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 AJPS  Vol.6 No.5 , March 2015
Molecular Characterization of Type II Transposable Elements in Cowpea [Vigna unguiculata (L.) Walp]
Olufisayo Kolade1,2*, Adebola Raji3, Iyiola Fawole1,4, Ivan Ingelbrecht5
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Abstract: Previous genetic studies in cowpea [Vigna unguiculata (L.) Walp] have shown that an active bipartite transposable element (TE) is responsible for a range of mutant phenotypes of its leaf, stem and flower. Since type II TEs have not been characterized at the molecular level in cowpea, this study was initiated to survey the presence of type II TEs in the cowpea genome. Type II TEs: Enhancer/Suppressor-mutator (En/Spm) and Miniature Inverted-repeat Transposable Elements (MITEs) were isolated and characterized. The sequence identity between the EnSpm TE clones was 46% at the nucleotide level (NL) and 30% at the amino acid level (AL) while that of MITEs was 71% at NL and 63% at AL. These cowpea En/Spm TEs were 80% homologous with En/Spm elements of other crops at NL and 46% at AL. The MITEs were 96% similar at NL and 18% homologous at AL. DNA gel blot analysis confirmed the presence of the En/Spm TEs in cowpea. RT-PCR (reverse transcriptase polymerase chain reaction) analysis showed that the VuEnSpm-3 and the MITE clone, VuPIF-1 were actively transcribed in wild type and mutant cowpea tissues. Overall, our data show that multiple, divergent lineages of En/Spm and MITEs are present in the cowpea genome, some of which are actively transcribed. Our findings also offer new molecular resource to further investigate the genetic determinants underlying previously described mutant cowpea phenotypes.
Keywords: Cowpea, En/Spm, MITE, Transposable Element, Vigna unguiculata
Cite this paper: Kolade, O. , Raji, A. , Fawole, I. , Ingelbrecht, I. (2015) Molecular Characterization of Type II Transposable Elements in Cowpea [Vigna unguiculata (L.) Walp]. American Journal of Plant Sciences, 6, 767-776. doi: 10.4236/ajps.2015.65082.
References

[1]   Kunze, R., Saedler, H. and Lönnig, W.E. (1997) Plant Transposable Elements. Advances in Botanical Research, 27, 332-409.
http://dx.doi.org/10.1016/S0065-2296(08)60284-0

[2]   Stagginus, C., Huettel, B., Desel, C., Schmidt, T. and Kahl, G. (2001) A PCR-Based Assay to Detect En/Spm-Like Transposon Sequences in Plants. Chromosome Resources, 9, 591-605.
http://dx.doi.org/10.1023/A:1012455520353

[3]   Wessler, S. (2006) Transposable Elements and the Evolution of the Eukaryotic Genome. Proceeding of National Academy of Science, 103, 17600-17601.
http://dx.doi.org/10.1073/pnas.0607612103

[4]   McClintock, B. (1948) Mutable Loci in Maize. Carnegie Institution of Washington Year Book, 47, 155-169.

[5]   Fedoroff, N. (1983) Controlling Elements in Maize. In: Shapiro, J., Ed., Mobile Genetic Elements, Academic Press, New York, 63 p.
http://dx.doi.org/10.1016/B978-0-12-638680-6.50005-3

[6]   Griffith, A.J.F., Miller, J.H., Suzuki, D.T., Lewontin, R.C. and Gelbart, W.M. (1999) Introduction to Genetic Analysis. 7th Edition, WH Freeman and Co., New York.

[7]   Zhang, X., Jiang, N., Feschotte, C. and Wessler, S.R. (2004) PIF- and Pong-Like Elements: Distribution, Evolution and Relationship with Tourist Like Miniature Inverted Repeat Transposable Elements. Genetics, 166, 971-986.
http://dx.doi.org/10.1534/genetics.166.2.971

[8]   Bennetzen, J.L. (2000) Transposable Element Contributions to Plant Gene and Genome Evolution. Plant Molecular Biology, 42, 251-269.
http://dx.doi.org/10.1023/A:1006344508454

[9]   Shapiro, J.A. (1999) Transposable Elements as the Key to a 21st Century View of Evolution. Genetica, 107, 171-179.
http://dx.doi.org/10.1023/A:1003977827511

[10]   Fedoroff, N. (2000) Transposons and Genome Evolution in Plants. Proceedings of National Academy of Science USA, 97, 7002-7007.
http://dx.doi.org/10.1073/pnas.97.13.7002

[11]   Gray, Y.H.M. (2000) It Takes Two Transposons to Tango: Transposable Element-Mediated Chromosomal Rearrangements. Trends in Genetics, 16, 461-468.
http://dx.doi.org/10.1016/S0168-9525(00)02104-1

[12]   Holmes, I. (2002) Transcendent Elements: Whole Genome Transposon Screens and Open Evolutionary Questions. Genome Research, 12, 1152-1155.
http://dx.doi.org/10.1101/gr.453102

[13]   Grimanelli, D. (2000) Identification of Genes for Tolerance to Striga in Maize Using Transposable Elements. In: Haussmann, B.I.G., Hess, D.E., Koyama, M.L., Grivet, L., Rattunde, H.F.W. and Geiger, H.H., Eds., Breeding for Striga Resistance in Cereals, Proceedings of a Workshop, IITA, Ibadan, 18-20 August 1999, 187.

