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The Open Access Israeli Journal of Aquaculture – Bamidgeh The Open Access Israeli Journal of Aquaculture – Bamidgeh As from January 2010 The Israeli Journal of Aquaculture - Bamidgeh (IJA) will be published exclusively as an on-line Open Access (OA) quarterly accessible by all AquacultureHub (http://www.aquaculturehub.org) members and registered individuals and institutions. Please visit our website (http://siamb.org.il) for free registration form, further information and instructions. This transformation from a subscription printed version to an on-line OA journal, aims at supporting the concept that scientific peer-reviewed publications should be made available to all, including those with limited resources. The OA IJA does not enforce author or subscription fees and will endeavor to obtain alternative sources of income to support this policy for as long as possible. Editor-in-Chief Published under auspices of Dan Mires The Society of Israeli Aquaculture and Marine Biotechnology (SIAMB), Editorial Board University of Hawaii at Manoa Library Sheenan Harpaz Agricultural Research Organization and Beit Dagan, Israel University of Hawaii Aquaculture Zvi Yaron Dept. of Zoology Program in association with Tel Aviv University AquacultureHub Tel Aviv, Israel http://www.aquaculturehub.org Angelo Colorni National Center for Mariculture, IOLR Eilat, Israel Rina Chakrabarti Aqua Research Lab Dept. of Zoology University of Delhi Ingrid Lupatsch Swansea University Singleton Park, Swansea, UK Jaap van Rijn The Hebrew University Faculty of Agriculture Israel Spencer Malecha Dept. of Human Nutrition, Food and Animal Sciences University of Hawaii Daniel Golani The Hebrew University of Jerusalem Jerusalem, Israel Emilio Tibaldi Udine University Udine, Italy ISSN 0792 - 156X Israeli Journal of Aquaculture - BAMIGDEH. Copy Editor Ellen Rosenberg PUBLISHER: Israeli Journal of Aquaculture - BAMIGDEH - Kibbutz Ein Hamifratz, Mobile Post 25210, ISRAEL Phone: + 972 52 3965809 http://siamb.org.il The Israeli Journal of Aquaculture – Bamidgeh 60(4), 2008, 237-242. 237 Genetic Diversity and Population Structure of the Peanut Worm (Sipunculus nudus) in Southern China as Inferred from Mitochondrial 16S rRNA Sequences Du Xiaodong*, Chen Zian, Deng Yuewen, Wang Qingheng and Huang Ronglian Fishery College, Guangdong Ocean University, 524025 Zhanjiang, China (Received 26.4.06, Accepted 8.7.06) Key words: peanut worm, Sipunculus nudus, genetic diversity, population structure, 16S rRNA gene Abstract Genetic diversity and population structure of the peanut worm (Sipunculus nudus) were investi- gated by using 536 base-pair fragments of the mitochondrial 16S ribosomal gene. Populations were collected from three locations along the southern coast of China - Beihai, Sanya, and Xiamen. Amplified polymerase chain reaction products were sequenced in both directions and data were analyzed using ClustalX, Arlequin, and MEGA. A total of 69 polymorphic sites and 21 distinct haplotypes were revealed. The mean haplotype and nucleotide diversity of the three pop- ulations were 0.814% and 0.37%, respectively. The Beihai population had the greatest haplo- type and nucleotide diversity, followed by the Xiamen and Sanya populations. Analysis of mole- cular variance (AMOVA) showed significant genetic differentiation among the three populations (Fst = 0.0619, p<0.05) and distinct population structures among the three sites. Introduction Genetic diversity, the fundamental hierarchy markers include nuclear and mitochondrial of species and ecosystem diversities, is the markers. Mitochondrial DNA (mtDNA) has a primary subject of biodiversity research (Avise high mutation rate relative to single-copy and Himrick, 1996). Documentation of genetic nuclear DNA (Brown et al., 1979) and, under diversity is needed to utilize and manage equilibrium conditions, maternal inheritance genetic resources. Genetic diversity can be contributes one quarter of nuclear DNA (Birky assessed by using morphological, cytological, et al., 1983). Thus population differentiation is physiological, biochemical, and molecular expected to evolve more rapidly within mtDNA markers. The most frequently used molecular than in allozymes and other coding regions of * Corresponding author. E-mail: [email protected] 238 Xiaodong et al. nuclear DNA, making mtDNA a more sensi- 3’ (Zhang and Ryder, 1993). Amplification tive indicator of population structure. was performed in a 50 µl reaction volume con- Mitochondrial DNA markers are frequently taining 1 µl DNA dilution, 25 pmol primers, 5 µl used to evaluate genetic diversity in marine 10x reaction buffer, 25 mM MgCl2, 200 µM invertebrates (e.g., Boulding et al., 1993; Su dNTP, and 2 U Taq polymerase (Sangon, et al., 2005; Kumar et al., 2007). Shanghai). The cycling conditions were 2 min In China, the peanut worm, Sipunculus denaturation at 94°C, 35 cycles of 45 s denat- nudus, is mainly distributed along the southern uration at 94°C, 1 min annealing at 50°C, 1 coast. The species is widely cultured in south- min extension at 72°C, and a final extension ern regions of China, especially in Beihai, at 72°C for 5 