Genetic Diversity and Structure Analysis of Phascolosoma esculenta in the Coastal Zone of South-eastern China Based on Mitochondrial Cyt b Gene

Phascolosoma esculenta is a newly developed mariculture species in south-eastern China. However, its wild populations are diminishing because of marine environmental pollution, beach reclamation, and overexploitation. To investigate the genetic diversity and genetic structure of the wild populations of P. esculenta, the entire sequence (1136 bp) of its mitochondrial cytochrome b (Cyt b) gene were sequenced and analyzed in 80 organisms sampled from four areas. A total of 59 variable sites and 49 haplotypes (61.25% of the total samples) were detected from the sequence, indicating a high level of polymorphism. High haplotype diversity (0.976±0.007) and low nucleotide diversity (0.00439±0.00027) were detected. Topologies of neighbor-joining trees were shallow and the clustering of haplotypes was not correlated with their geographical distributions. Both AMOVA and pairwise Fst analyses showed that the genetic differentiation between populations was relatively weak, which might be influenced by its life history, paleoclimate, and recent human activity. The neutrality test and mismatch-distribution analysis revealed that the expansion of P. esculenta populations occurred approximately 0.046 million years ago.

Kaynakça

Alzohairy, A.M. (2011). BioEdit: An important software for molecular biology. Gerf Bulletin of Biosciences, 2(1), 60-61.

Barrett, R.D.H. & Schluter, D. (2008). Adaptation from standing genetic variation. Trends in Ecology & Evolution, 23(1), 38-44. http://dx.doi.org/10.1016/j.tree.2007.09.008

Deng, Y., Song, N., Liu, M. & Gao, T.X. (2014). Population genetic analysis of Perinereis aibuhitensis based on the mitochondrial DNA Cyt b. Acta Hydrobiologica Sinica, 38(3), 597-601. http://dx.doi.org/10.7541/2014.85

Dong, Z.G., Li, X.Y., Wang, P.L., Wang, W.J., Zhang, Q.Q., Yan, B.L. & Sun, X.W. (2013). Genetic diversity and genetic differentiation of swimming crab (Portunus trituberculatus) from six geographical populations of China Sea based on mitochondrial D-loop gene. Journal of Fisheries of China, 09, 1304-1312. http://dx.doi.org/10.3724/SP.J.1231.2013.38630 Du, X.D., Chen, Z., Deng, Y.W. & Wang, Q.H. (2009). Comparative analysis of genetic diversity and population structure of Sipunculus nudus as revealed by mitochondrial COI sequences. Biochemical Genetics, 47(11-12), 884-891. http://dx.doi.org/10.1007/s10528-009-9291-x

Excoffier, L., Laval, G. & Schneider, S. (2005). Arlequin (version 3.0): an integrated software package for population genetics data analysis. Evolutionary bioinformatics online, 1, 47-50.

Fu, Y.X. (1997). Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection. Genetics, 147, 915-925.

Gillooly, J.F., Allen, A.P., West, G.B. & Brown, J.H. (2005). Metabolic rate calibrates the molecular clock: reconciling molecular and fossil estimates of evolutionary divergence. Proceedings of the National Academy of Sciences, 102, 140-145.

Grant, W.S. & Bowen, B.W. (1998). Shallow population histories in deep evolutionary lineages of marine fishes: Insights from sardines and anchovies and lessons for conservation. Journal of Heredity, 89(5), 415-426. https://doi.org/10.1093/jhered/89.5.415

Hewitt, G. (2000). The genetic legacy of the Quaternary ice ages. Nature, 405(6789), 907-913. http://dx.doi.org/10.1038/35016000

Huang, Z., Liu, N., Xiao, Y.A., Cheng, Y., Mei, W., Wen, L., Yu, X. (2009). Phylogenetic relationships of four endemic genera of the Phasianidae in China based on mitochondrial DNA control-region genes. Molecular phylogenetics and evolution, 53(2), 378-383. http://dx.doi.org/10.1016/j.ympev.2009.07.002

Imbrie, J., Berger, A., Boyle, E.A., Clemens, S.C., Duffty, A., Howard, W.R., Mcintyre A, et al. (1992). On the structure and origin of major glaciation cycles 1. Linear responses to Milankovitch forcing. Paleoceanography, 7(6), 701-738.http://dx.doi.org/10.1029/92PA02253

Jin, C.H., Zhu, J.Q., Xu, S.J. & Wang, W. (2011). Study on the embryonic and larval development of Phascolosoma esculenta. Oceanologia et Limnologia Sinica, 42(1), 94-100.

Lei, S.Y., Lu, M.M., Ding, L.F. & Zhu, J.Q. (2013). The morphology of the digestive tract of Phascoloma esculeuta. Journal of Biology, 30(2), 33-36(39). http://dx.doi.org/10.3969/j.issn.2095-1736.2013.02.033

Librado, P. & Rozas, J. (2009). DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics, 25(11), 1451-1452. http://dx.doi.org/10.1093/bioinformatics/btp187

Li, F.L. (1988). Studies on the genus Phascolosoma (sipuncula) off the China coasts. Journal of Ocean University of Qingdao, 19(3), 78-90.

