Bioinformatic approach in the identification of arabidopsis gene homologous in amaranthus

Authors

  • Jana Žiarovská Slovak University of Agriculture in Nitra, Faculty of Agrobiology and Food Resources, Department of Genetics and Plant Breeding, Tr. A. Hlinku 2, 949 76 Nitra
  • Michal Záhorský Slovak Academy of Sciences, Institute of Plant Genetics and Biotechnology, Akademická 2, 949 01 Nitra
  • Zdenka Gálová Slovak University of Agriculture in Nitra, Faculty of Biotechnology and Food Sciences, Department of Biochemistry and Biotechnology, Tr. A. Hlinku 2, 949 76 Nitra
  • Andrea Hricová Slovak Academy of Sciences, Institute of Plant Genetics and Biotechnology, Akademická 2, 949 01 Nitra

DOI:

https://doi.org/10.5219/467

Keywords:

BLAST analysis, alightment, Rml-C like cupins, Amaranthus, PCR identification

Abstract

Bioinfomatics offers an efficient tool for molecular genetics applications and sequence homology search algorithms became an inevitable part for many different research strategies. Appropriate managing of known data that are stored in public available databases can be used in many ways in the research. Here, we report the identification of RmlC-like cupins superfamily protein DNA sequence than is known in Arabidopsis genome for the Amaranthus - plant specie where this sequence was still not sequenced. A BLAST based approach was used to identify the homologous sequences in the nucleotide database and to find suitable parts of the Arabidopsis sequence were primers can be designed. In total, 64 hits were found in nucleotide database for Arabidopsis RmlC-like cupins sequence. A query cover ranged from 10% up to the 100% among RmlC-like cupins nucleotides and its homologues that are actually stored in public nucleotide databases. The most conserved region was identified for matches that posses nucleotides in the range of 1506 up to the 1925 bp of RmlC-like cupins DNA sequence stored in the database. The in silico approach was subsequently used in PCR analysis where the specifity of designed primers was approved. A unique, 250 bp long fragment was obtained for Amaranthus cruentus and a hybride Amaranthus hypochondriacus x hybridus in our analysis. Bioinformatic based analysis of unknown parts of the plant genomes as showed in this study is a very good additional tool in PCR based analysis of plant variability. This approach is suitable in the case for plants, where concrete genomic data are still missing for the appropriate genes, as was demonstrated for Amaranthus

Downloads

Download data is not yet available.

References

Brown, D. R., Southern, L. L. 1985. Effect of citric acid and ascorbic acids on performance and intestinal pH of chicks. Poultry Science, vol. 64, no. 7, p. 1390-1401. https://doi.org/10.3382/ps.0641399 PMid:4022914

Altschul, S. F., Madden, T. L., Schäffer, A. A., Zhang, J., Zhang, Z., Miller, W., Lipman, D. J. 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Research, vol. 25, no. 17, p. 3389-3402. https://doi.org/10.1093/nar/25.17.3389 PMid:9254694

Aravind, L., Koonin, E. V. 1999. Gleanin non-trivial structural, functional and evolutionary information about proteins by interactive database searches. J. Mol. Biology, vol. 287, no. 5, p. 1023-1040. https://doi.org/10.1006/jmbi.1999.2653 PMid:10222208

Bailey, T. L. 2008. Discovering sequence motifs. Methods Mol. Biology. vol. 452, p. 231-251. https://doi.org/10.1007/978-1-60327-159-2_12 PMid:18566768

Bäumlein, H., Braun, H., Kakhovskaya, I. A., Shutov. A. D. 1995. Seed storage proteins of spermatophytes share a common ancestor with desiccation proteins of fungi. Journal of Molecular Evolution, vol. 41, no. 6, p. 1070-1075. https://doi.org/10.1007/BF00173188 PMid:8587105

Dasu, S., Williams, A., Fofanov, Y., Putonti, C. 2010. csPCR: A computational tool for the simulation of the Polymerase Chain Reaction. Online Journal of Bioinformatics, vol. 11, no. 1, p. 34-37. [cit. 2015-03-03] Available at: http://onljvetres.com/cspcrabs2010.htm