[14]   Lee, J.J., Kwon, S.J., Park, K.C. and Kim, N.S. (2005) Isaac-CACTA Transposons: New Genetic Markers in Maize and Sorghum. Genome, 48, 455-460.
http://dx.doi.org/10.1139/g05-013

[15]   Kumar, A., Pearce, S.R., McLean, K., Harrison, G., Heslop-Harrison, J.S., Waugh, R. and Flavell, A.J. (1997) The Ty1-copia Group of Retrotransposons in Plants: Genomic Organisation, Evolution, and Use as Molecular Markers. Genetica, 100, 205-217.
http://dx.doi.org/10.1023/A:1018393931948

[16]   Nevers, P., Sheperd, N.A. and Saedler (1986) Plant Transposable Elements. Advances in Botanical Research, 12, 102-203.

[17]   Osborne, B. and Baker, B. (1995) Movers and Shakers: Maize Transposons as Tools for Analyzing Other Plant Genomes. Current Opinion in Cell Biology, 7, 406-413.

[18]   Sundaresan, V., Springer, P., Volpe, T., Haward, S., Jones, J.D., Dean, C., Ma, H. and Martienssen, R. (1995) Patterns of Gene Action in Plant Development Revealed by Enhancer Trap and Gene Trap Transposable Elements. Genes & Development, 9, 1797-1810.
http://dx.doi.org/10.1101/gad.9.14.1797

[19]   Peterson, P.A. (1953) A Mutable Pale-Green Locus in Maize. Genetics, 38, 682-683.

[20]   McClintock, B. (1954) Mutations in Maize and Chromosomal Aberrations in Neurospora. In: Carnegie Institution of Washington, Yearbook No. 53, 254-260.

[21]   Wessler, S.R., Nagel, A. and Casa, A. (2001) Miniature Inverted Repeat Transposable Elements Help Create Genomic Diversity in Maize and Rice. In: Khush, G.S., Brar, D.S. and Hardy, B., Eds., Rice Genetics IV, Science, Manila, 107-116.

[22]   Altinkut, A., Raskina, O., Nevo, E. and Belyayev, A. (2006) En/Spm-Like Transposons in Poaceae Species: Transposase Sequence Variability and Chromosomal Distribution. Cellular and Molecular Biology Letters, 11, 214-229.
http://dx.doi.org/10.2478/s11658-006-0017-3

[23]   Gbadegesin, M.A., Reilly, K. and Beeching, J.R. (2005) Mutator-Like Transposable Element of Cassava (Manihot esculenta Crantz) Is Highly Methylated. FEBS Journal, 272, 476.

[24]   Feschotte, C., Zhang, X. and Wessler, S.R. (2002) Miniature Inverted-Repeat Transposable Elements (MITEs) and Their Relationship with Established DNA Transposons. In: Craig, N.L., Craigie, R., Gellert, M. and Lambowitz, A.M., Eds., Mobile DNA II, American Society for Microbiology Press, Washington DC, 1147-1158.

[25]   Fawole, I. (1988) A Non-Petiolate Leaf Mutant in Cowpea, Vigna unguiculata (L.) Walp. Journal of Heredity, 79, 484-487.

[26]   Fawole, I. (1998) Two Unstable Dominant Genes in Cowpea, Vigna unguiculata (L.) Walp. Eighteenth International Congress of Genetics, Beijing, 10-15 August 1998, 29.

[27]   Fawole, I. (1997) Inheritance of Crinkled Leaf in Cowpea, Vigna unguiculata (L) Walp. Nigerian Journal of Science, 31, 35-40.

[28]   Fawole, I. (2001) Genetic Analysis of Mutations at Loci Controlling Leaf Form in Cowpea (Vigna unguiculata L. Walp). Journal of Heredity, 92, 43-50.
http://dx.doi.org/10.1093/jhered/92.1.43

[29]   Fawole, I. (2010) Origin, Morphology & Inheritance of Dominant Mutations Affecting Flower Form and Colour in Cowpea. Nigerian Journal of Science, 44, 77-87.

