Comparative analysis of Aegilops speltoides and wheat repetitive elements and development of S genome-specific FISH painting
<i>Aegilops speltoides</i> (2n=2x=14, genome SS) is a wild relative of wheat and a donor of useful traits for wheat improvement. Several whole-genome studies compared genic regions of <i>Aegilops</i> from the <i>Sitopsis</i> section and wheat and found that <i>Ae. speltoides</i> is most closely related to the wheat B subgenome but is not its direct progenitor. The results showed that a B subgenome ancestor diverged from <i>Ae. speltoides</i> more than 4 MYA and either has not yet been discovered, or is extinct. To further explore the evolutionary relationship between wheat and <i>Ae. speltoides</i> and develop <i>Ae. speltoides</i> chromosome paints, we performed comparative analysis of repetitive fractions of the S genome and three subgenomes of hexaploid wheat. The low coverage sequence data was analyzed with RepeatExplorer pipeline to annotate repeats and estimate their content. The LTR-retrotransposons comprised about 80% of repeats in <i>Ae. speltoides</i> and wheat datasets and about two-third of them were LTR/Ty3-Gypsy. <i>Ae. speltoides</i> had 1.5 times more LTR/Ty-Copia repeats and 1.5 times less DNA transposons than wheat subgenomes. Several S genome-specific dispersed repeats were found and annotated. Their sequences were used to develop S genome-specific paints for detecting <i>Ae. speltoides</i> chromatin in the wheat background using fluorescent <i>in situ</i> hybridization.