Arbuscular mycorrhiza fungi of soil samples from North Caucasus were identified via Illumina Miseq and universal primers for ITS region. It was shown, that both ITS1 and ITS2 are necessary for identification.
Проведено молекулярно-филогенетическое исследование гибридогенного рода × Trisetokoeleria Tzvelev и некоторых предполагаемых предковых таксонов с использованием маркерных последовательностей ITS1-5.8S рДНК-ITS2, trnL-trnF и trnK-rps16. Кроме того, было проведено секвенирование нового поколения (NGS) на платформе Illumina последовательности ITS1 и начала гена 5.8S рРНК. Секвенирование по Сэнгеру выявило частичное совпадение с классическими представлениями о происхождении рода, причем × T. jurtzevii группируется с Koeleria asiatica и K. macrantha, а × T. taimyrica монофилетична с Trisetum spicatum. По данным NGS-секвенирования все виды × Trisetokoeleria содержат в своем геноме последовательности ITS T. spicatum –они самые массовые. Другие субгеномы различны у разных видов и не всегда соответствуют данным морфологического анализа
A molecular phylogenetic study of weed-field species of the genus Avena L. using marker sequences ITS1–5.8S rRNA gene–ITS2 was undertaken. In addition, next-generation sequencing (NGS) was performed on the Illuminaplatform for the ITS1 sequence and the beginning of the gene 5.8S rRNA. Sanger sequencing results revealed the separateclade of microspecies with a good level of support and small level of difference between themselves. According to NGSsequencing data, the two most abundant subgenomes in terms of the number of sequences were identified. Among thecommon sequences of hexaploids, those associated with the C-genome were not found. The presence of unique ribotypeswas shown for A. persica and A. georgica.
For diploid (2x) species with the A-genome, as well as for hexaploid (6x) from the genus Avena, a locus-specific next-generation sequencing (NGS) of the sequence of the region of the internal transcribed spacer ITS1 and the beginning of the 5.8S rRNA gene was carried out on the Illumina platform. The high diversity and heterogeneity of the genomes of diploid species are shown. It was revealed that the genomes of modern diploid oat species are relatively far removed from the hexaploid species. It was found that A. canariensis occupies an isolated position among other diploid species, and also takes only an insignificant role in the formation of hexaploid genomes.
For the first time, using next generation sequencing (NGS) on the Illumina platform of the ITS1 sequence and the beginning of the 5.8S rRNA gene, the current state of genomic compositions of complex cultivated oat hybrids based on the Avena macrostachya was studied. It was shown that A. sativa х A. macrostachya hybrid used for further hybridization with other oat species actually acts as a “pure” A. sativa in the next generations of hybridization. The most represented ribotypes (abundant by the number of marker sequences reads) are inherited from the hexaploid A. sativa (ACD genome). Other parental taxa, such as hexaploids A. byzantina, A. sterilis (ACD-genome), tetraploids A. magna, A. murphyi (AC-genome), as a rule, form the second most abundant ribotype in hybrids. Also, this ribotype includes the minor components of A. sativa rDNA (probably left over from common ancestors). We assume that this is due to the harsh consequences of the reorganization of genomes in interspecific hybrids from crossing cultivated oat with wild ones, as a result of which the number of sequences of these species in the genomic set of hybrids naturally gradually decreases. It especially manifests in the artificial hybridization of hexaploids of the A. sativa group (A. sativa and A. fatua, ACD-genome) and A. macrostachya (homotetraploid CmCm). In such hybrids, according to our data, the loss of entire chromosomes of A. macrostachya sometimes occurs, due to which we do not see rDNA sequences of this species at all.
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