Differentially Amplified Repetitive Sequences Among Aegilops tauschii Subspecies and Genotypes

Abstract

Genomic repetitive sequences commonly show species-specific sequence type, abundance, and distribution patterns, however, their intraspecific characteristics have been poorly described. We quantified the genomic repetitive sequences and performed single nucleotide polymorphism (SNP) analysis between 29 Ae. tauschii genotypes and subspecies using publicly available raw genomic Illumina sequence reads and used fluorescence in situ hybridization (FISH) to experimentally analyze some repeats. The majority of the identified repetitive sequences had similar contents and proportions between anathera, meyeri, and strangulata subspecies. However, two Ty3/gypsy retrotransposons (CL62 and CL87) showed significantly higher abundances, and CL1, CL119, CL213, CL217 tandem repeats, and CL142 retrotransposon (Ty1/copia type) showed significantly lower abundances in subspecies strangulata compared with the subspecies anathera and meyeri. One tandem repeat and 45S ribosomal DNA (45S rDNA) abundances showed a high variation between genotypes but their abundances were not subspecies specific. Phylogenetic analysis using the repeat abundances of the aforementioned clusters placed the strangulata subsp. in a distinct clade but could not discriminate anathera and meyeri. A near complete differentiation of anathera and strangulata subspecies was observed using SNP analysis; however, var. meyeri showed higher genetic diversity. FISH using major tandem repeats couldn’t detect differences between subspecies, although (GAA)10 signal patterns generated two different karyotype groups. Taken together, the different classes of repetitive DNA sequences have differentially accumulated between strangulata and the other two subspecies of Ae. tauschii that is generally in agreement with spike morphology, implying that factors affecting repeatome evolution are variable even among highly closely related lineages.

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

“…From another side, chromosomal breaks causing chromosomal rearrangements often occur at sites enriched with repetitive DNA (Raskina et al, 2008;Molnár et al, 2011;Murat et al, 2017;Pollak et al, 2018). Owing to this, many researchers studying genome evolution and speciation in plants were focused on analysis repetitive DNA (Liu et al, 2019;Song et al, 2020;Ebrahimzadegan et al, 2021;Waminal et al, 2021). Fluorescence in situ hybridization is one of the most broadly exploited approaches in this field.…”

“…strangulata and D subgenome chromosomes of common wheat differed from that in the D 1 and D 2 chromosomes, suggesting that these differences may exist in the genome of diploid progenitor. This assumption is legitimate, as many molecular ( Luo et al, 2007 ; Wang et al, 2013 ; Li et al, 2018 ; Singh et al, 2019 ; Gaurav et al, 2021 ) and cytogenetic ( Majka et al, 2017 ; Zhao et al, 2018 ; Badaeva et al, 2019a ; Ebrahimzadegan et al, 2021 ) data supported significant genome divergence between two Ae . tauschii subspecies.…”

“…The D subgenome is also present in two polyploid Aegilops species and in four exaploidy bread wheat Triticum aestivum (2n = 6x = BBAADD). According to molecular analysis of nuclear genome ( Dvořák et al, 1998 ; Luo et al, 2017 ; Singh et al, 2019 ) and hybridization pattern of pAs1 probe ( Badaeva et al, 1996 , 2019a ; Zhao et al, 2018 ; Ebrahimzadegan et al, 2021 ), the D subgenome of polyploid wheat was inherited from Ae . tauschii subsp.…”

Intraspecific divergence of diploid grass Aegilops comosa is associated with structural chromosome changes

“…tauschii. Chromosomes of these species contain only little amounts of microsatellite sequences or do not possess them at all (Badaeva et al 2015a(Badaeva et al , 2019aLinc et al 2017;Li et al 2018;Zhao et al 2018;Ebrahimzadegan et al 2021).…”

Structural Polymorphisms of Chromosome 3Am Containing Lr63 Leaf Rust Resistance Loci Reflect the Geographical Distribution of Triticum monococcum L. and Related Diploid Wheats

“…For example, differences in the proximity of retrotransposons to genes could contribute to the significant phenotypic differences between wild and cultivated sunflowers [43]. Recently, Ebrahizadegan et al [44] reported that different classes of repetitive DNA sequences have differentially accumulated between Aegilops tauschii subsp. strangulata and the other two subspecies of Ae.…”