Abstract
In this study, complete chloroplast and mitochondrial genomes of wild ( Hordeum vulgare subsp. spontaneum ) and cultivated ( Hordeum vulgare subsp. vulgare ) barley forms were compared to evaluate the diversity of these genomes within the species. NGS (next generation sequencing) was conducted for mixtures of chloroplast and mitochondrial DNA of 17 barley samples. The chloroplast DNA was obtained from the fraction of these organelles, isolated by differential centrifugation. Such fraction contained an admixture of mitochondrial DNA, which made it possible to conduct sequencing of both genomes simultaneously. The NGS data processing algorithm included some features to prevent mistakes during the alignment of reads from the homology regions within and between the genomes. Five sequences of barley chloroplast genome and two sequences of mitochondrial genome accessible in NCBI GenBank were also involved in the full-genome comparative analysis. Comparison of 22 complete barley chloroplast genome sequences revealed a high level of diversity of these genomes within Hordeum vulgare . There were 107 polymorphic loci: 9 INDELs, 79 SNPs and 19 polymorphisms of SSR-regions (simple sequence repeats). Twenty from 79 found SNPs were located in coding sequences. Analysis of 19 complete sequences of mitochondrial genomes (8 H. vulgare subsp. vulgare and 11 H. vulgare subsp. spontaneum ) showed a lower level of variability of these organelles: 1 INDEL and 22 SNP (4 in coding sequences). Two SNPs were found in one of the genes of the small subunit of ribosomes and two were located in the exon of a pseudogene. The results of the study proved the applicability of NGS of chloroplast and mitochondrial DNA mixtures to the obtaining of complete sequences of these genomes. Revealed polymorphic loci could be used for barley intraspecific identification and phylogeny.
Highlights
NGS was conducted for mixtures of chloroplast and mitochondrial DNA of 17 barley samples
Сomparison of 22 complete barley chloroplast genome sequences revealed a high level of diversity of these genomes within Hordeum vulgare
The results of the study proved the applicability of NGS of chloroplast and mitochondrial DNA mixtures to the obtaining of complete sequences of these genomes
Summary
В ходе исследования был оптимизирован алгоритм обработки данных NGS для получения полных последовательностей хп и мт геномов ячменя при секвенировании смесей органельной ДНК, полученной из фракции хлоропластов Данный алгоритм содержит стандартные этапы обработки NGS-прочтений при ресеквенировании геномов (очистка прочтений, выравнивание на референсную последовательность, получение и фильтрация VCF-файлов), однако включает особенности, необходимые для исключения ошибки выравнивания прочтений, относящихся к гомологичным областям генома Результаты тестирования метода подтвердили его применимость для обработки данных NGS смесей хп и мт ДНК с различными соотношениями их концентраций. В результате обработки данных NGS получены полные нуклеотидные последовательности хп и мт геномов 17 образцов, несущих цитоплазму 5 диких форм А также последовательностей хп и мт геномов из базы данных NCBI GenBank 1) был проведен анализ изменчивости органельных геномов ячменя, результаты которого представлены в табл. Для которых получены полные последовательности хп и мт геномов Table 2. Barley samples with obtained complete sequences of сp and mt genomes
Sign-in/Register to view highlights & summary Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callMore From: Proceedings of the National Academy of Sciences of Belarus, Biological Series
Disclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
