{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,20]],"date-time":"2026-08-20T04:26:28Z","timestamp":1787199988097,"version":"build-2736575974"},"reference-count":72,"publisher":"MDPI AG","issue":"16","license":[{"start":{"date-parts":[[2026,8,17]],"date-time":"2026-08-17T00:00:00Z","timestamp":1786924800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100003443","name":"Ministry of Education and Science of Russian Federation","doi-asserted-by":"crossref","award":["124020100136-0"],"award-info":[{"award-number":["124020100136-0"]}],"id":[{"id":"10.13039\/501100003443","id-type":"DOI","asserted-by":"crossref"}]},{"award":["124020100136-0"],"award-info":[{"award-number":["124020100136-0"]}],"id":[{"id":"https:\/\/ror.org\/00ghqgy32","id-type":"ROR","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Int. J. Mol. Sci.","IJMS"],"abstract":"<jats:p>Locus-specific Illumina NGS was used to analyze the polymorphism of the partial 18S rDNA, spacer ITS1, and partial 5.8S rDNA sequences across 25 cactus species (53 accessions) of the subtribes Hylocereinae and Echinocereinae. To ensure data reliability, only ribotypes (zero-radius operational taxonomic units, ZOTUs) with a minimum read depth of 10 reads within each genome-read pool were retained. A single ribotype was identified in 18 analyzed genomes. In 23 accessions, two or three ribotypes were detected, typically consisting of a major ribotype (98\u201399%) and one or two minor ribotypes. In the remaining samples, two distinct ribotypes were present in approximately equal proportions, suggesting that these individuals are recent hybrids. Ribotype patterns clearly distinguish the genus Deamia from Selenicereus, Hylocereus, and Epiphyllum. Putative pseudogenes with deletions in the 18S and 5.8S rDNA, as well as deletions and insertions in the ITS1 spacers, were detected. Their abundance was generally low (usually &lt;1%), except in two Deamia species (5\u201315%). In ITS1 of some minor ribotypes, deletions eliminated cleavage sites B1, B2, and A3, which are important for pre-rRNA processing. Consequently, the products of these putative pseudogenes could not participate in ribosome formation. In addition, pseudogenic copies exhibited a strong transition bias and A\/T enrichment in the ITS1 region.<\/jats:p>","DOI":"10.3390\/ijms27167351","type":"journal-article","created":{"date-parts":[[2026,8,17]],"date-time":"2026-08-17T16:35:08Z","timestamp":1786984508000},"page":"7351","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Intragenomic and Interspecific Polymorphism of 35S rDNA Internal Transcribed Spacer 1 (ITS1) in Selenicereus and Related Species (Cactaceae: Cactoideae: Phyllocacteae)"],"prefix":"10.3390","volume":"27","author":[{"given":"Alexander V.","family":"Rodionov","sequence":"first","affiliation":[{"name":"Komarov Botanical Institute of the Russian Academy of Sciences, St. Petersburg 197376, Russia"},{"name":"Faculty of Biology, St. Petersburg State University, St. Petersburg 199034, Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yuri G.","family":"Kalugin","sequence":"additional","affiliation":[{"name":"Komarov Botanical Institute of the Russian Academy of Sciences, St. Petersburg 197376, Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Evgenia L.","family":"Romanova","sequence":"additional","affiliation":[{"name":"Komarov Botanical Institute of the Russian Academy of Sciences, St. Petersburg 197376, Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2102-4568","authenticated-orcid":false,"given":"Peter M.","family":"Zhurbenko","sequence":"additional","affiliation":[{"name":"Komarov Botanical Institute of the Russian Academy of Sciences, St. Petersburg 197376, Russia"},{"name":"Weizmann Institute of Science, Rehovot 7610001, Israel"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9745-4604","authenticated-orcid":false,"given":"Elizaveta O.","family":"Punina","sequence":"additional","affiliation":[{"name":"Komarov Botanical Institute of the Russian Academy of Sciences, St. Petersburg 197376, Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alexander G.","family":"Dyomin","sequence":"additional","affiliation":[{"name":"Komarov Botanical Institute of the Russian Academy of Sciences, St. Petersburg 197376, Russia"},{"name":"Biological Station Rybachy, Zoological