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1Academic Journal
Συγγραφείς: E. S. Balakirev, Е. С. Балакирев
Συνεισφορές: This study received budget support within the framework of the Research Study entitled “World Ocean biodiversity: taxonomy, barcoding, phylogenetics, reproductive and evolutionary biology, biogeography” (State registry no. 121082600036-9, Ministry of Science and Higher Education of the Russian Federation) conducted by A.V. Zhirmunsky National Scientific Center of Marine Biology, Far Eastern Branch, Russian Academy of Sciences, Vladivostok, Russia.
Πηγή: Vavilov Journal of Genetics and Breeding; Том 29, № 2 (2025); 259-267 ; Вавиловский журнал генетики и селекции; Том 29, № 2 (2025); 259-267 ; 2500-3259 ; 10.18699/vjgb-25-20
Θεματικοί όροι: генетическая дивергенция, Protosalanx, taxonomic misidentification, mitochondrial genomes, CytB, single-marker sequences, genetic divergence, таксономические ошибки идентификации, митохондриальные геномы, маркерные последовательности
Περιγραφή αρχείου: application/pdf
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Misidentified mitogenomes of two Lycodes species (Perciformes: Zoarcidae) in GenBank. Russ J Genet. 2024;60(10):1375-1382. doi 10.1134/S1022795424700911; Betancur-R R., Wiley E.O., Arratia G., Acero A., Bailly N., Miya M., Lecointre G., Ortí G. Phylogenetic classification of bony fishes. BMC Evol Biol. 2017;17:162. doi 10.1186/s12862-017-0958-3; Botero-Castro F., Delsuc F., Douzery E.J.P. Thrice better than once: quality control guidelines to validate new mitogenomes. Mitochondrial DNA A DNA Mapp Seq Anal. 2016;27(1):449-454. doi 10.3109/19401736.2014.900666; Cheng J., Ma G.-Q., Song N., Gao T.-X. Complete mitochondrial genome sequence of bighead croaker Collichthys niveatus (Perciformes, Sciaenidae): a mitogenomic perspective on the phylogenetic relationships of Pseudosciaeniae. Gene. 2012;491(2):210-223. doi 10.1016/j.gene.2011.09.020; Collins R.A., Boykin L.M., Cruickshank R.H., Armstrong K.F. Barcoding’s next top model: an evaluation of nucleotide substitution models for specimen identification. Methods Ecol Evol. 2012;3: 457-465. doi 10.1111/j.2041-210x.2011.00176.x; Cunha R.L., Nicastro K.R., Zardi G.I., Madeira C., McQuaid C.D., Cox C.J., Castilho R. Comparative mitogenomic analyses and gene rearrangements reject the alleged polyphyly of a bivalve genus. PeerJ. 2022;10:e13953. doi 10.7717/peerj.13953; Edgar R.C. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004;32:1792-1797. doi 10.1093/nar/gkh340; Fu C., Luo J., Wu J., López J.A., Zhong Y., Lei G., Chen J. Phylogenetic relationships of salangid fishes (Osmeridae, Salanginae) with comments on phylogenetic placement of the salangids based on mitochondrial DNA sequences. Mol Phylogenet Evol. 2005;35:76-84. doi 10.1016/j.ympev.2004.11.024; Fu C., Guo L., Xia R., Li J., Lei G. A multilocus phylogeny of Asian noodlefishes Salangidae (Teleostei: Osmeriformes) with a revised classification of the family. Mol Phylogenet Evol. 2012;62(3):848- 855. doi 10.1016/j.ympev.2011.11.031; Giribet G., Wheeler W.C. On gaps. Mol Phylogenet Evol. 1999;13(1): 132-143. doi 10.1006/mpev.1999.0643; Guo L., Li J., Wang Z., Fu C. Phylogenetic relationships of noodlefishes (Osmeriformes: Salangidae) based on four mitochondrial genes. Acta Hydrobiol. 