min. PCR products were sepa- Guangxi. Sipunculus nudus culture relies rated on 1.5% agarose gels; bands were entirely on seed collected from the wild, which stained with rhodium bromide and viewed may result in over-exploitation of wild popula- under a UV light source. tions. Therefore, it is urgent to obtain informa- A total of 5 µl of each PCR product was tion on the genetic diversity of wild populations used for 1.5% agarose gel electrophoresis to so as to manage commercial species. confirm the amplified fragment length with a Data on population genetics of S. nudus marker. Here, bands were made visible using have been reported on the basis of random ultraviolet light after an ethidium bromide amplified polymorphic DNA (Wang et al., bath. The remainder of each PCR product 2006). In the present study, genetic diversity was used as a template for automated and the population structures of S. nudus col- sequencing reactions performed with a T3 lected from three locations along the coast of Thermocycler and run on an ABI 310 DNA southern China were investigated using 16S sequencer. The primers used for sequencing rRNA gene sequence analysis. The objective reactions were the same as those for PCR was to provide useful information for resource amplification. Sequence data are available conservation and fishery management of the from GeneBank (accession numbers species. EU260100-EU260120). Data analysis. A total of 536 bp sequences Materials and Methods from 30 individuals were aligned by using Sample collection. Wild samples of S. nudus ClustalX (Thompson et al., 1997). Data were were collected from Beihai in Guangxi, Sanya analyzed using Arlequin vers. 3.0 (Excoffier et in Hainan, and Xiamen in Fujian, all in the al., 2005). The numbers of transition, trans- South China Sea. Fresh tissues from the mus- version, and haplotype, as well as haplotype cle and whole individuals were preserved in diversity (h), and nucleotide diversity (pi) val- 70% ethanol. ues (Nei, 1987), were calculated for separate Total DNA extraction. Total DNA was and combined populations. The total number extracted from the ethanol-preserved muscle of nucleotide differences, mean sequence tissues. The tissues were incubated overnight divergence values, and Jukes-Cantor genetic in lysis buffer with proteinase K at 37°C. DNA distances (Jukes and Cantor, 1969) were cal- was purified using phenol-chloroform accord- culated for each pair using molecular evolu- ing to Wang et al. (2006). Isolated DNA was tionary genetics analysis (MEGA vers. 2.1; dissolved in 50-100 µl distilled water. This Kumar et al., 2004). solution was further diluted in distilled water to Analysis of molecular variance (AMOVA) 100 ng/µl for polymerase chain reaction was used to partition the total genetic varia- (PCR). tion into variance components and produce Amplification and sequencing. A 536-bp fixation indices (Fst). Fst values were calcu- segment of 16S rRNA was amplified by PCR. lated for the three populations separately and The primers were: 16SAR (forward) 5’-CGC- together for all pairs of populations on the CTGTTTATCAAAAACAT3’ and 16SBR basis of information regarding haplotypes and (reverse) 5’CCGGTTTGAACTCAGATCATG- their frequencies. The statistical significance Genetic diversity and population structure of the peanut worm 239 of the Fst values was tested by permutation (Kong et al., 2003) and in 500-bp 16S rRNA tests (10,000 replicates). AMOVA was con- gene sequences of the oyster, Crassostrea ducted by using Arlequin vers. 3.0 (Excoffier rivularis, there were 12 haplotypes in 105 et al., 2005). samples at 23 polymorphic sites (Su et al., 2005). Possible explanations for the high level Results of variation in S. nudus are higher mutation in Mitochondrial DNA 16S rRNA polymorphism. the 16S rRNA gene sequence and large effec- The 536 bp sequences of the 16S rRNA gene tive population sizes of the species. from 30 individuals produced 69 polymorphic The mean haplotype and nucleotide diver- sites that defined 21 haplotypes (Table 1). sity of the three populations were 0.814 and One haplotype (F) was shared by the Beihai 0.37%, respectively. These results are com- and Sanya populations while the remaining parable with those on other marine inverte- twenty (95.2%) were unique to one of the brates, for example, 0.57 and 0.14% in three populations. Forty (58.0%) of the Crassostrea virginica from the Atlantic Ocean nucleotide substitutions in the 16S rRNA gene (Reeb and Avise, 1990) and 0.07-0.55 and were synonymous and 29 were non-synony- 0.08%-0.6% for Penaeus monodon from the mous. Variant substitutions of parsimony Indian Ocean (Kumar et al., 2007). The high informative sites appeared in the 21 haplo- level of genetic diversity in the present study types at position 482 (A↔G, A↔T, T↔G, indicates that the 16S rRNA gene sequence three variants). might be useful as a genetic marker for aqua- Haplotype, nucleotide diversity, and other culture purposes such as maintaining stock population-specific diversity indices are diversity and distinguishing hatchery stocks showed in Table 2. For all indices, the Beihai from wild populations.
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