Institute, Russian Academy of Sciences, Rybachy 238535, Kaliningrad Oblast, Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ivan N.","family":"Shulzhenko","sequence":"additional","affiliation":[{"name":"Komarov Botanical Institute of the Russian Academy of Sciences, St. Petersburg 197376, Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5264-5594","authenticated-orcid":false,"given":"Alexander A.","family":"Gnutikov","sequence":"additional","affiliation":[{"name":"Komarov Botanical Institute of the Russian Academy of Sciences, St. Petersburg 197376, Russia"},{"name":"N.I. Vavilov All-Russian Institute of Plant Genetic Resources (VIR), St. Petersburg 190000, Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nikolai N.","family":"Nosov","sequence":"additional","affiliation":[{"name":"Komarov Botanical Institute of the Russian Academy of Sciences, St. Petersburg 197376, Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,8,17]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"5088","DOI":"10.1073\/pnas.74.11.5088","article-title":"Phylogenetic structure of the prokaryotic domain: The primary kingdoms","volume":"74","author":"Woese","year":"1977","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"621","DOI":"10.1042\/BJ20082063","article-title":"The origin, evolution and structure of the protein world","volume":"417","author":"Wang","year":"2009","journal-title":"Biochem. J."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"1801","DOI":"10.1002\/1873-3468.12682","article-title":"Comparison of preribosomal RNA processing pathways in yeast, plant and human cells\u2013focus on coordinated action of endo-and exoribonucleases","volume":"591","author":"Tomecki","year":"2017","journal-title":"FEBS Lett."},{"key":"ref_4","doi-asserted-by":"crossref","unstructured":"Hemleben, V., Grierson, D., Borisjuk, N., Volkov, R.A., and Kovarik, A. (2021). Personal perspectives on plant ribosomal RNA genes research: From precursor-rRNA to molecular evolution. Front. Plant Sci., 12.","DOI":"10.3389\/fpls.2021.797348"},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"911","DOI":"10.1016\/j.ympev.2007.01.013","article-title":"Better the devil you know? Guidelines for insightful utilization of nrDNA ITS in species-level evolutionary studies in plants","volume":"44","year":"2007","journal-title":"Mol. Phylogenet. Evol."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"573","DOI":"10.1111\/1755-0998.12325","article-title":"ITS1: A DNA barcode better than ITS2 in eukaryotes?","volume":"15","author":"Wang","year":"2015","journal-title":"Mol. Ecol. Resour."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"e155","DOI":"10.3989\/ajbm.624","article-title":"Is ITS2 more successful in angiosperm DNA barcoding than the entire ITS, ITS1, matK and trnH-psbA regions? A review","volume":"82","year":"2025","journal-title":"An. Jard. Bot. Madr."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"509","DOI":"10.1007\/BF00015882","article-title":"Ribosomal RNA genes in plants: Variability in copy number and in the intergenic spacer","volume":"9","author":"Rogers","year":"1987","journal-title":"Plant Mol. Biol."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"884","DOI":"10.1038\/ng.2678","article-title":"Massive genomic variation and strong selection in Arabidopsis thaliana lines from Sweden","volume":"45","author":"Long","year":"2013","journal-title":"Nat. Genet."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"356","DOI":"10.1038\/hdy.2014.111","article-title":"Silenced rRNA genes are activated and substitute for partially eliminated active homeologs in the recently formed allotetraploid, Tragopogon mirus (Asteraceae)","volume":"114","author":"Leitch","year":"2015","journal-title":"Heredity"},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"1201","DOI":"10.1534\/g3.117.040204","article-title":"Unstable inheritance of 45S rRNA genes in Arabidopsis thaliana","volume":"7","author":"Rabanal","year":"2017","journal-title":"G3 Genes Genomes Genet."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"1020","DOI":"10.1111\/tpj.13442","article-title":"Cytogenetic features of rRNA genes across land plants: Analysis of the plant rDNA database","volume":"89","author":"Garcia","year":"2016","journal-title":"Plant J."