2011;35:449-459. doi 10.3724/SP.J.1035.2011.00449; Hoang D.T., Chernomor O., von Haeseler A., Minh B.Q., Vinh L.S. UFBoot2: improving the ultrafast bootstrap approximation. Mol Biol Evol. 2018;35:518-522. doi 10.1093/molbev/msx281; Hofstetter V., Buyck B., Eyssartier G., Schnee S., Gindro K. The unbearable lightness of sequenced-based identification. Fungal Divers. 2019;96:243-284. doi 10.1007/s13225-019-00428-3; Houbraken J., Visagie C.M., Frisvad J.C. Recommendations to prevent taxonomic misidentification of genome-sequenced fungal strains. Microbiol Resour Ann. 2021;10:e01074-20. doi 10.1128/MRA.01074-20; Kartavtsev Y.P. Sequence divergence at mitochondrial genes in animals: applicability of DNA data in genetics of speciation and molecular phylogenetics. Mar Genomics. 2011;4(2):71-81. doi 10.1016/j.margen.2011.02.002; Kartavtsev Y.P., Rozhkovan K.V., Masalkova N.A. Phylogeny based on two mtDNA genes (Co-1, Cyt-B) among sculpins (Scorpaeniformes, Cottidae) and some other scorpionfish in the Russian Far East. Mitochondrial DNA A DNA Mapp Seq Anal. 2016;27(3):2225-2240. doi 10.3109/19401736.2014.984164; Kim D.E., Kim P., Lee H., Kim N.H., Kim D., Lee M.J., Ban Y.G., Jang B., Park J. Comprehensive analysis of the complete mitochondrial genome of Melanoplus differentialis (Acrididae: Melanoplinae) captured in Korea. Entomol Res. 2023;53:66-81. doi 10.1111/1748-5967.12633; Li X., Shen X., Chen X., Xiang D., Murphy R.W., Shen Y. Detection of potential problematic Cytb gene sequences of fishes in GenBank. Front Genet. 2018;9:30. doi 10.3389/fgene.2018.00030; Mohamed W.M.A., Moustafa M.A.M., Kelava S., Barker D., Matsuno K., Nonaka N., Shao R., Mans B.J., Barker S.C., Nakao R. Reconstruction of mitochondrial genomes from raw sequencing data provides insights on the phylogeny of Ixodes ticks and cautions for species misidentification. Ticks Tick Borne Dis. 2022;13(1):101832. doi 10.1016/j.ttbdis.2021.101832; Mulder K.P., Lourenço A., Carneiro M., Velo-Antón G. The complete mitochondrial genome of Salamandra salamandra (Amphibia: Urodela: Salamandridae). Mitochondrial DNA Part B. 2016;1:880- 882. doi 10.1080/23802359.2016.1253042; Nguyen L.T., Schmidt H.A., von Haeseler A., Minh B.Q. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum likelihood phylogenies. Mol Biol Evol. 2015;32:268-274. doi 10.1093/molbev/msu300; Nielsen M.K., Wang J., Davis R., Bellaw J.L., Lyons E.T., Lear T.L., Goday C. Parascaris univalens – a victim of large-scale misidentification? Parasitol Res. 2014;113:4485-4490. doi 10.1007/s00436-014-4135-y; Nilsson R.H., Ryberg M., Kristiansson E., Abarenkov K., Larsson K.H., Koljalg U. Taxonomic reliability of DNA sequences in public sequence databases: a fungal perspective. PLoS One. 2006;1(1):e59. doi 10.1371/journal.pone.0000059; Oleinik A.G., Skurikhina L.A., Kukhlevsky A.D. Clarification of taxonomic assignment of smelt complete mitochondrial genome: GenBank accession number KP281293.1 (NC_026566.1). Mitochondrial DNA Part B. 2019;4:1696-1697. doi 10.1080/23802359.2019.1607578; Ožana S., Dolný A., Pánek T. Nuclear copies of mitochondrial DNA as a potential problem for phylogenetic and population genetic studies of Odonata. Syst Entomol. 2022;47:591-602. doi 10.1111/syen.12550; Roberts T.R. 