The In Silico Predicton of the Chloroplast Maturase K Gene Polymorphism in Several Barley Varieties

ADZHUBEI, I.A. - SCHMIDT, S. - PESHKIN, L. - RAMENSKY, V.E. - GERASIMOVA, A. - BORK, P. - KONDRASHOV, A.S. - SUNYAEV, SR. 2010. A method and server for predicting damaging missense mutations. In Nature Methods, vol. 7, no. 4, pp. 248-249. DOI: 10.1038/nmeth0410-24810.1038/nmeth0410-248285588920354512Open DOISearch in Google Scholar

AL-SHUHAIB, M.B. 2017. A Universal, rapid, and inexpensive method for genomic DNA isolation from the whole blood of mammals and birds. In Journal of Genetics, vol. 96, no 1, pp. 171-176. DOI: 10.1007/s12041-017-0750-610.1007/s12041-017-0750-628360403Open DOISearch in Google Scholar

BARTHET, M.M. - HILU, K.W. 2007. Expression of matK: functional and evolutionary implications. In American Journal of Botany, vol. 94, no. 8, pp. 1402-1412. DOI: 10.3732/ajb.94.8.140210.3732/ajb.94.8.140221636508Open DOISearch in Google Scholar

BARTHET, M.M. - MOUKARZEL, K. - SMITH, K.N. - PATEL, J. - HILU, K.W. 2015. Alternative translation initiation codons for the plastid maturase MatK: unraveling the pseudogene misconception in the Orchidaceae. In BMC Evolutionary Biology, vol. 15, pp. 210. DOI: 10.1186/s12862-015-0491-110.1186/s12862-015-0491-1458786026416561Open DOISearch in Google Scholar

BYUN, S. - FANG, Q. - ZHOU, H. - HICKFORD, J. 2009. An effective method for silver-staining DNA in large numbers of polyacrylamide gels. In Analytical Biochemistry, vol. 385, pp. 174-175. DOI: 10.1016/j.ab.2008.10.02410.1016/j.ab.2008.10.02419013423Open DOISearch in Google Scholar

CAPRIOTTI, E. - FARISELLI, P. - CASADIO, R. 2005. I-Mutant 2.0: predicting stability changes upon mutation from the protein sequence or structure. In Nucleic Acids Research vol. 33, pp. 306-310. DOI: 10.1093/nar/gki37510.1093/nar/gki375116013615980478Search in Google Scholar

CHOI, Y. - SIMS, G.E. - MURPHY, S. - MILLER, J.R. - CHAN, A.P. 2012. Predicting the functional effect of amino acid substitutions and indels. In PLOS ONE, vol. 7, pp. e46688. DOI: 10.1371/journal.pone.004668810.1371/journal.pone.0046688346630323056405Search in Google Scholar

CRUSIO, W. 1987. A note on the analysis of reciprocal effects in diallel crosses. In Journal of Genetics, vol. 66, pp. 177-185. DOI: 10.1007/BF0292771110.1007/BF02927711Open DOISearch in Google Scholar

DE ALENCAR, S.A. - LOPES, J.C.D. 2010. A comprehensive in silico analysis of the functional and structural impact of SNPs in the IGF1R gene. In Journal of Biomedical Biotechnology ID 715139, 8 pages. DOI:10.1155/2010/71513910.1155/2010/715139289685820625407Search in Google Scholar

GASSER, R.B. - HU, M. - CHILTON, N.B. - CAMPBELL, B.E. - JEX, A.J. - ONTRANTO, D. - CAFARCHIA, C. - BEVERIDGE, I. - ZHU, X. 2006. Single-strand conformation polymorphism (SSCP) for the analysis of genetic variation. In Nature Protocols, vol. 1, no. 8, pp. 3121-8. DOI:10.1038/nprot.2006.48510.1038/nprot.2006.48517406575Search in Google Scholar

HILU, K.W. - LIANG, H. 1997. The matK gene: sequence variation and application in plant systematics. In American Journal of Botany, vol. 84, pp. 830-839. url: https://www.ncbi.nlm.nih.gov/pubmed/2170863510.2307/2445819Search in Google Scholar

ISHIDA, T. - KINOSHITA, K. 2007. PrDOS: prediction of disordered protein regions from amino acid sequence. In Nucleic Acids Research, vol. 35, pp. W460-464. DOI: 10.1093/nar/gkm36310.1093/nar/gkm363193320917567614Open DOISearch in Google Scholar

