Abstract
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, rpoC1, 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.
Highlights
Barley is one of the most important cereals in the world, after wheat and rice
We explored alloplasmic barley lines with cytoplasm of H. spontaneum and H. vulgare, as we lack the original seeds of H. spontaneum and H. vulgare donors of cytoplasm
It displays the diversity of chloroplast genomes of H. vulgare and H. spontaneum, which allows to subdivide the plasmotypes in the study set of barley
Summary
Barley is one of the most important cereals in the world, after wheat and rice. The history of its cultivation stretches from ancient times (Pankin, von Korf, 2017). Peculiar distribution of different nuclear and cytoplasmic gene loci of barley across localities occurred together with the process of migration of humans (Saisho, Purugganan, 2007). In parallel with the process of barley spreading from the centers of origin to different climatic zones, definite changes in nuclear and cytoplasmic genes have happened. This led to change in the interactions of the nucleus and cytoplasm, the establishment of new nuclearcytoplasmic relations. Chloroplasts and mitochondria are essential organelles in plant cells and play an important role in sustaining life. The genomes of organelles have a number of properties that make them indispensable for studying in various areas of modern biology: a large number of copies per cell; relatively conservative sequences; lack of recombination; maternal inheritance; coding the proteins for photosynthesis and respiration; endosymbiotic origin (Danilenko, Davydenko, 2003; Daniell et al, 2016)
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