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Mitochondrial genome announcements need to consider existing short sequences from closely related species to prevent taxonomic errors. Conserv Genet Resour. 2021;13:359-365. doi 10.1007/s12686-021-01214-7; The National Center for Biotechnology Information. Available online: https://www.ncbi.nlm.nih.gov/ (accessed on July 29, 2024); Yang Y., Sui Z., Liu K., Liu Y. The complete mitochondrial DNA sequence of Linyi small icefish (Neosalanx taihuensis). GenBank submission: 24-NOV-2020. Genbank accession number: MW291630; Zhang J., Li M., Xu M., Takita T., Wei F. Molecular phylogeny of icefish Salangidae based on complete mtDNA cytochrome b sequences, with comments on estuarine fish evolution. Biol J Linn Soc. 2007;91:325-340. doi 10.1111/j.1095-8312.2007.00785.x; Zhao L., Zhang J., Liu Z., Funk S.M., Wei F., Xu M., Li M. Complex population genetic and demographic history of the Salangid, Neosalanx taihuensis, based on cytochrome b sequences. 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2Academic Journal
Συγγραφείς: S. V. Shekhovtsov, G. V. Vasiliev, R. Latif, T. V. Poluboyarova, S. E. Peltek, I. B. Rapoport, С. В. Шеховцов, Г. В. Васильев, Р. Латиф, Т. В. Полубоярова, С. Е. Пельтек, И. Б. Рапопорт
Συνεισφορές: This study was supported by the grant of the Russian Foundation for Basic Research No. 20-54-5603_Iran_t and of the Iran National Science Foundation No. 99003929, as well as by the State Budget Projects No. АААА-А18-122011900453-0 and FWNR-2022-0022
Πηγή: Vavilov Journal of Genetics and Breeding; Том 27, № 2 (2023); 146-152 ; Вавиловский журнал генетики и селекции; Том 27, № 2 (2023); 146-152 ; 2500-3259 ; 10.18699/VJGB-23-1
Θεματικοί όροι: митохондриальные геномы, Lumbricidae, Dendrobaena tellermanica, mitochondrial genomes
Περιγραφή αρχείου: application/pdf
Relation: https://vavilov.elpub.ru/jour/article/view/3679/1693; 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. SPAdes: A new genome assembly algorithm and its applications to single-cell sequencing. J. Comput. Biol. 2012;19(5): 455-477. DOI:10.1089/cmb.2012.0021.; Benson G. Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res. 1999;27(2):573-580. DOI:10.1093/nar/27.2.573.; Bernt M., Donath A., Jühling F., Externbrink F., Florentz C., Fritzsch G., Pütz J., Middendorf M., Stadler P.F. MITOS: Improved de novo metazoan mitochondrial genome annotation. Mol. Phylogenet. Evol. 2013;69(2):313-319. DOI:10.1016/j.ympev.2012.08.023.; Blouin M., Hodson M.E., Delgado E.A., Baker G., Brussaard L., Butt K.R., Dai J., Dendooven L., Peres G., Tondoh J.E., Cluzeau D., Brun J.-J. A review of earthworm impact on soil function and ecosystem services. Eur. J. Soil Sci. 2013;64(2):161-182. DOI:10.1111/ejss.12025.; Bolger A.M., Lohse M., Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 2014;30(15):2114-2120. DOI:10.1093/bioinformatics/btu170.; Boore J.L., Brown W.M. Complete sequence of the mitochondrial DNA of the annelid worm Lumbricus terrestris. Genetics. 1995;141(1): 305-319. DOI:10.1093/genetics/141.1.305.; Castresana J. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol. Biol. Evol. 2000;17(4): 540-552. DOI:10.1093/oxfordjournals.molbev.a026334.; Clayton D.A. Transcription and replication of animal mitochondrial DNAs. Int. Rev. Cytol. 