JENNA, N.K. - STEPHEN, D.B. 2014. In silico analysis of functional single nucleotide polymorphisms in the human TRIM22 gene. In PLoS One, vol. 9, no. 7, pp. e101436. DOI: 10.1371/journal.pone.010143610.1371/journal.pone.0101436407780324983760Search in Google Scholar

JOHNSON, L.A, - SOLTIS, D.E. 1995. Phylogenetic inference in saxifragaceae sensu stricto and gilia (Polemoniaceae) using matK sequences. In Annals of the Missouri Botanical Garden, vol. 82, pp.149-175. DOI: 10.2307/239987510.2307/2399875Open DOISearch in Google Scholar

KALLBERG, M. - WANG, H. - WANG, S. - PENG, J. - WANG, Z. - LU, H. - XU, J. 2012. Template-based protein structure modeling using the RaptorX web server. In Nature Protocols, vol. 7, no. 8, pp. 1511-1522. DOI: 10.1038/nprot.2012.08510.1038/nprot.2012.085473038822814390Open DOISearch in Google Scholar

KUHN, D. - MOTAMAYOR, J. - MEEROW, A. - BORRONE, J. - SCHNELL, R. 2008. SSCP markers provide a useful alternative to microsatellites in genotyping and estimating genetic diversity in populations and germplasm collections of plant specialty crops. In Electrophoresis, vol. 29, no. 19, pp. 4096-5108. DOI: 10.1002/elps.20070093710.1002/elps.20070093718958880Open DOISearch in Google Scholar

LIANG, H. - HILU, K.W. 1996. Application of the matK gene sequences to grass systematics. In Canadian Journal of Botany, vol. 74, pp. 125-134. url: http://www.nrcresearchpress.com/doi/pdf/10.1139/b96-017 10.1139/b96-017Open DOISearch in Google Scholar

LIAO, P.Y. - LEE, K.H. 2010. From SNPs to functional polymorphism: The insight into biotechnology applications. In Biochemical Engineering Journal, vol. 49, pp. 149-158. https://doi.org/10.1016/j.bej.2009.12.02110.1016/j.bej.2009.12.021Open DOISearch in Google Scholar

MOHR, G. - PERLMAN, P. - LAMBOWITZ, A. 1993. Evolutionary relationships among group II intron-encoded proteins and identification of a conserved domain that may be related to maturase function. In Nucleic Acids Research, vol. 21, pp. 4991-4997. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC310608/10.1093/nar/21.22.49913106088255751Open DOISearch in Google Scholar

MULLER, K.F. - BORSCH, T. - HILU, K.W. 2006. Phylogenetic utility of rapidly evolving DNA at high taxonomical levels: contrasting matK, trnT-F and rbcL in basal angiosperms. In Molecular Phylogenetics and Evolution, vol. 41, pp. 99-117. DOI: 10.1016/j.ympev.2006.06.01710.1016/j.ympev.2006.06.01716904914Open DOISearch in Google Scholar

NG, P.C. - HENICKOFF, S. 2006. Predicting the effects of amino acid substitutions on protein function. In Annual Review of Genomics and Human Genetics, vol. 7, pp. 61-80. DOI: 10.1146/annurev.genom.7.080505.11563010.1146/annurev.genom.7.080505.115630Open DOISearch in Google Scholar

OFRAN, Y. - ROST, B. 2007. ISIS: interaction sites identified from sequence. In Bioinformatics, vol. 23, pp. e13-e16. DOI: 10.1093/bioinformatics/btl30310.1093/bioinformatics/btl303Open DOISearch in Google Scholar

PATEL, S.M. - KORINGA, P.G. - REDDY, B.B. - NATHANI, N.M. - JOSHI, C.G. 2015. In silico analysis of consequences of non-synonymous SNPs of Slc11a2 gene in Indian bovines. In Genomics Data, vol. 5, pp. 72-79. DOI: 10.1016/j. gdata.2015.05.01510.1016/j.gdata.2015.05.015Open DOISearch in Google Scholar

PALINE, C.N. - STEVEN, H. 2003. SIFT: predicting amino acid changes that affect protein function. In Nucleic Acids Research, vol. 31, pp. 3812-73814. DOI: 10.1093/nar/gkg50910.1093/nar/gkg509Search in Google Scholar

RAFALSKI, A. 2002. Applications of single nucleotide polymorphisms in crop genetics. In Current Opinion in Plant Biology, vol. 5, pp. 94-100. DOI: 10.1016/S1369- 5266(02)00240-610.1016/S1369-5266(02)00240-6Open DOISearch in Google Scholar