Dunwell, J. M. 1998. Cupins: a new superfamily of functionally diverse proteins that include germins and plant storage proteins. Biotechnol. Genet. Eng. Rev., vol. 15, no. 1, p.1-32. https://doi.org/10.1080/02648725.1998.10647950 PMid:9573603

Hertz, G. Z., Stormo, G. D. 1999. Identifying DNA and protein patterns with statistically significant alignments of multiple sequences. Bioinformatics, vol. 15, no. 7-8, p. 563-577. https://doi.org/10.1093/bioinformatics/15.7.563 PMid:10487864

Kalendar, R., Lee, D., Schulman, A. H. 2011. Java web tools for PCR, in silico PCR, and oligonucleotide assembly and analysis. Genomics, vol. 98, no. 2, p. 137-144. https://doi.org/10.1016/j.ygeno.2011.04.009 PMid:21569836

Karpov, P. A., Nadezhdina, E. S., Yemets, A. I., Matusov, V. G., Nyporko, A. Y., Shashina, N. Y., Blume, Y. B. 2010. Bioinformatic search of plant microtubule-and cell cycle related serine-threonine protein kinases. BMC Genomics, vol. 11, Suppl. 1, S14; https://doi.org/10.1186/1471-2164-11-S1-S14

Khuri, S., Bakker, F. T., Dunwell, J. M. 2001. Phylogeny, Function, and Evolution of the Cupins, a Structurally Conserved, Functionally Diverse Superfamily of Proteins. Molecular Biology and Evolution, vol. 18, no. 4, p. 593-605. https://doi.org/10.1093/oxfordjournals.molbev.a003840 PMid:11264412

La, D., Livesay, D. R. 2005. Predicting functional sites with an automated algorithm suitable for heterogeneous datasets. BMC Bioinformatics, vol. 6, p. 116. https://doi.org/10.1186/1471-2105-6-116 PMid:15890082

Lin, I. 2012. Discovering Transcription Factor Binding Motif Sequences. Bioc218 Final Report. [cit. 2015-03-03] Available at: http://biochem218.stanford.edu/Projects%202012/Lin.pdf

Rasouli, H., Kahrizi, D., Ghadernia, P. 2013. Identification of conserved domains and motifs for TaWdhn13 gene in Triticum aestivum by in silico analysis. Advances in Environmental Biology, vol. 7, p. 586-590.

Shea, N., Gardner, S. H., Slezak, T. 2014. Simulate_PCR for amplicon prediction and annotation from multiplex, degenerate primers and probes. BMC Bioinformatics, vol. 15, p. 237. https://doi.org/10.1186/1471-2105-15-237 PMid:25005023

Woo, E.-J., Dunwell, J. M, Goodenough, P. W., Marvier, A. C., Pickersgill, R. W. 2000. Germin is a manganese containing homohexamer with oxalate oxidase and superoxide dismutase activities. Nat. Struct. Biol. vol. 7, no. 11, p. 1036-1040. https://doi.org/10.1038/80954 PMid:11062559

Ye, J., Coulouris, G., Zaretskaya, I., Cutcutache, I., Rozen, S., Madden, T. L. 2012. Primer-BLAST: A tool to design target-specific primers for polymerase chain reaction. BMC Bioinformatics, vol. 13, p. 134. https://doi.org/10.1186/1471-2105-13-134 PMid:22708584

Zhang, Z., Schwartz, S., Wagner, L., Miller, W. A. 2000. A greedy algorithm for aligning DNA sequences. Journal of Computational Biology, vol. 7, no. 1-2, p. 203-214. https://doi.org/10.1089/10665270050081478 PMid:10890397

Downloads

Published

2015-05-15

How to Cite

Žiarovská, J. ., Záhorský, M. ., Gálová, Z. ., & Hricová, A. . (2015). Bioinformatic approach in the identification of arabidopsis gene homologous in amaranthus. Potravinarstvo Slovak Journal of Food Sciences, 9(1), 149–153. https://doi.org/10.5219/467

Most read articles by the same author(s)

1 2 3 4 > >>