161
Views
0
CrossRef citations to date
0
Altmetric
Articles

Development and characterisation of novel polymorphic microsatellite loci in the freshwater mussel Lamellidens marginalis (Lamarck, 1819) using next generation sequencing

, , ORCID Icon, , , & show all
Pages 308-312 | Received 09 Nov 2019, Published online: 02 Aug 2020

References

  • Bachtrog, D., Agís, M., Imhof, M. & Schlötterer, C. (2000) Microsatellite variability differs between dinucleotide repeat motifs-evidence from Drosophila melanogaster. Molecular Biology and Evolution 17, 1277–1285. doi: 10.1093/oxfordjournals.molbev.a026411
  • Bankevich, A., Nurk, S., Antipov, D., Gurevich, A.A., Dvorkin, M., Kulikov, A.S., Lesin, V.M., Nikolenko, S.I., Pham, S., Prjibelski, A.D., Pyshkin, A.V., Sirotkin, A.V., Vyahhi, N., Tesler, G., Alekseyev, M.A. & Pevzner, P.A. (2012) SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. Journal of Computational Biology 19, 455–477. doi: 10.1089/cmb.2012.0021
  • Barbara, T., Palma-Silva, C., Paggi, G.M., Bered, F., Fay, M.F. & Lexer, C. (2007) Cross-species transfer of nuclear microsatellite markers: potential and limitations. Molecular Ecology 16, 3759–3767. doi: 10.1111/j.1365-294X.2007.03439.x
  • Bauer, G. (1987) Reproductive strategy of the freshwater pearl mussel Margaritifera margaritifera. Journal of Animal Ecology 56, 691–704. doi: 10.2307/5077
  • Beier, S., Thiel, T., Münch, T., Scholz, U. & Mascher, M. (2017) MISA-web: a web server for microsatellite prediction. Bioinformatics 33, 2583–2585. doi: 10.1093/bioinformatics/btx198
  • Callen, D.F., Thompson, A.D., Shen, Y., Phillips, H.A., Richards, R.I. & Mulley, J.C. (1993) Incidence and origin of ‘null’ alleles in the (AC)n microsatellite markers. American Journal of Human Genetics 52, 922–927.
  • Chakraborty, R., Kimmel, M., Stivers, D.N., Davison, L.J. & Deka, R. (1997) Relative mutation rates at di-, tri-, and tetranucleotide microsatellite loci. Proceedings of the National Academy of Sciences of the U.S.A. 94, 1041–1046. doi: 10.1073/pnas.94.3.1041
  • Chakraborty, S., Ray, M. & Ray, S. (2008) Sodium arsenite induced alteration of hemocyte density of Lamellidens marginalis – an edible mollusk from India. Clean Soil Air Water 36, 195–200. doi: 10.1002/clen.200600032
  • Cruz, F., Pérez, M. & Presa, P. (2005) Distribution and abundance of microsatellites in the genome of bivalves. Gene 346, 241–247. doi: 10.1016/j.gene.2004.11.013
  • Dakin, E.E. & Avise, J.C. (2004) Microsatellite null alleles in parentage analysis. Heredity 93, 504–509. doi: 10.1038/sj.hdy.6800545
  • Deng, Y., Lei, Q., Tian, Q., Xie, S., Du, X., Li, J., Wang, L. & Xiong, Y. (2014) Denovo assembly, gene annotation, and simple sequence repeat marker development using illumina paired-end transcriptome sequences in the pearl oyster Pinctada maxima. Bioscience, Biotechnology, and Biochemistry 78, 1685–1692. doi: 10.1080/09168451.2014.936351
  • Du, R., Zhang, D., Wang, Y., Wang, W. & Gao, Z. (2016) Cross-species amplification of microsatellites in genera Megalobrama and Parabramis. Journal of Genetics 93, 106–109. doi: 10.1007/s12041-013-0308-1
  • Gagneux, P., Boesch, C. & Woodruff, D.S. (1997) Microsatellite scoring errors associated with noninvasive genotyping based on nuclear DNA amplified from shed hair. Molecular Ecology 6, 861–868. doi: 10.1111/j.1365-294X.1997.tb00140.x
  • Hossain, M.A., Sultana, N., Azimuddin, K., Hussain, M.G. & Mazid, M.A. (2004) Selection of freshwater pearl mussel species for mantle transportation in Bangladesh. Bangladesh Journal of Fisheries Research 8, 113–116.
  • Janakiram, K. (2008) Freshwater pearl culture technology development in India. Journal of Applied Aquaculture 13, 341–349. doi: 10.1300/J028v13n03_07
  • Jerry, D.R., Kvingedal, R., Lind, C.E., Evans, B.S., Taylor, J.J.U. & Safari, A.E. (2012) Donor-oyster derived heritability estimates and the effect of genotype x environment interaction on the production of pearl quality traits in the silver-lip pearl oyster, Pinctada maxima. Aquaculture 338-341, 66–71. doi: 10.1016/j.aquaculture.2012.02.001
  • Kalinowski, S.T. (2004) Counting alleles with rarefaction: private alleles and hierarchical sampling designs. Conservation Genetics 5, 539–543. doi: 10.1023/B:COGE.0000041021.91777.1a
  • Madhyastha, A., Budha, P.B. & Daniel, B.A. (2010) Lamellidens marginalis. The IUCN Red List of Threatened Species 2010, e.T166731A6270763. Available online at http://dx.doi.org/10.2305/IUCN.UK.2010-4.RLTS.T166731A6270763.en. [Accessed on 6 August 2019].
