Geodesic
Multiplex \emph{in silico} RAPD-analysis for genome barcoding
Matematičeskaâ biologiâ i bioinformatika, Tome 17 (2022) no. 2, pp. 208-229.

Voir la notice de l'article provenant de la source Math-Net.Ru

In this work, we propose a new method for identifying organisms of multiplex polymerase chain reaction (PCR) with arbitrary primers in silico (multiplex in silico RAPD-analysis) for the unique identification of living organisms. The results of computer modeling search of possible primer annealing sites in genomic DNA, and their convertation into the genomic barcode format, are proposed. These data with information about used primers that can be unique for genomes. A comparative analysis of genomic barcodes of species of related plant species was carried out in order to classify them on the level of species and lines in the future. A pairwise analysis of the location of the same or similar amplicons within different subgenomes and genomes is presented. The genomes of wheat and Aegilops in FASTA files format are presented as the research samples. The proposed method makes possible to predict the success of the multiplex polymerase chain reaction using special primers in the laboratory. This technology allows the analysis of the entire genomic DNA, rather than fragments of the genome. 
@article{MBB_2022_17_2_a4,
     author = {O. Y. Kiryanova and I. I. Kiryanov and B. R. Kuluev and R. R. Garafutdinov and A. V. Chemeris and I. M. Gubaydullin},
     title = {Multiplex \emph{in silico} {RAPD-analysis} for genome barcoding},
     journal = {Matemati\v{c}eska\^a biologi\^a i bioinformatika},
     pages = {208--229},
     publisher = {mathdoc},
     volume = {17},
     number = {2},
     year = {2022},
     language = {ru},
     url = {http://geodesic.mathdoc.fr/item/MBB_2022_17_2_a4/}
}
TY  - JOUR
AU  - O. Y. Kiryanova
AU  - I. I. Kiryanov
AU  - B. R. Kuluev
AU  - R. R. Garafutdinov
AU  - A. V. Chemeris
AU  - I. M. Gubaydullin
TI  - Multiplex \emph{in silico} RAPD-analysis for genome barcoding
JO  - Matematičeskaâ biologiâ i bioinformatika
PY  - 2022
SP  - 208
EP  - 229
VL  - 17
IS  - 2
PB  - mathdoc
UR  - http://geodesic.mathdoc.fr/item/MBB_2022_17_2_a4/
LA  - ru
ID  - MBB_2022_17_2_a4
ER  - 
%0 Journal Article
%A O. Y. Kiryanova
%A I. I. Kiryanov
%A B. R. Kuluev
%A R. R. Garafutdinov
%A A. V. Chemeris
%A I. M. Gubaydullin
%T Multiplex \emph{in silico} RAPD-analysis for genome barcoding
%J Matematičeskaâ biologiâ i bioinformatika
%D 2022
%P 208-229
%V 17
%N 2
%I mathdoc
%U http://geodesic.mathdoc.fr/item/MBB_2022_17_2_a4/
%G ru
%F MBB_2022_17_2_a4
O. Y. Kiryanova; I. I. Kiryanov; B. R. Kuluev; R. R. Garafutdinov; A. V. Chemeris; I. M. Gubaydullin. Multiplex \emph{in silico} RAPD-analysis for genome barcoding. Matematičeskaâ biologiâ i bioinformatika, Tome 17 (2022) no. 2, pp. 208-229. http://geodesic.mathdoc.fr/item/MBB_2022_17_2_a4/

[1] N. L. Bolotova, “Biologicheskoe raznoobrazie i problemy ego sokhraneniya”, Nauka – shkole, Sbornik nauchnykh publikatsii, 2017, 119–174

[2] P. D.N. Hebert, A. Cywinska, S. L. Ball, J. R. deWaard, “Biological identifications through DNA barcodes”, Proceedings of the Royal Society, 270:1512 (2003), 313–321 | DOI

[3] P. D.N. Hebert, T. R. Gregory, “The Promise of DNA Barcoding for Taxonomy”, Systematic. Biology, 54:5 (2005), 852–859

[4] J. W.O. Ballard, M. C. Whitlock, “The incomplete natural history of mitochondria”, Molecular. Ecology, 13:4 (2004), 729–744 | DOI

[5] C. Schoch, K. Seifert, S. Huhndorf, R. Vincent, J. Spouge, A. Levesque, C. Wen, “Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi”, Proceedings of the National Academy of Sciences, 109:16 (2012), 6241–6246 | DOI

[6] P. Forrest L. Spouge J. Hollingsworth, M. Hajibabaei, S. Ratnasingham, M. van der Bank, M. Chase, R. Cowan, “A DNA barcode for land plants”, Proceedings of the National Academy of Sciences, 106:31 (2009), 12794–12797

[7] N. Nehal, B. Choudhary, A. Nagpure, R. K. Gupta, “DNA barcoding: a modern age tool for detection of adulteration in food”, Critical Reviews in Biotechnology, 41:5 (2021), 767–791 | DOI

[8] K. Chatpiyaphat, S. Sumruayphol, J. P. Dujardin, Y. Samung, A. Phayakkaphon, L. Cui, J. Ruangsittichai, S. Sungvornyothin, J. Sattabongkot, P. Sriwichai, “Geometric morphometrics to distinguish the cryptic species Anopheles minimus and An. harrisoni in malaria hot spot villages, western Thailand”, Medical and Veterinary Entomology, 35:3 (2021), 293–301 | DOI

[9] V. V. Panyukov, S. S. Kiselev, O. V. Alikina, N. N. Nazipova, O. N. Ozoline, “Short unique sequences in bacterial genomes as strain- and species-specific signatures”, Mathematical Biology and Bioinforatics, 12:2 (2017), 547–558 | DOI

