Alexander A. Gnutikov

For the first time, locus-specific next-generation sequencing (NGS) of the internal transcribed spacer (ITS1) and the 5.8S rRNA gene start sequences was performed on the Illumina platform for specimens of species from the taxonomically complex genera Koeleria and Trisetum. Over 10,000 marker sequence reads per rDNA pool were obtained for 13 Koeleria and two Trisetum spicatum samples from different geographic regions of Russia. Intragenomic polymorphism of the obtained sequences was studied. According to NGS data, the rDNA of Koeleria samples forms ribotypes, which include sequences from species from different sections. Extensive intersectional hybridization was revealed between Koeleria species. One ribotype of K. polonica was shown to be identical to minor ribotypes of K. glauca, K. brevis, and one Trisetum spicatum sample. The major ribotype of K. theodoriana, K. spryginii, and K. luerssenii was identical to that of K. glauca, while the major ribotype of K. cristata was identical to those of K. altaica and K. asiatica. The major ribotype of K. delavignei was found to be identical to that of K. brevis and one of the ribotypes of K. glauca.

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 (98–99%) 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 Deamia species (5–15%). 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.

The nuclear ITS1–5.8S rDNA–ITS2 region is among the most widely used markers for phylogenetic studies in plants. We sequenced the ITS1–5.8S rDNA–ITS2 region in several species of Selenicereus, two species of Deamia and Epiphyllum chrysocardium. The newly generated sequences were found to be more closely related to ITS and 5.8S rDNA sequences from representatives of other cactus tribes than to the Selenicereus ITS sequences previously deposited in GenBank by research group O. Plume. Importantly, all these sequences retained three conserved motifs of the 5.8S rRNA gene that are commonly used to distinguish functional copies from pseudogenes. Then we analyzed available genome assemblies representing 12 species of Cactaceae. In contrast to the ribotypes identified in this study, the previously reported 5.8S rDNA variants in the assembled genomes of Selenicereus and Carnegiea were represented by a single copy flanked by highly degraded 18S and 28S rDNA sequences. Phylogenetic analyses based on the newly generated ITS sequences and Genbank data supported the monophyly of the subtribes Hylocereinae, Rhipsalideae, and Trichocereinae, as well as the tribes Rhipsalideae, Notocacteae, and Cylindropuntieae. These results demonstrate that the functional ITS1-5.8S rDNA–ITS2 region represents an informative marker for phylogenetic studies within the Cactaceae.

All taxa of plants have undergone several rounds of whole-genome duplication (WGD), accompanying interspecific and intergeneric crosses; subsequently, some part of one or both parent genomes in hybrid plants can be eliminated. The objective of this study was to evaluate the relationships of the intergeneric hybrid ×Agrotrigia (Poaceae) species with the taxa of parental genera Agropyron and Elytrigia and to determine the distribution as well as conservation or loss of parental genomes in the genomes of hybrid species. Molecular phylogenetic analysis of nuclear (ITS, ETS) and several chloroplast DNA markers confirmed that the most likely parents of this hybrid were really species of Agropyron and Elytrigia. The compositions of ribotypes (sequences of the 18S–ITS1–5.8S rDNA region) assessed by next-generation sequencing (NGS) showed that the genomes of hybrid species of ×Agrotrigia hajastanica and of the sample of ×A. androssovii from Turkmenistan carry ribotypes of both Agropyron and Elytrigia. However, the samples of ×A. kotovii and ×A. androssovii from Pskov Oblast bear ribotypes of the Elytrigia type only, whereas the genome of one sample of the ×Agrotrigia genus collected in Stavropol Krai consists exclusively of two clusters of Agropyron-type ribotypes (P genome) and may represent a new species. Therefore, these two (or three) species may be subject to the elimination of portions of the genome of one of the parents, though the extent of elimination may be different.

This article presents information on the botanical composition, geographic diversity, and breeding level of the active oat collection of VIR, which has served as the initial material for oat breeding in the Russian Federation more than a century-long period. Here is a description of the genetic collection including alleles of identified genes for various morphological, biological, and biochemical traits. To expand the genetic basis of cultivated oats, the article presents the results of a comprehensive study of all wild species of the genus Avena L. in terms of evolution, phylogeny, and breeding value. It also presents the results of a field study of a wide range of economically valuable traits in the active oat collection, conducted within the VIR experimental network in various ecological and geographical zones of our country. In addition to describing the identified sources of economically valuable traits, it provides an overview of a number of developed donors of semi-dwarfness and lodging resistance with various alleles of the semi-dwarf gene. The article also summarizes the results of fruitful collaboration with Russian breeding institutions in terms of distributing source material based on a comprehensive study of the active oat collection for various oat breeding directions. Thus, the active oat collection of VIR is comprehensively studied, reliably preserved, and sustainably used for breeding purposes in the Russian Federation.