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"21610","DOI":"10.1038\/s41598-022-25954-0","article-title":"Hybridization and diversity of aquatic macrophyte Sparganium L. (Typhaceae) as revealed by high-throughput nrDNA sequencing","volume":"12","author":"Belyakov","year":"2022","journal-title":"Sci. Rep."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"179","DOI":"10.1038\/s41437-023-00634-5","article-title":"Intragenomic rDNA variation\u2014The product of concerted evolution, mutation, or something in between?","volume":"131","author":"Wang","year":"2023","journal-title":"Heredity"},{"key":"ref_15","doi-asserted-by":"crossref","unstructured":"Gnutikov, A.A., Nosov, N.N., Zuev, E.V., Lysenko, N.S., Shneyer, V.S., Troitsky, A.V., and Rodionov, A.V. (2025). Genomic composition of the artificial hybrid \u00d7 Trititrigia cziczinii (Hordeeae, Poaceae) and related taxa according to molecular phylogenetic data. Plants, 15.","DOI":"10.3390\/plants15010070"},{"key":"ref_16","first-page":"131","article-title":"Intragenomic polymorphism of 35S rDNA internal transcribed spacers: Verification of the hypothesis on the hybridogenic origin of tetraploid Pulsatilla vulgaris","volume":"91","author":"Punina","year":"2026","journal-title":"Biochemistry"},{"key":"ref_17","first-page":"1","article-title":"The repair of double-strand breaks in plants: Mechanisms and consequences for genome evolution","volume":"56","author":"Puchta","year":"2005","journal-title":"J. Exp. Bot."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"985","DOI":"10.1007\/s00294-018-0820-1","article-title":"Fidelity of DNA replication\u2014A matter of proofreading","volume":"64","year":"2018","journal-title":"Curr. Genet."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"1726","DOI":"10.1073\/pnas.1613375114","article-title":"Multiple horizontal transfers of nuclear ribosomal genes between phylogenetically distinct grass lineages","volume":"114","author":"Mahelka","year":"2017","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"1246","DOI":"10.1111\/nph.18171","article-title":"Intact ribosomal DNA arrays of Potentilla origin detected in Erythronium nucleus suggest recent eudicot-to-monocot horizontal transfer","volume":"235","author":"Bartha","year":"2022","journal-title":"New Phytol."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"903","DOI":"10.1093\/oxfordjournals.molbev.a025658","article-title":"Phylogenetic evidence for horizontal transmission of group I introns in the nuclear ribosomal DNA of mushroom-forming fungi","volume":"13","author":"Hibbett","year":"1996","journal-title":"Mol. Biol. Evol."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"evad114","DOI":"10.1093\/gbe\/evad114","article-title":"Ribosomal intergenic spacers are filled with transposon remnants","volume":"15","author":"Bendich","year":"2023","journal-title":"Genome Biol. Evol."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"477","DOI":"10.1534\/genetics.107.071399","article-title":"Finely orchestrated movements: Evolution of the ribosomal RNA genes","volume":"175","author":"Eickbush","year":"2007","journal-title":"Genetics"},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"184","DOI":"10.1101\/gr.5457707","article-title":"Highly efficient concerted evolution in the ribosomal DNA repeats: Total rDNA repeat variation revealed by whole-genome shotgun sequence data","volume":"17","author":"Ganley","year":"2007","journal-title":"Genome Res."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"734","DOI":"10.1016\/j.tig.2019.07.006","article-title":"Mechanisms of rDNA copy number maintenance","volume":"35","author":"Nelson","year":"2019","journal-title":"Trends Genet."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"7245","DOI":"10.1038\/s41467-022-34989-w","article-title":"Varying strength of selection contributes to the intragenomic diversity of rRNA genes","volume":"13","author":"Sultanov","year":"2022","journal-title":"Nat. Commun."},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"414","DOI":"10.1038\/s41580-022-00573-9","article-title":"Regulation of ribosomal RNA gene copy number, transcription and nucleolus organization in eukaryotes","volume":"24","author":"Hori","year":"2023","journal-title":"Nat. Rev. Mol. Cell Biol."