Molecular study of mollusca in Bandar Lengeh using 18S rRNA gene

Document Type : Research paper


1 Biotechnology Department, Faculty of Agriculture and Natural Resources, Imam Khomeini International University, P. O. Box. 34149-16818, Qazvin, Iran

2 Cellular and Molecular Research Center, Birjand University of Medical Sciences, Birjand, Iran

3 Department of Medical Biotechnology, Faculty of Medicine, Birjand University of Medical Sciences, Birjand, Iran

4 Department of Biomedical Sciences, Alzahra University, Tehran, Iran

5 Persian Gulf & Oman Sea Ecological Research Institute, Bandar Abbas, Iran

6 Postdoc Position in Parasitology, Birjand University of Medical Sciences, Birjand, Iran


Mollusca are one of the most diverse animal phyla whose phylogeny is considered as a controversial subject. Although some groups were traditionally classified as mollusca, they need to be identified again. High diversity of mollusca has created considerable taxonomic problems and despite their importance in marine biota, deep phylogenetic relationships of mollusca have scarcely been investigated. The aim of this study was to determine genetic diversity and differences between mollusca species in waters of Bandar Lengeh (Persian Gulf) of Iran. A clone library of the ribosomal small subunit RNA gene (18S rDNA) in the nuclear genome was constructed by PCR, and then, after examining the clones, selected clones were sequenced. The determined clone sequences were analyzed by a similarity search of the NCBI GenBank database using BLAST. Also, the fixation index (FST) factor was used in order to measure and understand the genetic differences between studied populations. In this study, seventeen sequences were identified belonging to two classes of Bivalvia and Gastropoda and they were used for phylogenetic analysis. According to the allele frequencies at each locus, FST value was significant in samples of Bandar Lengeh meaning that migration is in the lowest rate in the studied region. The present research project exhibited that clone library of 18S rDNA might be accounted as a beneficial tool to identify marine specimens and estimate the actual species diversity in marine environments. Moreover, these findings confirmed the effective role of molecular studies for the identification and taxonomy of speciesfrom the natural resources to obtain reliable data.