  • Min, J.J., Ye, R.H., Zhang, G.F. & Zheng, R.Q. (2015) Microsatellite analysis of genetic diversity and population structure of freshwater mussel (Lamprotula leai). Zoological Research 36, 34–40.
  • Nesemann, H., Sharma, S., Sharma, G., Khanal, S.N., Pradhan, B., Shah, D.N. & Tachamo, R.D. (2007) Aquatic Invertebrates of the Ganga River System: Mollusca, Annelida, Crustacea (in part). Chandi, Khatmandu.
  • Patnaik, B.B., Wang, T.H., Kang, S.W., Hwang, H.-J., Park, S.Y., Park, E.B., Chung, J.M., Song, D.K., Kim, C., Kim, S., Lee, J.S., Han, Y.S., Park, H.S. & Lee, Y.S. (2016) Sequencing, de novo assembly, and annotation of the transcriptome of the endangered freshwater pearl bivalve, Cristaria plicata, provides novel insights into functional genes and marker discovery. PLoS One 11, e0148622. doi: 10.1371/journal.pone.0148622
  • Peakall, R. & Smouse, P.E. (2006) Genalex 6: genetic analysis in Excel, population genetic software for teaching and research. Molecular Ecology Notes 6, 288–295. doi: 10.1111/j.1471-8286.2005.01155.x
  • Pino-Querido, A., Alvarez-Castro, J., Vera, M., Pardo, B., Fuentes, J. & Martınez, P. (2015) A molecular tool for parentage analysis in the Mediterranean mussel (Mytilus galloprovincialis). Aquatic Research 46, 1721–1735. doi: 10.1111/are.12329
  • Renaut, S., Guerra, D., Hoeh, W.R., Stewart, D.T., Bogan, A.E., Ghiselli, F., Milani, L., Passamonti, M. & Breton, S. (2018) Genome survey of the freshwater mussel Venustoconcha ellipsiformes (Bivalvia:Unionida) using a hybrid de novo assembly approach. Genome Biology and Evolution 10, 1637–1646. doi: 10.1093/gbe/evy117
  • Rousset, F. (2008) Genepop’007: a complete reimplementation of the Genepop software for Windows and Linux. Molecular Ecology Resources 8, 103–106. doi: 10.1111/j.1471-8286.2007.01931.x
  • Santos, M.F., Souza, I.G.B., Gomes, S.O., Silva, G.R., Bentzen, P. & Diniz, F.M. (2018) Isolation and characterisation of microsatellite markers in the spiny lobster, Panulirus echinatus Smith, 1869 (Decapoda: Palinuridae) by Illumina MiSeq sequencing. Journal of Genetics 97, e25–e30. doi: 10.1007/s12041-018-0895-y
  • Schmieder, R. & Edwards, R. (2011) Quality control and preprocessing of metagenomic datasets. Bioinformatics 27, 863–864. doi: 10.1093/bioinformatics/btr026
  • Siddique, M.A., Khatun, M.A., Rahman, M.M., Ahmed, G.U., Moniruzzaman, M. & Uddin, M.J. (2020) Annual gametogenic cycle of the freshwater pearl mussel, Lamellidens marginalis (Lamarck, 1819) collected from a perennial lentic habitat of Bangladesh. Molluscan Research 40, 36–43. doi: 10.1080/13235818.2019.1682954
  • Srivastava, S., Avvaru, A.K., Sowpati, T.D. & Mishra, R.K. (2019) Patterns of microsatellite distribution across eukaryotic genomes. BMC Genomics 20, 153. doi: 10.1186/s12864-019-5516-5
  • Teaniniuraitemoana, V., Huvet, A., Levy, P., Klopp, C., Lhuillier, E., Gaertner-Mazouni, N., Gueguen, Y. & Moullac, G.L. (2014) Gonad transcriptome analysis of pearl oyster Pinctada margaritifera: identification of potential sex differentiation and sex determining genes. BMC Genomics 15, 491. doi: 10.1186/1471-2164-15-491
  • Thomas, E.I. (1974) The bionomics, anatomy and development of the freshwater mussel, Lamellidens marginalis (Lamarck). Annales Zoologici Fennici 10, 71–169.
  • Untergasser, A., Cutcutache, I., Koressaar, T., Ye, J., Faircloth, B.C., Remm, M. & Rozen, S.G. (2012) Primer3-new capabilities and interfaces. Nucleic Acids Research 40, e115. doi: 10.1093/nar/gks596
  • Van Oosterhout, C., Hutchinson, W.F., Wills, D.P.M. & Shipley, P. (2004) Micro-checker: software for identifying and correcting genotyping errors in microsatellite data. Molecular Ecology Notes 4, 535–538. doi: 10.1111/j.1471-8286.2004.00684.x
  • Zhang, D.X. & Hewitt, G.M. (2003) Nuclear DNA analyses in genetic studies of populations: practice, problems and prospects. Molecular Ecology 12, 563–584. doi: 10.1046/j.1365-294X.2003.01773.x
  • Zhang, A.J., Liu, S.L., Zhu, J.Y., Gu, Z.M., Zhou, Z.M., Zhang, G.F. & Lu, K.H. (2016) Transcriptome analysis of the freshwater pearl mussel, Hyriopsis cumingii (Lea) using illumina paired-end sequencing to identify genes and markers. Iranian Journal of Fisheries Sciences 15, 479–496.

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.