},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"168","DOI":"10.1016\/j.ympev.2009.11.020","article-title":"High nrDNA ITS polymorphism in the ancient extant seed plant Cycas: Incomplete concerted evolution and the origin of pseudogenes","volume":"55","author":"Xiao","year":"2010","journal-title":"Mol. Phylogenet. Evol."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"683","DOI":"10.1007\/s00412-015-0556-3","article-title":"Astonishing 35S rDNA diversity in the gymnosperm species Cycas revoluta Thunb","volume":"125","author":"Wang","year":"2016","journal-title":"Chromosoma"},{"key":"ref_30","doi-asserted-by":"crossref","unstructured":"Zhang, J., Chi, X., Zhong, J., Fernie, A., Alseekh, S., Huang, L., and Qian, D. (2022). Extensive nrDNA ITS polymorphism in Lycium: Non-concerted evolution and the identification of pseudogenes. Front. Plant Sci., 13.","DOI":"10.3389\/fpls.2022.984579"},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"e718","DOI":"10.7717\/peerj.718","article-title":"Intragenomic polymorphisms among high-copy loci: A genus-wide study of nuclear ribosomal DNA in Asclepias (Apocynaceae)","volume":"3","author":"Weitemier","year":"2015","journal-title":"PeerJ"},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"579","DOI":"10.1016\/j.ympev.2006.05.036","article-title":"Non-concerted ITS evolution in Mammillaria (Cactaceae)","volume":"41","author":"Harpke","year":"2006","journal-title":"Mol. Phylogenet. Evol."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"261","DOI":"10.1007\/s10265-008-0156-x","article-title":"Extensive 5.8S nrDNA polymorphism in Mammillaria (Cactaceae) with special reference to the identification of pseudogenic internal transcribed spacer regions","volume":"121","author":"Harpke","year":"2008","journal-title":"J. Plant Res."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"124","DOI":"10.1007\/s002390010200","article-title":"Extensive ribosomal DNA genic variation in the columnar cactus Lophocereus","volume":"53","author":"Hartmann","year":"2001","journal-title":"J. Mol. Evol."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"451","DOI":"10.1111\/j.1095-8312.2008.01141.x","article-title":"Galapagos\u2019 Opuntia (prickly pear) cacti: Extensive morphological diversity, low genetic variability","volume":"96","author":"Helsen","year":"2009","journal-title":"Biol. J. Linn. Soc."},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"668","DOI":"10.1016\/j.ympev.2012.07.027","article-title":"Molecular phylogeny and character evolution in terete-stemmed Andean opuntias (Cactaceae\u2212Opuntioideae)","volume":"65","author":"Ritz","year":"2012","journal-title":"Mol. Phylogenet. Evol."},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"737","DOI":"10.1600\/036364413X670421","article-title":"Testing a hypothesis of intergeneric allopolyploidy in vine cacti (Cactaceae: Hylocereeae)","volume":"38","author":"Plume","year":"2013","journal-title":"Syst. Bot."},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"300","DOI":"10.1139\/B07-134","article-title":"5.8S motifs for the identification of pseudogenic ITS regions","volume":"86","author":"Harpke","year":"2008","journal-title":"Botany"},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"595","DOI":"10.1093\/molbev\/msv274","article-title":"On the causes of evolutionary transition: Transversion bias","volume":"33","author":"Stoltzfus","year":"2015","journal-title":"Mol. Biol. Evol."},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"1957","DOI":"10.1093\/plcell\/koac052","article-title":"Maize RNA 3\u2032-terminal phosphate cyclase-like protein promotes 18S pre-rRNA cleavage and is important for kernel development","volume":"34","author":"Wang","year":"2022","journal-title":"Plant Cell"},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"1657","DOI":"10.1046\/j.1365-294x.2000.01020.x","article-title":"TCS: A computer program to estimate gene genealogies","volume":"9","author":"Clement","year":"2000","journal-title":"Mol. Ecol."