1992;141:217-232. DOI:10.1016/S00747696(08)62067-7.; Conrado A.C., Arruda H., Stanton D.W.G., James S.W., Kille P., Brown G., Silva E., Dupont L., Taheri S., Morgan A.J., Simõe N., Rodrigues A., Montiel R., Cunha L. The complete mitochondrial DNA sequence of the pantropical earthworm Pontoscolex corethrurus (Rhinodrilidae, Clitellata): Mitogenome characterization and phylogenetic positioning. ZooKeys. 2017;688:1-13. DOI:10.3897/zookeys.688.13721.; Csuzdi C., Koo J., Hong Y. The complete mitochondrial DNA sequences of two sibling species of lumbricid earthworms, Eisenia fetida (Savigny, 1826) and Eisenia andrei (Bouché, 1972) (Annelida, Crassiclitellata): comparison of mitogenomes and phylogenetic positioning. ZooKeys. 2022;1097:167-181. DOI:10.3897/zookeys.1097.80216.; Gendron P., Lemieux S., Major F. Quantitative analysis of nucleic acid three-dimensional structures. J. Mol. Biol. 2001;308(5):919-936. DOI:10.1006/jmbi.2001.4626.; Hendrix P.F., Callaham M.A., Drake J.M., Huang C.-Y., James S.W., Snyder B.A., Zhang W. Pandora’s box contained bait: the global problem of introduced earthworms. Annu. Rev. Ecol. Evol. Syst. 2008;39(1):593-613. DOI:10.1146/annurev.ecolsys.39.110707.173426.; Hong Y., Kim M.J., Wang A.R., Kim I. Complete mitochondrial genome of the earthworm. Amynthas jiriensis (Clitellata: Megascolecidae). Mitochondrial DNA A DNA Mapp. Seq. Anal. 2017;28(2): 163-164. DOI:10.3109/19401736.2015.1115491.; Jamieson B.G.M., Tillier S., Tillier A., Justine J.-L., Ling E., James S., McDonald K., Hugall A.F. Phylogeny of the Megascolecidae and Crassiclitellata (Annelida, Oligochaeta): combined versus partitioned analysis using nuclear (28S) and mitochondrial (12S, 16S) rDNA. Zoosystema. 2002;24(4):707-734.; Kim M.J., Hong Y. Complete mitochondrial genome of the earthworm Amynthas seungpanensis (Clitellata: Megascolecidae). Mitochondrial DNA B Resour. 2022;7(6):989-991. DOI:10.1080/23802359.2022.2080604.; Klarica J., Kloss-Brandstätter A., Traugott M., Juen A. Comparing four mitochondrial genes in earthworms – Implications for identification, phylogenetics, and discovery of cryptic species. Soil Biol. Biochem. 2012;45:23-30. DOI:10.1016/j.soilbio.2011.09.018.; Kvavadze E.Sh. The Earthworms (Lumbricidae) of the Caucasus. Tbilisi: Metsniereba Publ., 1985. (in Russian); Lavelle P., Spain A., Blouin M., Brown G., Decaëns T., Grimaldi M., Jiménez J.J., McKey D., Mathieu J., Velasquez E., Zangerlé A. Ecosystem engineers in a self-organized soil. Soil Sci. 2016;181(3/4): 91-109. DOI:10.1097/SS.0000000000000155.; Liu H., Xu N., Zhang Q., Wang G., Xu H., Ruan H. Characterization of the complete mitochondrial genome of Drawida gisti (Metagynophora, Moniligastridae) and comparison with other Metagynophora species. Genomics. 2020;112(5):3056-3064. DOI:10.1016/j.ygeno.2020.05.020.; Liu H., Zhang Y., Xu W., Fang Y., Ruan H. Characterization of five new earthworm mitogenomes (Oligochaeta: Lumbricidae): mitochondrial phylogeny of Lumbricidae. Diversity. 2021;13(11):580. DOI:10.3390/d13110580.; Marchán D.F., Cosín D.J.D., Novo M. Why are we blind to cryptic species? Lessons from the eyeless. Eur. J. Soil Biol. 2018;86:49-51. DOI:10.1016/j.ejsobi.2018.03.004.; Marchán D.F., Decaëns T., Domínguez J., Novo M. Perspectives in earthworm molecular phylogeny: recent advances in Lumbricoidea and standing questions. Diversity. 