ROMERO, P.R. - ZAIDI, S. - FANG, Y.Y. - UVERSKY, V.N. - RADIVOJAC, P. - OLDFIELD, C.J. - CORTESE, M.S. - LEGALL, T. - OBRADOVIC, Z. - DUNKER, A.K. 2006. Alternative splicing in concert with protein intrinsic disorder enables increased functional diversity in multicellular organisms. In Proceedings of the National Academy10.1073/pnas.0507916103148250316717195Search in Google Scholar

of Sciences USA, vol. 103, pp. 8390-8395. DOI: 10.1073/pnas.050791610310.1073/pnas.0507916103Open DOISearch in Google Scholar

SALDANHA, R. - CHEN, B. - WANK, H. - MATSUURA, M. - EDWARDS, J. - LAMBOWITZ, A.M. 1999. RNA and protein catalysis in group II intron splicing and mobility reactions using purified components. In Biochemistry, vol. 38, pp. 9069-9083. DOI: 10.1021/bi982799l10.1021/bi982799l10413481Open DOISearch in Google Scholar

SAUNA, Z.E. - KIMCHI-SARFATY, C. 2011. Understanding the contribution of synonymous mutations to human disease. In Nature Review Genetics, vol. 12, pp. 638-691. DOI: 10.1038/nrg305110.1038/nrg305121878961Open DOISearch in Google Scholar

SCHLESSINGER, A. - PUNT, A.M. - YACHDAV, G. - KAJAN, L. - ROST, B. 2009. Improved disorder prediction by combination of orthogonal approaches. In PLoS One, vol. 4, no. 2, pp. e4433. DOI: http://dx.doi.org/10.1371/journal.pone.000443310.1371/journal.pone.0004433263596519209228Open DOISearch in Google Scholar

SCHNEIDER, K. - WEISSHAAR, B. - BORCHARDT, D.C. - SALAMINI, F. 2001. SNP frequency and allelic haplotype structure of Beta vulgaris expressed genes. In Molecular Breeding, vol. 8, pp. 63-74. DOI: 10.1023/A:101190291619410.1023/A:1011902916194Search in Google Scholar

SCHOLTZ, S. - LORZ, H. - LUTTICKE, S. 2001. Transposition of maize transposable element Ac in barley (Hordeum vulgare L.). In Molecular and General Genetics, vol. 264, pp. 653‒661. DOI: 10.1007/s00438000035110.1007/s00438000035111212920Open DOISearch in Google Scholar

SMIGIELSKI, E.M. - SIROTKIN, K. - WARD, M. - SHERRY, S.T. 2000. dbSNP: a database of single nucleotide polymorphisms. In Nucleic Acids Research, vol. 28, no. 1, pp. 52‒355. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC102496/pdf/gkd114.pdf10.1093/nar/28.1.35210249610592272Search in Google Scholar

VON BOTHMER, R. - SATO, K. - KOMATSUDAM, T. - YASUDA, S. - FISCHBECK, G. 2003. The domestication of cultivated barley. In von BOTHMER, R. - VAN HINTUM, T. - KNÜPFFER, H. - SATO, K. (Eds.) Diversity in barley (Hordeum vulgare). Amsterdam: Elsevier Science BV, pp. 9-27.10.1016/S0168-7972(03)80004-XSearch in Google Scholar

WARD, J.J. - SODHI, J.S. - MCGUFFIN, L.J. - BUXTON, B.F. - JONES, D.T. 2004. Prediction and functional analysis of native disorder in proteins from the three kingdoms of life. In Journal of Molecular Biology, vol. 337, pp. 635-645. DOI: 10.1016/j.jmb.2004.02.00210.1016/j.jmb.2004.02.00215019783Open DOISearch in Google Scholar

YU, J. - XUE, J.H. - ZHOU, S.L. 2011. New universal matK primers for DNA barcoding angiosperms. In Journal of Systematic Evolution, vol. 49, no. 3, pp. 176. DOI: 10.1111/j.1759-6831.2011.00134.x10.1111/j.1759-6831.2011.00134.xOpen DOISearch in Google Scholar

ZOSCHKE, R. - NAKAMURA, M. - LIERE, K. - SUGIURA, M. - BORNER, T. - SCHMITZ-LINNEWEBER, C. 2010. An organellar maturase associates with multiple group II introns. In Proceedings of the National Academy of Sciences USA, vol. 107, no. 7, pp. 3245. DOI: 10.1073/pnas.090940010710.1073/pnas.0909400107284029020133623Open DOISearch in Google Scholar