[10] V. Panyukov, S. Kiselev, O. Ozoline, “Unique k-mers as strain-specific barcodes for phylogenetic analysis and natural microbiome profiling”, Int. J. Mol. Sci, 21:3 (2020), 944 | DOI

[11] J. M.S. Bartlett, D. Stirling, “A Short History of the Polymerase Chain Reaction”, PCR Protocols, 226 (2003), 3–6

[12] B. R. Kuluev, An. Kh. Baimiev, G. A. Geraschenkov, D. A. Chemeris, V. V. Zubov, A. R. Kuluev, Al. Kh. Baimiev, A. V. Chemeris, “Metody PTsR dlya vyyavleniya multilokusnogo polimorfizma DNK u eukariot, osnovannye na sluchainom praimirovanii”, Genetika, 54 (2018), 495–511 | DOI

[13] J. G. Williams, A. R. Kubelik, K. J. Livak, J. A. Rafalski, S. V. Tingey, “DNA polymorphisms amplified by arbitrary primers are useful as genetic markers”, Nucleic Acids Res, 18 (1990), 6531–6535

[14] G. E. Corley-Smith, C. J. Lim, G. B. Kalmar, B. P. Brandhorst, “Efficient Detection of DNA Polymorphisms by Fluorescent RAPD Analysis”, BioTechniques, 22:4 (1997), 690–699 | DOI

[15] N. E. Morton, “Parameters of the human genome”, Proc. Natl. Acad. Sci, 88 (1991), 7474–7476

[16] D. A. Chemeris, O. Yu. Kiryanova, I. M. Gubaidullin, A. V. Chemeris, “Dizain praimerov dlya polimeraznoi tsepnoi reaktsii (kratkii obzor kompyuternykh programm i baz dannykh)”, Biomika, 8:3 (2016), 215–238

[17] O. Yu. Kiryanova, I. I. Kiryanov, B. R. Kuluev, A. V. Chemeris, R. R. Garafutdinov, I. M. Gubaidullin, ABCDNA_GS (AMPLIFIED BAR-CODED DNA GENOME/SPECIMEN), svidetelstvo o registratsii programmy dlya EVM No 2020610703 ot 17.01.2020

[18] R. R. Garafutdinov, A. Kh. Baimiev, G. V. Maleev, Ya. I. Alekseev, V. V. Zubov, D. A. Chemeris, O. Yu. Kiryanova, I. M. Gubaidullin, R. T. Matniyazov, A. R. Sakhabutdinova, Yu. M. Nikonorov, B. R. Kuluev, A. Kh. Baimiev, A. V. Chemeris, “Raznoobrazie praimerov dlya PTsR i printsipy ikh podbora”, Biomika, 11:1 (2019), 23–70

[19] Python, (data obrascheniya 15.09.2022) https://www.python.org/downloads/release/python-360/

[20] D. A. Benson, I. Karsch-Mizrachi, D. J. Lipman, J. Ostell, D. L. Wheeler, “GenBank”, Nucleic Acids Res, 36 (2007), D25-D30 | DOI

[21] 1001Genomes, (data obrascheniya 15.09.2022) https://1001genomes.org/data-center.html

[22] National Library of Medicine, (data obrascheniya 15.09.2022) https://www.ncbi.nlm.nih.gov/

[23] D. Knuth, J. H. Morris, V. Pratt, “Fast pattern matching in strings”, SIAM Journal on Computing, 6:2 (1977), 323–350 | DOI

[24] O. Yu. Kiryanova, B. R. Kuluev, A. R. Kuluev, I. S. Mardanshin, I. M. Gubaidullin, A. V. Chemeris, “Multipleksnyi in silico RAPD-analiz ryada rodstvennykh rastenii s otlichayuschimisya razmerami genomov i perspektivy takogo podkhoda dlya DNK-pasportizatsii sortov selskokhozyaistvennykh rastenii”, Biomika, 12:2 (2020), 194–210 | DOI

[25] A. R. Kuluev, R. T. Matniyazov, D. A. Chemeris, A. V. Chemeris, “Sovremennye predstavleniya o rodstvennykh vzaimootnosheniyakh v pshenichno-egilopsnom alyanse (s kratkoi istoricheskoi spravkoi)”, Biomika, 8:4 (2016), 297–310

[26] O. Yu. Kiryanova, R. R. Garafutdinov, D. A. Chemeris, Yu. R. Giniyatov, I. M. Gubaidullin, A. V. Chemeris, “Polimorfizm DNK sobak (canis familiaris l). II. RAPD-analiz”, Biomika, 13:3 (2021), 309–320 | DOI

[27] R. R. Garafutdinov, K. P. Gainullina, O. Yu. Kiryanova, A. V. Yurina, I. Yu. Dolmatova, O. N. Loginov, A. V. Chemeris, “Polimorfizm DNK loshadi Equus Caballus i metody ego vyyavleniya”, Biomika, 12:2 (2020), 272–299 | DOI

[28] V. V. Zubov, D. A. Chemeris, R. G. Vasilov, V. E. Kurochkin, Ya. I. Alekseev, “Kratkaya istoriya metodov vysokoproizvoditelnogo sekvenirovaniya nukleinovykh kislot”, Biomika, 13:1 (2021), 27–46 | DOI

[29] B. R. Kuluev, An. Kh. Baimiev, G. A. Geraschenkov, U. B. Yunusbaev, R. R. Garafutdinov, Ya. I. Alekseev, Al. Kh. Baimiev, A. V. Chemeris, “Sto let gaploidnym genomam. Seichas nastupaet vremya diploidnykh”, Biomika, 12:4 (2020), 411–434 | DOI