2022;14(1):30. DOI:10.3390/d14010030.; Mezhzherin S.V., Garbar A.V., Vlasenko R.P., Onishchuk I.P., Kotsyuba I.Yu., Zhalai E.I. The Evolutionary Paradox of Parthenogenetic Earthworms. Kiev: Naukova Dumka Publ., 2018. (in Ukrainian); Michaelsen W. Die Lumbriciden des Kaukasischen Museums in Tiflis. Mitteilungen des Kaukasischen Museums. 1907;3:81-93.; Perel T.S. Earthworms in forest soils of the Northwestern Caucasus. In: The Impact of Animals on the Productivity of Forest Cenoses. Moscow: Nauka Publ., 1966;146-165. (in Russian); Seto A., Endo H., Minamiya Y., Matsuda M. The complete mitochondrial genome sequences of Japanese earthworms Metaphire hilgendorfi and Amynthas yunoshimensis (Clitellata: Megascolecidae). Mitochondrial DNA B. Resour. 2021;6(3):965-967. DOI:10.1080/23802359.2020.1830728.; Shekhovtsov S., Berman D.I., Bazarova N.E., Bulakhova N.A., Porco D., Peltek S.E. Cryptic genetic lineages in Eisenia nordenskioldi pallida (Oligochaeta, Lumbricidae). Eur. J. Soil Biol. 2016;75:151156. DOI:10.1016/j.ejsobi.2016.06.004.; Shekhovtsov S.V., Golovanova E.V., Ershov N.I., Poluboyarova T.V., Berman D.I., Bulakhova N.A., Szederjesi T., Peltek S.E. Phylogeny of the Eisenia nordenskioldi complex based on mitochondrial genomes. Eur. J. Soil Biol. 2020a;96:103137. DOI:10.1016/j.ejsobi.2019.103137.; Shekhovtsov S.V., Peltek S.E. The complete mitochondrial genome of Aporrectodea rosea (Annelida: Lumbricidae). Mitochondrial DNA Part B. 2019;4(1):1752-1753. DOI:10.1080/23802359.2019.1610091.; Shekhovtsov S.V., Rapoport I.B., Poluboyarova T.V., Geraskina A.P., Golovanova E.V., Peltek S.E. Morphotypes and genetic diversity of Dendrobaena schmidti (Lumbricidae, Annelida). Vavilovskii Zhurnal Genetiki i Selektsii = Vavilov Journal of Genetics and Breeding. 2020b;24(1):48-54. DOI:10.18699/VJ20.594. (in Russian); Shekhovtsov S.V., Shipova A.A., Poluboyarova T.V., Vasiliev G.V., Golovanova E.V., Geraskina A.P., Bulakhova N.A., Szederjesi T., Peltek S.E. Species delimitation of the Eisenia nordenskioldi complex (Oligochaeta, Lumbricidae) using transcriptomic data. Front. Genet. 2020c;11:1508. DOI:10.3389/fgene.2020.598196.; Stamatakis A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics. 2014;30(9): 1312-1313. DOI:10.1093/bioinformatics/btu033.; Vallès Y., Boore J.L. Lophotrochozoan mitochondrial genomes. Integr. Comp. Biol. 2006;46(4):544-557. DOI:10.1093/icb/icj056.; Viktorov A.G. Diversity of polyploid races in the family Lumbricidae. Soil Biol. Biochem. 1997;29(3-4):217-221. DOI:10.1016/S00380717(96)00086-7.; Vsevolodova-Perel T.S. The Earthworms of the Russian Fauna: Cadaster and Key. Moscow: Nauka Publ., 1997. (in Russian); Vsevolodova-Perel T.S. Addition to the fauna of earthworms (Oligochaeta, Lumbricidae) of the Northern Caucasus. Zoologicheskiy Zhurnal = Zoological Journal. 