Li, H.M., Lv, Z.M., Liu, L.Q., Wu, C.W. & Zhang, J.S. (2013) Genetic structure in 4 Octopus variabilis populations from China coastal waters based on mitochondrial Cyt b gene sequence. Oceanologia et Limnologia Sinica, 03, 626-631.

Li, J.J., Ye, Y.Y., Wu, C.W., Qi, P.Z., Guo, B.Y. & Chen, Y.J. (2013). Genetic variation of Mytilus coruscus Gould (Bivalvia: Mytilidae) populations in the East China Sea inferred from mtDNA COI gene Sequence. Biochemical Systematics and Ecology, 50(1), 30-38. http://dx.doi.org/10.1016/j.bse.2013.03.033

Liu, H.J., Liu, M., Ge, S.S., Wang, Q.X., Yu, D.D. & Guan, S.G. (2012a). Population structuring and historical demography of a common clam worm Perinereris aibuhitensis near the coasts of Shandong Peninsula. Biochemical Systematics and Ecology, 44, 70-78. http://dx.doi.org/10.1016/j.bse.2012.04.019

Liu, L.W., Xu, Q.H. & Chen, X.J. (2012b). Population genetic structure of Ommastrephes bartramii in the North Pacific Ocean based on the COI and Cyt b gene sequences analysis. Journal of Fisheries of China, 36(11), 1675-1684. http://dx.doi.org/10.3724/SP.J.1231.2012.27955

Liu, Y., Li, C.H., Su, X.R., Wang, M.Q., Li, Y.Y., Li, Y. & Li, T.W. (2013) Cloning and characterization of hemerythrin gene from Sipuncula Phascolosoma esculenta. Genes & Genomics, 35(1), 95-100. http://dx.doi.org/10.1007/s13258-013-0073-9

Long, L.L., Lu, M.M. & Zhu, J.Q. (2014a). Distribution and structural features of nephridial cilia in the sipunculan Phascolosoma esculenta. Chinese Journal of Zoology, 49(2), 253-260. http://dx.doi.org/10.13859/j.cjz.2014.02.012

Long, L.L., Sheng, Z., Lu, M.M., Ding, L.F. & Zhu, J.Q. (2014b). Structural features of musculature in the nephridium of Phascolosoma esculeuta. Chinese Journal of Zoology, 31(2), 9-12. http://dx.doi.org/10.3969/j.issn.2095-1736.2014.02.009

Long, L.L., Sheng, Z., Xu, S.J., Wang, W. & Zhu, J.Q. (2015b). The cytological changes of sperm and oocyte nuclei during fertilization in Phascolosoma esculenta (Sipuncula: Phascolosomatidea). Italian Journal of Zoology, 82(3), 327-337.http://dx.doi.org/10.1080/11250003.2015.1045045

Long, L.L., Sheng, Z. & Zhu, J.Q. (2015a). Ultrastructural observations on spermiogenesis in the peanut worm, Phascolosoma esculenta (Sipuncula: Phascolosomatidea). Animal Cells and Systems, 19(3), 221-229.http://dx.doi.org/10.1080/19768354.2015.1026398

Maltagliati, F., Di, G.G., Barbieri, M., Castelli, A. & Dini,F. (2010). Phylogeography and genetic structure of the edible sea urchin Paracentrotus lividus (Echinodermata: Echinoidea) inferred from the mitochondrial cytochrome b gene. Biological Journal of the Linnean Society, 100(4), 910-923. http://dx.doi.org/10.1111/j.1095-8312.2010.01482.x

Mao, Y., Gao, T., Yanagimoto, T. & Xiao, Y. (2011).Molecular phylogeography of Ruditapes philippinarum in the Northwestern Pacific Ocean based on COI gene. Journal of Experimental Marine Biology and Ecology, 407(2), 171-181. http://dx.doi.org/10.1016/j.jembe.2011.06.002

Peng, B., Zhang, Q., Zhao, S. & Yue, X.L. (2010). Genetic diversity analysis of Larimichthys polyactis in coastal waters of China based on Cytochrome b gene. Guangdong Agricultural Sciences, 2, 131-135. http://dx.doi.org/10.16768/j.issn.1004-874x.2010.02.067

Polzin, T. & Daneshmand, S.V. (2003). On steiner trees and minimum spanning trees in hypergraphs. Operations Research Letters, 31, 12–20. http://dx.doi.org/10.1016/S0167-6377(02)00185-2

Shen, X., Ma, X., Ren, J. & Zhao, F. (2009). A close phylogenetic relationship between Sipuncula and Annelida evidenced from the complete mitochondrial genome sequence of Phascolosoma esculenta. BMC Genomics, 10(1), 1-11. http://dx.doi.org/10.1186/1471-2164-10-136

Song, Z.K., Li, M.Y., Nie, Z.P., Sun, F.Y., Zhao, P. & Su, Q. (2012). Population genetic structure and expansion analysis of green mud crab (Scylla paramamosain) from beibu gulf. Oceanologia et Limnologia Sinica, 43(4), 828-836.

