vavilovВавиловский журнал генетики и селекцииVavilov Journal of Genetics and Breeding2500-3259Institute of Cytology and Genetics of Siberian Branch of the RAS10.18699/VJ19.589vavilov-2475Research ArticleГЕНЕТИЧЕСКИЕ РЕСУРСЫ И БИОКОЛЛЕКЦИИPLANT GENETICSИзучение изменчивости ДНК органелл аллоплазматических линий ячменя в эпоху высокопроизводительного секвенированияThe study of organelle DNA variability in alloplasmic barley lines in the NGS erahttps://orcid.org/0000-0002-9800-4725СинявскаяМ. Г.SiniauskayaM. G.

Минск

Minsk

cytoplasmic@mail.ruМакаревичА. М.MakarevichA. M.

Минск

Minsk

ГолоенкоИ. М.GoloenkoI. M.

Минск

Minsk

ПанкратовВ. С.PankratovV. S.

Минск

Minsk

ЛевданскийО. Д.LiaudanskiA. D.

Минск

Minsk

ДаниленкоН. Г.DanilenkoN. G.

Минск

Minsk

ЛуханинаН. В.LukhaninaN. V.

Минск

Minsk

ШимкевичА. М.ShimkevichA. M.

Минск

Minsk

ДавыденкоО. Г.DavydenkoO. G.

Минск

Minsk

Институт генетики и цитологии, Национальная академия наук БеларусиБеларусьInstitute of Genetics and Cytology, National Academy of Sciences of BelarusBelarus2020170320202411219Copyright © Синявская М.Г., Макаревич А.М., Голоенко И.М., Панкратов В.С., Левданский О.Д., Даниленко Н.Г., Луханина Н.В., Шимкевич А.М., Давыденко О.Г., 20202020Синявская М.Г., Макаревич А.М., Голоенко И.М., Панкратов В.С., Левданский О.Д., Даниленко Н.Г., Луханина Н.В., Шимкевич А.М., Давыденко О.Г.Siniauskaya M.G., Makarevich A.M., Goloenko I.M., Pankratov V.S., Liaudanski A.D., Danilenko N.G., Lukhanina N.V., Shimkevich A.M., Davydenko O.G.This work is licensed under a Creative Commons Attribution 4.0 License.https://vavilov.elpub.ru/jour/article/view/2475

Аллоплазматические линии являются подходящей моделью для изучения молекулярной коэволюции и взаимодействий между генетическими системами растительной клетки. C использованием MiSeqSystem (Illumina) были определены полногеномные последовательности ДНК органелл клетки -хлоропластов и митохондрий. ДНК органелл выделена из 12 образцов коллекции аллоплазматических линий ячменя с цитоплазмами Hordeumvulgaressp. spontaneum (H. spontaneum) и H. vulgaressp. vulgare (H. vulgare), а также из сортов ячменя доноров ядра. Разработан и верифицирован подход к анализу результатов NGS смесей хлоропластной и митохондриальной ДНК для сборки новых полных сиквенсов пла-стидных и митохондриальных геномов H. vulgare и H. spontaneum. Проведено сравнительное изучение изменчивости геномов органелл, локализованы полиморфные участки. Выделено восемь типов хпДНК и пять типов мтДНК. Полученная информация сопоставлена с результатами предыдущих исследований этих же линий методом полиморфизма длин рестрикционных фрагментов ДНК органелл. На основании сравнения полногеномных последовательностей хпДНК и мтДНК аллоплазматических линий и сортов доноров ядерных геномов пересмотрены полученные для них ранее данные по формированию признаков, связанных с продуктивностью. Семнадцать полиморфных локусов обнаружено в экзонах пластидных генов. Семь из них расположены в генах Ndh комплекса. Несинонимические замены нуклеотидов идентифицированы в генах matK, rpoCI, ndhK, ndhG, infA. Вероятно, некоторые SNP являются точками, где происходит эдитинг, о чем свидетельствуют позиции замены в кодоне и тип аминокислотной замены. Проведенное исследование открывает новые перспективы для изучения ядерно-цитоплазматических взаимодействий на примере аллоплазматических линий.

Alloplasmic lines are a suitable model for studying molecular coevolution and interrelations between genetic systems of plant cells. Whole chloroplast (cp) and mitochondrial (mt) genome sequences were obtained by the MiSeq System (Illumina). Organelle DNA samples were prepared from a set of 12 alloplasmic barley lines with different cytoplasms of Hordeum vulgare ssp. spontaneum and H. vulgare ssp. vulgare, as well as from their paternal varieties. A bioinformatic approach for analysis of NGS data obtained on an organellar DNA mix has been developed and verified. A comparative study of Hordeum organelle genomes' variability and disposition of polymorphic loci was conducted. Eight types of chloroplast DNA and 5 types of mitochondrial DNA were distinguished for the barley sample set examined. These results were compared with the previous data of a restriction fragment length polymorphism (RFLP) study of organelle DNAs for the same material. Formerly established data about a field evaluation of alloplasmic barley lines were revised in the light of information about organelle genomes gained after NGS. Totally 17 polymorphic loci were found at exons of chloroplast genomes. Seven of the SNPs were located in the genes of the Ndh complex. The nonsynonymous changes of nucleotides were detected in the matK, rpoCI, ndhK, ndhG and infA genes. Some of the SNPs detected are very similar in codon position and in the type of amino acid substitution to the places where RNA editing can occur. Thus, these results outline new perspectives for the future study of nuclear-cytoplasmic interactions in alloplasmic lines.

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The authors declare that there are no conflicts of interest present.