[30]   Oluwatosin, O.B. (1997) Inheritance and Instability of Genes Controlling Anthocyanin Pigmentation, Seed Coat Colour and Leaf Form in Cowpea, Vigna unguiculata (L.) Walp. Dissertation, University of Ibadan, Ibadan.

[31]   Dellarporta, S.L., Wood, J. and Hicks, J.B. (1983) A Plant DNA Minipreparation: Version II. Plant Molecular Biology Reporter, 1, 19-21.
http://dx.doi.org/10.1007/BF02712670

[32]   Sambrook, J., Fritsch, E. and Maniatis, T. (1989) Molecular Cloning: A Laboratory Manual. 2nd Edition, Cold Spring Harbor Laboratory Press, Cold Spring Harbor.

[33]   Zhang, X. and Wessler, S.R. (2004) Genome-Wide Comparative Analysis of the Transposable Elements in the Related Species Arabidopsis thaliana and Brassica oleracea. Proceedings of the National Academy of Sciences of the United States of America, 101, 5589-5594.
http://dx.doi.org/10.1073/pnas.0401243101

[34]   Gorbunova, V. and Levy, A.A. (2000) Analysis of Extrachromosomal Ac/Ds Transposable Elements. Genetics, 155, 349-359.

[35]   Macas, J., Neuman, P. and Pozarkova, D. (2003) Zaba: A Novel Miniature Transposable Element Present in Genomes of Legume Plants. Molecular Genetics and Genomics, 269, 624-631.
http://dx.doi.org/10.1007/s00438-003-0869-4

[36]   Singer, T., Yordan, C. and Martienssien, R.A. (2001) Robertson’s Mutator Transposons in A. thaliana Are Regulated by the Chromatin-Remodeling Gene Decrease in DNA Methylation (DDM1). Genes & Development, 15, 591-602.
http://dx.doi.org/10.1101/gad.193701

[37]   Rozen, S. and Skaletsky, H.J. (2000) Primer 3 on the WWW for General Users and Biologist Programmers. In: Krawetz, S. and Misener, S., Eds., Bioinformatics Methods and Protocols: Methods in Molecular Biology, Humana Press, Totowa, 365-386.

[38]   Altschul, S.F., Gish, W., Miller, W., Mayers, E.W. and Lipman, D.J. (1990) Basic Local Alignment Search Tool. Journal of Molecular Biology, 215, 403-410.
http://dx.doi.org/10.1016/S0022-2836(05)80360-2

[39]   Higgins, D.G. and Sharp, P.M. (1988) CLUSTAL: A Package for Performing Multiple Sequence Alignment on a Microcomputer. Gene, 73, 237-244.
http://dx.doi.org/10.1016/0378-1119(88)90330-7

[40]   Tamura, K., Dudley, J., Nei, M. and Kumar, S. (2007) MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) Software Version 4.0. Molecular Biology and Evolution, 24, 1596-1599.
http://dx.doi.org/10.1093/molbev/msm092

[41]   Sammeth, M., Griebel, T., Tille, F. and Stoye, J. (2006) Panta rhei (QAlign2): An Open Graphical Environment for Sequence Analysis. Bioinformatics, 22, 889-890.
http://dx.doi.org/10.1093/bioinformatics/btl007

[42]   Jiang, N., Feschotte, C., Zhang, X. and Wessler, S.R. (2004) Using Rice to Understand the Origin and Amplification of Miniature Inverted Repeat Transposable Elements (MITEs). Current Opinion in Plant Biology, 7, 115-119.
http://dx.doi.org/10.1016/j.pbi.2004.01.004

[43]   Rhodes, P. and Vodkin, L. (1988) Organization of the Tgm Family of Transposable Element in Soybean. Genetics, 120, 597-604.

[44]   Snowden, K. and Napoli, C. (1998) Ps1: A Novel Spm-Like Transposable Element from Petunia hybrida. The Plant Journal, 14, 43-54.
http://dx.doi.org/10.1046/j.1365-313X.1998.00098.x

[45]   He, Z.H., Dong, J.X., Li, D.B. and Ronald, P.C. (2000) The Rice Rim2 Transcript Accumulates in Response to Magnaporthe grisea and Its Predicted Protein Product Shares Similarity with TNP2-Like Proteins Encoded by CACTA Transposons. Molecular and General Genetics MGG, 264, 2-10.
http://dx.doi.org/10.1007/s004380000278

[46]   Gbadegesin, M.A., Wills, M.A. and Beeching, J.R. (2008) Diversity of LTR-Retrotransposons and Enhancer/Suppressor Mutator-Like Transposons in Cassava (Manihot esculenta Crantz). Molecular Genetics and Genomics, 280, 305-317.
http://dx.doi.org/10.1007/s00438-008-0366-x

 
 
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