Song, Z.K., Liu, T., Yang, J.L., Cai, X.H., Liu, L.M., Wu, R. & Zhao, P. (2011). Genetic diversity and genetic structure of Sipunculus nudus in coastal Guangxi area. Fisheries Science, 31(12), 749-753. http://dx.doi.org/10.16378/j.cnki.1003-1111.2011.12.008

Su, B., Fu, Y.X., Wang, Y.X., Jin, L. & Chakraborty, R. (2001). Genetic diversity and population history of the red panda (Ailurus fulgens) as inferred from mitochondrial DNA sequence variations. Molecular Biology and Evolution, 18(6), 1070-1076. http://dx.doi.org/10.1093/oxfordjournals.molbev.a003 878

Tamura, K., Peterson, D., Peterson, N., Stecher, G., Nei, M. & Kumar, S. (2011). MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Molecular biology and evolution, 28(10), 2731-2739. http://dx.doi.org/10.1093/molbev/msr121

Wang, B., Jiang, J., Xie, F. & Li C. (2013). Phylogeographic patterns of mtDNA variation revealed multiple glacial refugia for the frog species Feirana taihangnica endemic to the Qinling Mountains. Journal of molecular evolution, 76(3), 112-128. http://dx.doi.org/10.1007/s00239-013-9544-5

Wang, M., Su, X., Li, Y., Jun, Z. & Li, T. (2010). Cloning and expression of the Mn-SOD gene from Phascolosoma esculenta. Fish & shellfish immunology, 29(5), 759-764. http://dx.doi.org/10.1016/j.fsi.2010.07.005

Wang, Q.H., Du, X.D. & Li, K. (2006). Genetic diversity of Sipunculus nudus as revealed by RAPD. Marine Fisheries Research, 27(3), 57-61.

Xia, Y.H., Zhang, Q., Gao, Z.Y., Chen, D.Y. & Li G.S. (2013). Genetic diversity analysis of Miichthys miiuy in coastal waters of China based on complete Cytochrome b gene sequences. Guangdong Agricultural Sciences, 3, 101-105

Yang, X., Ye, Q., Xin, T., Zou, Z. & Xia, B. (2016). Population genetic structure of Cheyletus malaccensis (Acari: Cheyletidae) in China based on mitochondrial COI and 12S rRNA genes. Experimental and Applied Acarology, 69(2), 117-128. http://dx.doi.org/10.1007/s10493-016-0028-3

Yang, Z.X., Mao, Y.L., Song, N., Gao, T.X., Cai, H.C. & Zhang, Z.H. (2014). Sequence analysis of mitochondrial COI gene of Mytilus coruscus along Chinese coast waters. Transactions of Oceanology and Limnology, 2, 82-88. http://dx.doi.org/10.13984/j.cnki.cn37-1141.2014.02.013

Ying, X.P., Dahms, H.U., Liu, X.M., Wu, H.X., Zhang, Y.P., Chen, C., Yang, W.X. (2009). Development of germ cells and reproductive biology in the sipunculid Phascolosoma esculenta. Aquaculture Research, 40(3), 305-314. http://dx.doi.org/10.1111/j.1365-2109.2008.02093.x

Zeng, H.X., Hong, P., Ding, L.F. & Zhu, J.Q. (2006). Tolerance of Phascolona esculenta to water temperature and salinity. Fisheries Science, 25(8), 422-423. http://dx.doi.org/10.16378/j.cnki.1003- 111.2006.08.017

Zhao, F., Zhuang, P., Zhang, L.Z. & Shi, Z.H. (2011). Population genetic structure of Pampus argenteus in the south yellow sea and East China Sea based on the mitochondrial Cyt b sequence. Acta Hydrobiologica Sinica, 35(5), 745-752. http://dx.doi.org/10.3724/SP.J.1035.2011.00745

Zhou, Y.S., Ding, L.F., Xu, J.L., Li, G.Y. & Yan, X.J. (2007). Analysis of main nutritional components in Phascolosoma esulenta. Acta Nutrimenta Sinica, 29(4), 413-414. http://dx.doi.org/10.13325/j.cnki.acta.nutr.sin.2007.04.017

Zhu, J.Q., Wang, W., Xu, S.J. & Zeng, H.X. (2007). Spermatogenesis and sperm morphology of Phascolosoma esculenta. Acta Zoologica Sinica, 53(4), 733-741.

Zhu, J.Q., Wang, W., Ying, X.P., Xu, S.J., Zeng, H.X. & Chen, H.Q. (2008). Cytological changes of fertilization and early cleavage in Phascolosoma esculenta. Acta Zoologica Sinica, 54(2), 290-298.

Kaynak Göster