},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"627","DOI":"10.1093\/bioinformatics\/btv636","article-title":"tcsBU: A tool to extend TCS network layout and visualization","volume":"32","author":"Cabezas","year":"2016","journal-title":"Bioinformatics"},{"key":"ref_43","doi-asserted-by":"crossref","unstructured":"Song, J., Shi, L., Li, D., Sun, Y., Niu, Y., Chen, Z., Luo, H., Pang, X., Sun, Z., and Liu, C. (2012). Extensive pyrosequencing reveals frequent intra-genomic variations of internal transcribed spacer regions of nuclear ribosomal DNA. PLoS ONE, 7.","DOI":"10.1371\/journal.pone.0043971"},{"key":"ref_44","doi-asserted-by":"crossref","unstructured":"Punina, E.O., Gnutikov, A.A., Nosov, N.N., Shneyer, V.S., and Rodionov, A.V. (2024). Hybrid origin of Leymotrigia bergrothii (Poaceae) as revealed by analysis of the internal transcribed spacer ITS1 and trnL sequences. Int. J. Mol. Sci., 25.","DOI":"10.3390\/ijms252211966"},{"key":"ref_45","first-page":"67","article-title":"Intragenomic polymorphism of the 35S rDNA internal transcribed spacers (ITS) in three species and three interspecific hybrids of Pulsatilla (Ranunculaceae)","volume":"27","author":"Punina","year":"2024","journal-title":"Turczaninowia"},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"17","DOI":"10.1016\/j.gde.2017.07.014","article-title":"Beyond speciation genes: An overview of genome stability in evolution and speciation","volume":"47","author":"Barbash","year":"2017","journal-title":"Curr. Opin. Genet. Dev."},{"key":"ref_47","doi-asserted-by":"crossref","first-page":"1025","DOI":"10.1134\/S1022795418090120","article-title":"Polymorphic sites in ITS1-5.8S rDNA-ITS2 region in hybridogenic genus \u00d7 Elyhordeum and putative interspecific hybrids Elymus (Poaceae: Triticeae)","volume":"54","author":"Rodionov","year":"2018","journal-title":"Russ. J. Genet."},{"key":"ref_48","first-page":"674","article-title":"Phenomenon of multiple mutations in the 35S rRNA genes of the C subgenome of polyploid Avena L. Russ","volume":"56","author":"Rodionov","year":"2020","journal-title":"J. Genet."},{"key":"ref_49","doi-asserted-by":"crossref","unstructured":"Bendixsen, D.P., Peris, D., and Stelkens, R. (2021). Patterns of genomic instability in interspecific yeast hybrids with diverse ancestries. Front. Fungal Biol., 2.","DOI":"10.3389\/ffunb.2021.742894"},{"key":"ref_50","doi-asserted-by":"crossref","unstructured":"Tel-Zur, N., Mouyal, J., Zurgil, U., and Mizrahi, Y. (2020). In support of Winge\u2019s theory of \u201chybridization followed by chromosome doubling\u201d. Front. Plant Sci., 11.","DOI":"10.3389\/fpls.2020.00954"},{"key":"ref_51","doi-asserted-by":"crossref","first-page":"33\u221237","DOI":"10.1086\/335887","article-title":"A cytological study of the Cactaceae of Puerto Rico","volume":"117","author":"Spencer","year":"1955","journal-title":"Bot. Gaz."},{"key":"ref_52","first-page":"108","article-title":"Cytological study of Deamia testudo (Karw.) Britt. & Rose: A cactus growing wild in west Bengal","volume":"36","author":"Bhattacharyya","year":"1970","journal-title":"Sci. Cult."},{"key":"ref_53","doi-asserted-by":"crossref","first-page":"1058\u22121065","DOI":"10.2307\/2657005","article-title":"Cytology and mating systems in the climbing cacti Hylocereus and Selenicereus","volume":"87","author":"Lichtenzveig","year":"2000","journal-title":"Am. J. Bot."},{"key":"ref_54","first-page":"527\u2212534","article-title":"Genetic relationships among Hylocereus and Selenicereus vine cacti (Cactaceae): Evidence from hybridization and cytological studies","volume":"94","author":"Abbo","year":"2004","journal-title":"Ann. Bot."},{"key":"ref_55","doi-asserted-by":"crossref","first-page":"26","DOI":"10.2985\/026.020.0106","article-title":"Karyotypes, heterochromatin and physical mapping of rDNA in vine Cactaceae (Hylocereineae)","volume":"2015","author":"Moreno","year":"2015","journal-title":"Haseltonia"},{"key":"ref_56","doi-asserted-by":"crossref","unstructured":"Zaman, Q.U., Hui, L., Nazir, M.F., Wang, G., Garg, V., Ikram, M., Raza, A., Lv, W., Khan, D., and Khokhar, A.A. (2024). Chromosome-level genome assembly of autotetraploid Selenicereus megalanthus and gaining genomic insights into the evolution of trait patterning in diploid and polyploid pitaya species. bioRxiv.","DOI":"10.1101\/2024.06.23.600268"},{"key":"ref_57","unstructured":"Innis, M.A., Gelfand, D.H., Sninsky, J.J., and White, T.T. (1990). Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. PCR Protocols: A Guide to Methods and Applications, Academic Press."