fisheries Sciences 6(2) 2020 3 et al., 2004; Husemann et al., 2012). In using the same PCR primers. Sequences the present study, we analyzed data of were aligned using CLUSTALX 1.83, fifteen complete mitochondrial genes Thompson et al. (1997) was used for gained, from fifteen individuals alignment and editing of sequences and collected from nine localities across the BioEdit 7.0.1, (Hall, 1999). Using CG Chinese coast. The sequences were View Server to draw the mtDNA ring examined to understand the genetic diagram. The neutrality test of diversity and phylogeny of A. fangsiao haplotype and nucleotide diversity and reveal the possible issues impacting indices their variances as well the phylogeographic pattern. The (Tajima’s D, Fu and Li’s D*, Fu and results of the present investigation Li’s F*) were calculated using DnaSP provide profound information for the version 5.0 software package, (Librado future management and conservation of and Rozas, 2009). Genetic distance this species. calculation and cluster analysis were carried out by using Mega 6.0 software. Materials and methods The phylogenetic tree was constructed Samples were collected from nine by UPGMA model and the bootstrap locations (Fig. 1). Thereafter, they were (repetition number 1000) was used to preserved in 95% ethanol and check the branch trust. Octopus Aegina transported to the laboratory. The total (NC_029702.1), (Zhang et al., 2015), genomic DNA was isolated from Octopus variabilis (NC_015896.1), muscle tissues using a standard protocol. (Cheng et al., 2012) Octopus vulgaris A set of 20 PCR primers were used to (NC_006353.1), (Yokobori et al., 2004), amplify overlapping fragments that Octopus bimaculoides (NC_028547.1), covered the whole mitochondrial Domínguez et al. (2015) mtDNA were genome of the Amphioctopus fangsiao. used as the out group in the Primarily, primers were designed on the Phylogeography analysis. The basis of complete mtDNA sequence haplotype networking was created using Gene Bank under accession number NETWORK software version 5.0.0.1 NC_007896.1 (Akasaki et al., 2006). (Bandelt et al., 1999). The genetic Later on, specific primers were structure of the population was assessed designed according to newly obtained using the FST statistic, and its sequences to facilitate primer walking. significance was repeated using Thermocycler conditions were as Arlequin 3.5 for 1 000 cycles. The Downloaded from sifisheriessciences.com at 17:05 +0330 on Thursday September 23rd 2021 [ DOI: 10.18331/SFS2020.6.2.1 ] follows: denaturation at 94 ◦C for 5 min, relationship between (1-FST) / 2-FST 35 cycles 94◦C for 30s, annealing at and the geographical distance of the 50◦C for 30s, extension at 72◦C for 30s, sample is plotted to determine whether and the final extension at 72◦C for 7 the population genetic structure min. Electrophoresis was performed on conforms to the geo-isolation model a 1.2% agarose gel and was sequenced (Slatkin, 1993). 4 Lashari et al., A mitogenomic phylogeny and genetic history of Amphioctopus fangsiao … Figure 1: Map showing collection sites of Amphioctopus fangsiao specimens. The genetic structure of the population negative and significantly deviated was further detected using the from neutral, (2) The use of nucleotide molecular variation analysis AMOVA mismatch distribution (mismatch method in Arlequin 3.5 software. distribution) analysis to test the Homoplasic sites were exposed by the existence of group expansion; unpaired use of the phylogeny network distribution test and neutral hypothesis investigation as applied in the Network test were used Arlequin3.01 software. Downloaded from sifisheriessciences.com at 17:05 +0330 on Thursday September 23rd 2021 [ DOI: 10.18331/SFS2020.6.2.1 ] 4.6 program. The differentiation time of the CO1 The historical dynamics of the gene and cytochrome b gene were population was carried out using two calculated by molecular clock theory. methods: (1) using Tajima's D and Fu's The evolution rate of CO1 gene was Fs test to determine whether the neutral calculated by 0.5% to 1. 4%/ million hypothesis was established, Tajima's D years (MY), and the evolution rate of and Fu's Fs neutral test results were Journal of Survey in Fisheries Sciences 6(2) 2020 5 cytochrome b gene were calculated by of 22 tRNA genes (tRNA-Lys, tRNA- 2.15% to 2.6% / MY, Zhao et al. (2013). Ala, tRNA-Arg, tRNA-Asn, tRNA-Ile, tRNA-Ser, tRNA-Asp, and tRNA-Thr) Results were located in the light chain and the A total of 15 complete mtDNA remainders were found in the other genomes of Amphioctopus fangsiao chain (Fig. 2). In the A. fangsiao were characterized (Gene Bank mtDNAs, 1642 positions were variable Accession No (MF 029678–MF and 1023 were parsimony-informative.
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