2003;82(2):275-280. (in Russian); Vsevolodova-Perel T.S., Bulatova N.Sh. Polyploid races of earthworms (Lumbricidae, Oligochaeta) in the East European Plain and Siberia. Biol. Bull. Russ. Acad. Sci. 2008;35(4):385-388. DOI:10.1134/S1062359008040092.; Wang A.R., Hong Y., Win T.M., Kim I. Complete mitochondrial genome of the Burmese giant earthworm, Tonoscolex birmanicus (Clitellata: Megascolecidae). Mitochondrial DNA. 2015;26(3):467-468. DOI:10.3109/19401736.2013.830300.; Weigert A., Golombek A., Gerth M., Schwarz F., Struck T.H., Bleidorn C. Evolution of mitochondrial gene order in Annelida. Mol. Phylogenet. Evol. 2016;94(Pt. A):196-206. DOI:10.1016/j.ympev.2015.08.008.; Zhang L., Jiang J., Dong Y., Qiu J. Complete mitochondrial genome of an Amynthas earthworm, Amynthas aspergillus (Oligochaeta: Megascolecidae). Mitochondrial DNA A DNA Mapp. Seq. Anal. 2014; 27(3):1-2. DOI:10.3109/19401736.2014.971267.; Zhang L., Jiang J., Dong Y., Qiu J. Complete mitochondrial genome of four pheretimoid earthworms (Clitellata: Oligochaeta) and their phylogenetic reconstruction. Gene. 2015;574(2):308-316. DOI:10.1016/j.gene.2015.08.020.; Zhang L., Jiang J., Dong Y., Qiu J. Complete mitochondrial genome of a Pheretimoid earthworm Metaphire vulgaris (Oligochaeta: Megascolecidae). Mitochondrial DNA. 2016a;27(1):297-298. DOI:10.3109/19401736.2014.892085.; Zhang L., Sechi P., Yuan M., Jiang J., Dong Y., Qiu J. Fifteen new earthworm mitogenomes shed new light on phylogeny within the Pheretima complex. Sci. Rep. 2016b;6:20096. DOI:10.1038/srep20096.; Zhang Q., Liu H., Zhang Y., Ruan H. The complete mitochondrial genome of Lumbricus rubellus (Oligochaeta, Lumbricidae) and its phylogenetic analysis. Mitochondrial DNA Part B. 2019;4(2):26772678. DOI:10.1080/23802359.2019.1644242.; Zhao H., Fan S., Aspe N.M., Feng L., Zhang Y. Characterization of four earthworm mitogenomes from Northeast China and phylogenetic implication (Oligochaeta: Lumbricidae, Moniligastridae). Diversity. 2022;14(9):714. DOI:10.3390/d14090714.; https://vavilov.elpub.ru/jour/article/view/3679
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3Academic Journal
Συγγραφείς: Левыкина, С.С., Рабчун, А.Ю.
Θεματικοί όροι: сравнительный анализ, митохондриальные геномы, Macrosiphum Albifrons, Macrosiphum Rosae
Περιγραφή αρχείου: application/pdf
Διαθεσιμότητα: https://rep.polessu.by/handle/123456789/34301
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4Academic Journal
Συγγραφείς: Golovanova, E. V., Ershov, N. I., Poluboyarova, T. V., Berman, Daniil I., Bulakhova, Nina A., Szederjesi, T., Peltek, Sergey E., Shekhovtsov, S. V.
Πηγή: European journal of soil biology. 2020. Vol. 96. P. 103137 (1-7)
Θεματικοί όροι: 0301 basic medicine, 0303 health sciences, 03 medical and health sciences, митохондриальные геномы, филогения, земляные черви
Περιγραφή αρχείου: application/pdf
Συνδεδεμένο Πλήρες ΚείμενοΣύνδεσμος πρόσβασης: https://www.sciencedirect.com/science/article/abs/pii/S1164556319302663
https://pubag.nal.usda.gov/catalog/6762523
http://vital.lib.tsu.ru/vital/access/manager/Repository/vtls:000794661 -
5Dissertation/ Thesis
Συγγραφείς: Федотовская, Виктория Дмитриевна
Συνεισφορές: Садовский, Михаил Георгиевич, Институт фундаментальной биологии и биотехнологии, Кафедра биофизики
Θεματικοί όροι: структура, функция, нуклеотидные последовательности, упругие карты, метод динамических ядер, митохондриальные геномы грибов, 34.17
Relation: Федотовская, Виктория Дмитриевна. Выявление связей между таксономией. Функцией и триплетным составом митохондриальных генов некоторых грибов [Электронный ресурс] : выпускная квалификационная работа бакалавра : 03.03.02 / В. Д. Федотовская. — Красноярск : СФУ, 2020.
Διαθεσιμότητα: https://elib.sfu-kras.ru/handle/2311/136507