Abdolkarim M., Torabi M., Rezaee S., and Afshari F. (2011). Virulence genes and pathotypes of Puccinia hordei Otth causing leaf rust on barley in some areas of Iran. Seed and Plant Improvement Journal, 27(1): 89–102.
Alemzadeh E., Haddad R., and Ahmadi A. R. (2014). Phytoplanktons and DNA barcoding: Characterization and molecular analysis of phytoplanktons on the Persian Gulf. Iranian Journal of Microbiology, 6(4): 296–302.
Avise J. C. (1994). Molecular markers, natural history and evolution. Chapman & Hall: New York. ISBN: 978-0-412-03781-8 207.
Azizpour J., Chegini V., Khosravi M., and Einali A. (2014). Study of the physical oceanographic properties of the Persian gulf, strait of Hormuz and gulf of Oman
based on PG-GOOS CTD measurements. Journal of the Persian Gulf, 5(18): 12/37–48.
Beardmore J. A., Mair G. C., and Lewis R. I. (1997). Biodiversity in aquatic systems in relation to aquaculture. Aquaculture Research, 28(10): 829–839.
Bhatia G., Patterson N., Sankararaman S., and Price A. L. (2013). Estimating and interpreting FST: The impact of rare variants. Genome Research, 23: 1514–1521.
Chapman A. D. (2009). Numbers of living species in Australia and the world. 2nd Edition, Canberra: Australian Biological Resources Study. ISBN: 9780642568601.
Czarnecki D. M., Rao M. N., Norcini J. G., Gmitter F. G., and Deng Z. (2008). Genetic diversity and differentiation among natural, production, and introduced populations of the narrowly endemic species Coreopsis leavenworthii (Asteraceae). Journal of the American Society for Horticultural Science, 33(2): 234–241.
Doyle J. J., and Doyle J. L. (1987). A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochemical Bulletin, 19: 13–15.
Elderkin C. L., Clewing C., Wembo Ndeo O., and Albrecht C. (2016). Molecular phylogeny
and DNA barcoding confirm cryptic species in the African freshwater oyster
Etheria elliptica Lamarck, 1807 (Bivalvia: Etheriidae). Biological Journal of the Linnean Society, 118(2): 369–381.
Fontoura-da-Silva V., de Souza Danta R. J., and Caetano C. H. S. (2013). Foraging tactics in mollusca: a review of the feeding behavior of their most obscure classes (Aplacophora, Polyplacophora, Monoplacophora, Scaphopoda and Cephalopoda). Oecologia Australis,17(3): 358–373.
Goloboff P. A., Catalano S. A., Mirande J. M., Szumik C. A., Arias J. S., Källersjö M., and Farris J. S. (2009). Phylogenetic analysis of 73 060 taxa corroborates major eukaryotic groups. Cladistics, 25(3): 211–230.
Haddad R, Alemzadeh E, Ahmadi A.A., Hosseini R., and Moezzi M. (2014). Identification of Chlorophyceae based on 18S rDNA sequences from Persian Gulf. Iranian Journal of Microbiology, 6(6): 437–442.
Harris J. K., Kelley S. T., and Pace N. R. (2004). New perspective on uncultured bacterial phylogenetic division OP11. Applied and Environmental Microbiology, 70(2): 845–849.
Hauquier F., Verleyen E., Tytgat B., and Vanreusel A. (2018). Regional-scale drivers of marine nematode distribution in Southern Ocean continental shelf sediments. Progress in Oceanography, 165: 1–10.
Holsinger K. E., and Weir B. S. (2009). Genetics in geographically structured populations: defining, estimating and interpreting FST. Nature Reviews Genetics, 10(9): 639–650.
Iijima M., Akiba N., Sarashina I., Kuratani S., and Endo K. (2006). Evolution of Hox genes in molluscs: a comparison among seven morphologically diverse classes. Journal of Molluscan Studies, 72(3): 259–266.
Klompmaker A. A., Kelley P. H., Chattopadhyay D., Clements J. C., Huntley J. W., and Kowalewski M. (2019). Predation in the marine fossil record: Studies, data, recognition, environmental factors, and behavior. Earth-Science Reviews, 194: 472–520.
Kocot K. K. (2013). Recent advances and unanswered questions in deep molluscan phylogenetics. American Malacological Bulletin, 31(1): 195–208.
Larkin M. A., Blackshields G., Brown N. P., Chenna R., McGettigan P. A., McWilliam H., Valentin F., Wallace I. M., Wilm A., Lopez R., Thompson J. D., Gibson T. J., and Higgins D. G. (2007). Clustal W and Clustal X version 2.0. Bioinformatics, 23: 2947–2948.
Leaché A. D., Harris R. B., Rannala B., and Yang Z. (2014). The influence of gene flow on species tree estimation: a simulation study. Systematic Biology, 63(1): 17–30.
 Lee S., Oak J. H., Chung I. K., and Lee J. A. (2010). Effective molecular examination of eukaryotic plankton species diversity in environmental seawater using environmental PCR, PCR-RFLP, and sequencing. Journal of Applied Phycology, 22(6): 699–707.