×Trititrigia cziczinii Tzvelev is a promising crop developed through distant hybridization between Elytrigia intermedia (Host) Nevski (=Thinopyrum intermedium (Host) Barkworth & D.R. Dewey) and Triticum aestivum L., followed by backcrossing with wheat. This study elucidates the genomic composition of this hybrid and its parental taxa using molecular phylogenetic analysis of nuclear (ITS, ETS) and chloroplast (trnK–rps16, ndhF) DNA markers, complemented by Next-Generation Sequencing (NGS) of the 18S–ITS1–5.8S rDNA region. Results from Sanger sequencing revealed that the primary nuclear ribosomal DNA (rDNA) of the hybrid originates from Triticum aestivum; a finding strongly supported by both Bayesian inference and Maximum Likelihood analyses. Chloroplast DNA data unequivocally indicate maternal inheritance from T. aestivum. In contrast, ETS sequence analysis showed phylogenetic affinity to Elytrigia intermedia, suggesting complex genomic reorganization or chimeric sequence formation in the hybrid. NGS data corroborate the dominance of T. aestivum-like ribotypes in the hybrid’s rDNA pool, with only a minor fraction identical to the main ribotype of E. intermedia. Genetic structure analysis further revealed geographic heterogeneity in the genomic composition of E. intermedia populations. The predominance of the wheat genome in ×T. cziczinii is likely a consequence of stabilizing backcrosses and illustrates a case of rDNA elimination from one parental genome during hybridization. This research underscores the complex genomic dynamics in artificial hybrids and the utility of multi-marker phylogenetic approaches for clarifying their origins.

The genus Gagea exhibits high morphological diversity and complex taxonomy. In this study, we analyzed the phylogenetic relationships and morphological differentiation within Gagea using ITS sequences from 32 species across 9 sections. Bayesian analysis revealed 3 main clades, partially congruent with morphological traits. Our results highlight both the value of molecular data for species delimitation and the need for taxonomic revision due to cases of morphological convergence and incongruence. This study contributes to a deeper understanding of evolutionary patterns in Gagea.

The possible origin of four cultivated species of the genus Avena of different ploidy and different subgenome composition (A. strigosa, A. abyssinica, A. byzantina, and A. sativa) from possible wild species was investigated. The region of the internal transcribed spacer ITS1 and the 5.8S rRNA gene in the cultivated species was studied with next-generation sequencing (NGS), and the patterns of occurrence and distribution of the ribotypes were compared among them and with those of the wild species. According to these data diploid, A. strigosa is more closely related to the diploid A. hirtula than to polyploid oats, and it could have evolved independently of polyploid cultivated species. The tetraploid Avena abyssinica could be a cultivated derivative of A. vaviloviana. Two hexaploid cultivated species, A. byzantina and A. sativa, could have a different origin; A. sativa could be the cultivated form of A. fatua, whereas A. byzantina could originate independently. It was found that the oat species with the A and C subgenomes, even with strong morphological and karyological differences, could intercross and pass the further stages of introgression producing a new stable combination of genomes. Our data show that almost all species of Avena could form an introgressive interspecies complex.

×Leymotrigia bergrothii is a presumed hybrid of Leymus arenarius and Elytrigia repens. This article investigates the hybrid origin and genome composition of this species. These plants are sterile, do not undergo pollination, and do not produce seeds; occasionally, underdeveloped stamens containing abortive pollen grains form in individual spikelets. The karyotype analysis of root meristem cells revealed a diploid chromosome number of 49 in ×L. bergrothii, reported here for the first time. Subsequently, we examined the intragenomic polymorphism of the transcribed spacer ITS1 in several species of Elytrigia, Elymus, Leymus, Hordeum, and Psathyrostachys, and compared the ribotype patterns of these species with those of ×L. bergrothii. It is shown that the St-ribotype variants found in Elytrigia repens and Elytrigia pseudocaesia, as well as the ribotypes of the La family, which dominate in the genome of Leymus arenarius, correspond to major ribotypes in ×L. bergrothii. The ribotypes of the St and La families are present in the nuclear genome of ×L. bergrothii in almost equal proportions. A comparison of intron and exon sequences of the trnL gene in the chloroplast DNA of Leymus arenarius, Elytrigia repens, and ×L. bergrothii showed that this region in ×L. bergrothii is identical or very close to that of Elytrigia repens, suggesting that Elytrigia repens was the cytoplasmic donor to ×L. bergrothii. Thus, our study confirms the hypothesis that this species represents a sterile first-generation hybrid of Leymus arenarius and Elytrigia repens, reproducing vegetatively.