The repetitive DNA landscape in Avena (Poaceae): chromosome and genome evolution defined by major repeat classes in whole-genome sequence reads

• DOI: 10.1186/s12870-019-1769-z
• Publication Date: 2019-05-30T10:03:05Z
• Authors: Qing Liu; Xiaoyu Li; Xiangying Zhou; Mingzhi Li; Fengjiao Zhang; Trude Schwarzacher; John Seymour Hesl...
• Keywords: Repeated sequence; Retrotransposon; Avena; Noncoding DNA; Satellite DNA

Repetitive DNA motifs – not coding genetic information and repeated millions to hundreds of times make up the majority many genomes. Here, we identify nature, abundance organization all repetitive families in oats (Avena sativa, 2n = 6x 42, AACCDD), a recognized health-food, its wild relatives. Whole-genome sequencing followed by k-mer RepeatExplorer graph-based clustering analyses enabled assessment composition common oat relatives' Fluorescence situ hybridization (FISH)-based karyotypes are developed understand chromosome sequence evolution oat. We show that some 200 70% Avena genome, with less than 20 making 20% total. Retroelements represent major component, Ty3/Gypsy elements representing more 40% DNA, nearly three abundant Ty1/Copia elements. transposons about 5% total, while tandemly repeated, satellite sequences fit into 55 2% genome. The species monophyletic, but both bioinformatic comparisons repeats different genomes, metaphase chromosomes from hexaploid species, shows repeat specific individual or A D genomes together. Notably, there terminal regions showing rest chromosome, suggesting presence translocations between relatively small number evolutionary constraints on their nature amplification, mechanisms leading homogenization, characterization is useful providing genome markers assist future assemblies this large (c. 4100 Mb diploid). frequency inter-genomic suggests optimum strategies exploit variation diploid for improvement may differ those used widely bread wheat.