Lemer S., González V. L., Bieler R., and Giribet G. (2016). Cementing mussels to oysters in the pteriomorphian tree: a phylogenomic approach. Proceedings of the Royal Society B: Biological Sciences, 283(1833): 20160857.
Lopes-Lima M., Froufe E., Do V. T., Ghamizi M., Mock K. E., Kebapçı Ü., Klishko O., Kovitvadhi S., Kovitvadhi U., Paulo O. S., Pfeiffer J. M., Raley M., Riccardi N., Şereflişan H., Sousa R., Teixeira A., Varandas S., Wu X., Zanatta D. T., Zieritz A., and Bogan A. E. (2017). Phylogeny of the most species-rich freshwater bivalve family (Bivalvia: Unionida: Unionidae): Defining modern subfamilies and tribes. Molecular Phylogenetics and Evolution, 106: 174–191.
Madigan M. T., Martinko J. M., Dunlap P. V., and Clark D. P. (2009). Brock biology of microorganisms. 12th EditionPearson/Benjamin Cummings: New York. ISBN 13: 9780132324601.
McArthur A. G., and Harasewych M. G. (2003). Molecular systematics of the major lineages of the Gastropoda. In Lydeard C., and Lindberg D. R., Molecular systematics and phylogeography of mollusks, Smithsonian Books. ISBN: 158834148 8 140.
Meyer A., Todt C., Mikkelsen N. T., and Lieb B. (2010). Fast evolving 18S rRNA sequences from Solenogastres (Mollusca) resist standard PCR amplification and give new insights into mollusk substitution rate heterogeneity. BMC Evolutionary Biology, 10: 70.
Osca D., Irisarri I., Todt C., Grande C., and Zardoya, R. (2014). The complete mitoc genome of Scutopus ventrolineatus (Mollusca: Chaetodermomorpha) supports the Aculifera hypothesis. BMC Evolutionary Biology, 14: 197.
Philippe B., Jean-Pierre R., Rüdiger B., Joseph C. G., and Eugene C. V. (2010). Nomenclator of Bivalve families with a classification of Bivalve families. Malacologia, 52(2): 1–184.
Prié V., and Puillandre, N. (2014). Molecular phylogeny, taxonomy, and distribution of
French Unio species (Bivalvia, Unionidae). Hydrobiologia, 735: 95–110.
Reynolds R. M., (1993). Physical Oceanography of the Gulf, Strait of Hormoz and the Gulf of Oman result from the Mt.Mitchell expedition. Marine Pollution Bulletin, 27: 35–59.
Rodrigues F. P., Carvalho S. C. S., Martinez C. B. R., Malafaia G., Carmen Luísa Barbosa Guedes C. L. B., and Jordão B. Q. (2019). Are the damaging effects of oil refinery effluents on Corbicula fluminea (mollusca) reversible after its transfer to clean water?. Ecological Indicators, 101: 1045–1054.
Rota-Stabelli O., Campbell L., Brinkmann H., Edgecombe G. D., Longhorn S. J., Peterson K. J., Pisani D., Philippe H., and Telford M. J. (2010). A congruent solution to arthropod phylogeny: phylogenomics, microRNAs and morphology support monophyletic Mandibulata. Proceedings of the Royal Society B: Biological Sciences, 278(1703): 298–306.
Ruzzante D. E., Taggart C. T., and Cook D. (1998). A nuclear DNA basis for shelf-and bank-scale population structure in northwest Atlantic cod (Gadus morhua). Molecular Ecology, 7(12): 1663–1680.
Sambrook J., and Russell D. W. (2001). Molecular cloning-a laboratory manual. 3rd Edition, Cold Spring Harbor Laboratory Press. ISBN-13: 978-0879695774.
Semmouri I, Schamphelaere K. A. C., Mees J., Janssen C. R., and Asselman J. (2020). Evaluating the potential of direct RNA nanopore sequencing: Metatranscriptomics highlights possible seasonal differences in a marine pelagic crustacean zooplankton community. Marine Environmental Research, 153: 104836.
Sperling E. A., Vinther J., Moy V. N., Wheeler B. M., Sémon M., and Briggs D. E. G. (2009). MicroRNAs resolve an apparent conflict between annelid systematics and their fossil record. Proceedings of the Royal Society B: Biological Sciences, 276(1677): 4315–4322.
Tamura K., Dudley J., Nei M., and Kumar S. (2007). MEGA 4: Molecular evolutionary genetics analysis (MEGA) software version 4.0. Molecular Biology and Evolution, 24(8): 1596–1599.
Valentin K., Mehl H., and Medlin L. K. (2005). Picoplankton culture assessment using single strand conformation polymorphism and partial 18S sequencing. Journal of Plankton Research, 27(11): 1149–1154.
Weersing K., and Toonen R. J. (2009). Population genetics, larval dispersal, and connectivity in marine systems. Marine Ecology Progress Series, 393: 1–12.
Wright S. (1978). Evolution and genetics of population, variability within and among natural populations. University of Chicago Press. ISBN: 0226910520580.
Yuan J., Chen M. Y., Shao P., Zhou H., Chen Y. Q., and Qu L. H. (2004). Genetic diversity of small eukaryotes from the coastal waters of Nansha Islands in China. FEMS Microbiology Letters, 240(2): 163–170.