},{"key":"ref_58","doi-asserted-by":"crossref","first-page":"234","DOI":"10.1002\/j.1537-2197.1996.tb12701.x","article-title":"A molecular phylogeny of Apiaceae subfamily Apioideae: Evidence from nuclear ribosomal DNA internal transcribed spacer sequences","volume":"83","author":"Downie","year":"1996","journal-title":"Am. J. Bot."},{"key":"ref_59","doi-asserted-by":"crossref","unstructured":"Ridgway, K.P., Duck, J.M., and Young, J.P.W. (2003). Identification of roots from grass swards using PCR-RFLP and FFLP of the plastid trnL (UAA) intron. BMC Ecol., 3.","DOI":"10.1186\/1472-6785-3-8"},{"key":"ref_60","doi-asserted-by":"crossref","unstructured":"Rodionov, A.V., Machs, E.M., Romanova, E.L., Dyomin, A.G., Shulzhenko, I.N., Gnutikov, A.A., Nosov, N.N., Shneyer, V.S., and Kalugin, Y.G. (2026). The nuclear ribosomal ITS1-5.8S rDNA-ITS2 region as a DNA Barcode for Selenicereus grandiflorus and related species (Cactaceae: Cactoideae: Phyllocacteae). Int. J. Mol. Sci., 27.","DOI":"10.3390\/ijms27167166"},{"key":"ref_61","doi-asserted-by":"crossref","first-page":"821","DOI":"10.1093\/genetics\/145.3.821","article-title":"The evolution of ribosomal DNA divergent paralogues and phylogenetic implications","volume":"145","author":"Buckler","year":"2007","journal-title":"Genetics"},{"key":"ref_62","doi-asserted-by":"crossref","unstructured":"Garcia, S., Crh\u00e1k Khaitov\u00e1, L., and Kova\u0159\u00edk, A. (2012). Expression of 5S rRNA genes linked to 35S rDNA in plants, their epigenetic modification and regulatory element divergence. BMC Plant Biol., 12.","DOI":"10.1186\/1471-2229-12-95"},{"key":"ref_63","doi-asserted-by":"crossref","first-page":"1371","DOI":"10.1093\/oxfordjournals.molbev.a026420","article-title":"Cytosine deamination plays a primary role in the evolution of mammalian isochores","volume":"17","author":"Fryxell","year":"2000","journal-title":"Mol. Biol. Evol."},{"key":"ref_64","doi-asserted-by":"crossref","unstructured":"Wendel, J.F., Greilhuber, J., Dole\u017eel, J., and Leitch, I.J. (2012). The variation of base composition in plant genomes. Plant Genome Diversity Volume 1: Plant Genomes, Their Residents, and Their Evolutionary Dynamics, Springer.","DOI":"10.1007\/978-3-7091-1130-7"},{"key":"ref_65","doi-asserted-by":"crossref","first-page":"e202209115","DOI":"10.1083\/jcb.202209115","article-title":"Quality control ensures fidelity in ribosome assembly and cellular health","volume":"222","author":"Parker","year":"2023","journal-title":"J. Cell Biol."},{"key":"ref_66","doi-asserted-by":"crossref","first-page":"2114","DOI":"10.1093\/bioinformatics\/btu170","article-title":"Trimmomatic: A flexible trimmer for Illumina sequence data","volume":"30","author":"Bolger","year":"2014","journal-title":"Bioinformatics"},{"key":"ref_67","doi-asserted-by":"crossref","first-page":"1166","DOI":"10.1093\/bioinformatics\/bts091","article-title":"Unipro UGENE: A unified bioinformatics toolkit","volume":"28","author":"Okonechnikov","year":"2012","journal-title":"Bioinformatics"},{"key":"ref_68","doi-asserted-by":"crossref","first-page":"e2584","DOI":"10.7717\/peerj.2584","article-title":"VSEARCH: A versatile open source tool for metagenomics","volume":"4","author":"Rognes","year":"2016","journal-title":"PeerJ"},{"key":"ref_69","doi-asserted-by":"crossref","first-page":"msae263","DOI":"10.1093\/molbev\/msae263","article-title":"MEGA 12: Molecular evolutionary genetics analysis version 12 for adaptive and green computing","volume":"41","author":"Kumar","year":"2024","journal-title":"Mol. Biol. Evol."},{"key":"ref_70","doi-asserted-by":"crossref","first-page":"1530","DOI":"10.1093\/molbev\/msaa015","article-title":"IQ-TREE 2: New models and efficient methods for phylogenetic inference in the genomic era","volume":"37","author":"Minh","year":"2020","journal-title":"Mol. Biol. Evol."},{"key":"ref_71","doi-asserted-by":"crossref","first-page":"539","DOI":"10.1093\/sysbio\/sys029","article-title":"MrBayes 3.2: Efficient Bayesian phylogenetic inference and model choice across a large model space","volume":"61","author":"Ronquist","year":"2012","journal-title":"Syst. Biol."},{"key":"ref_72","doi-asserted-by":"crossref","first-page":"111","DOI":"10.1007\/BF01731581","article-title":"A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences","volume":"16","author":"Kimura","year":"1980","journal-title":"J. Mol. 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