Abstract
BackgroundRepetitive DNA motifs – not coding genetic information and repeated millions to hundreds of times – make up the majority of many genomes. Here, we identify the nature, abundance and organization of all the repetitive DNA families in oats (Avena sativa, 2n = 6x = 42, AACCDD), a recognized health-food, and its wild relatives.ResultsWhole-genome sequencing followed by k-mer and RepeatExplorer graph-based clustering analyses enabled assessment of repetitive DNA composition in common oat and its wild relatives’ genomes. Fluorescence in situ hybridization (FISH)-based karyotypes are developed to understand chromosome and repetitive sequence evolution of common oat. We show that some 200 repeated DNA motifs make up 70% of the Avena genome, with less than 20 families making up 20% of the total. Retroelements represent the major component, with Ty3/Gypsy elements representing more than 40% of all the DNA, nearly three times more abundant than Ty1/Copia elements. DNA transposons are about 5% of the total, while tandemly repeated, satellite DNA sequences fit into 55 families and represent about 2% of the genome. The Avena species are monophyletic, but both bioinformatic comparisons of repeats in the different genomes, and in situ hybridization to metaphase chromosomes from the hexaploid species, shows that some repeat families are specific to individual genomes, or the A and D genomes together. Notably, there are terminal regions of many chromosomes showing different repeat families from the rest of the chromosome, suggesting presence of translocations between the genomes.ConclusionsThe relatively small number of repeat families shows there are evolutionary constraints on their nature and amplification, with mechanisms leading to homogenization, while repeat characterization is useful in providing genome markers and to assist with future assemblies of this large genome (c. 4100 Mb in the diploid). The frequency of inter-genomic translocations suggests optimum strategies to exploit genetic variation from diploid oats for improvement of the hexaploid may differ from those used widely in bread wheat.
Highlights
Repetitive DNA motifs – not coding genetic information and repeated millions to hundreds of times – make up the majority of many genomes
More than 70% of reads were assigned into just 200 graph clusters of highly related sequence reads (Additional file 2: Figure S2, Table 1), with 12 to 18 clusters representing more than 1% of all the reads (Additional file 15: Table S3b)
After manual verification by checking domain homology or satellite motifs (Additional file 16: Table S4), 65% of Avena genome reads were related to transposable elements [Transposable element (TE), including class I retrotransposons and class II DNA transposons], and tandem repeats [satellite DNA, Ribosomal DNA (rDNA), and telomere; average 2.70%] (Table 1, Additional file 17: Table S5 [33])
Summary
Repetitive DNA motifs – not coding genetic information and repeated millions to hundreds of times – make up the majority of many genomes. Several major groups of repetitive elements are found: ribosomal DNAs (rDNAs) [both 45S (18S–5.8S-26S) and 5S rDNAs with intergenic spacers], the telomeric repeats, class I retrotransposons (amplified through an RNA intermediate), class II DNA transposons (amplified through DNA copies), and tandem repeats (postulated to be generated/ modified by slippage replication, uneven crossing-over or rolling circle amplification) [7]. Their presence and similarity, variation in copy number and sequences, pose a major challenge to genome assembly and gene annotation [9]. Copy number variations in repeats, representing 5 to 10% of the human genome, are important for disease and population variation [10]
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