AUTHOR=Kroupin Pavel Yu. , Badaeva Ekaterina D. , Sokolova Victoria M. , Chikida Nadezhda N. , Belousova Maria Kh. , Surzhikov Sergei A. , Nikitina Ekaterina A. , Kocheshkova Alina A. , Ulyanov Daniil S. , Ermolaev Aleksey S. , Khuat Thi Mai Luong , Razumova Olga V. , Yurkina Anna I. , Karlov Gennady I. , Divashuk Mikhail G. 

TITLE=Aegilops crassa Boiss. repeatome characterized using low-coverage NGS as a source of new FISH markers: Application in phylogenetic studies of the Triticeae

JOURNAL=Frontiers in Plant Science

VOLUME=13

YEAR=2022

URL=https://www.frontiersin.org/journals/plant-science/articles/10.3389/fpls.2022.980764

DOI=10.3389/fpls.2022.980764

ISSN=1664-462X

ABSTRACT=<p><italic>Aegilops crassa Boiss</italic>. is polyploid grass species that grows in the eastern part of the Fertile Crescent, Afghanistan, and Middle Asia. It consists of tetraploid (4x) and hexaploid (6x) cytotypes (2<italic>n</italic> = 4x = 28, D<sup>1</sup>D<sup>1</sup>X<sup>cr</sup>X<sup>cr</sup> and 2n = 6x = 42, D<sup>1</sup>D<sup>1</sup>X<sup>cr</sup>X<sup>cr</sup>D<sup>2</sup>D<sup>2</sup>, respectively) that are similar morphologically. Although many <italic>Aegilops</italic> species were used in wheat breeding, the genetic potential of <italic>Ae</italic>. <italic>crassa</italic> has not yet been exploited due to its uncertain origin and significant genome modifications. Tetraploid <italic>Ae</italic>. <italic>crassa</italic> is thought to be the oldest polyploid <italic>Aegilops</italic> species, the subgenomes of which still retain some features of its ancient diploid progenitors. The D<sup>1</sup> and D<sup>2</sup> subgenomes of <italic>Ae</italic>. <italic>crassa</italic> were contributed by <italic>Aegilops</italic><italic>tauschii</italic> (2<italic>n</italic> = 2x = 14, DD), while the X<sup>cr</sup> subgenome donor is still unknown. Owing to its ancient origin, <italic>Ae</italic>. <italic>crassa</italic> can serve as model for studying genome evolution. Despite this, <italic>Ae</italic>. <italic>crassa</italic> is poorly studied genetically and no genome sequences were available for this species. We performed low-coverage genome sequencing of 4x and 6x cytotypes of <italic>Ae</italic>. <italic>crassa</italic>, and four <italic>Ae</italic>. <italic>tauschii</italic> accessions belonging to different subspecies; diploid wheatgrass <italic>Thinopyrum bessarabicum</italic> (J<sup>b</sup> genome), which is phylogenetically close to D (sub)genome species, was taken as an outgroup. Subsequent data analysis using the pipeline RepeatExplorer2 allowed us to characterize the repeatomes of these species and identify several satellite sequences. Some of these sequences are novel, while others are found to be homologous to already known satellite sequences of Triticeae species. The copy number of satellite repeats in genomes of different species and their subgenome (D<sup>1</sup> or X<sup>cr</sup>) affinity in <italic>Ae</italic>. <italic>crassa</italic> were assessed by means of comparative bioinformatic analysis combined with quantitative PCR (qPCR). Fluorescence <italic>in situ</italic> hybridization (FISH) was performed to map newly identified satellite repeats on chromosomes of common wheat, <italic>Triticum aestivum</italic>, 4x and 6x <italic>Ae</italic>. <italic>crassa</italic>, <italic>Ae</italic>. <italic>tauschii</italic>, and <italic>Th</italic>. <italic>bessarabicum</italic>. The new FISH markers can be used in phylogenetic analyses of the Triticeae for chromosome identification and the assessment of their subgenome affinities and for evaluation of genome/chromosome constitution of wide hybrids or polyploid species.</p>