Comparative genomic analysis and evolutionary study of repetitive DNA for estimating variation and mobility

Abstract

Repetitive DNA sequences, motifs repeated hundreds, thousands of times in the nuclear genome, represent typically half of the DNA and are some of the most rapidly evolving sequences. The objective of this study was to see how repetitive sequences differ and evolve between and within the wider Polygonaceae family and Malus domestica species. High volume DNA sequence reads from 12 Polygonaceae species were analysed using individual graphbased repeat clustering, revealing substantial differences in amount and composition of TEs. Many genus-specific repetitive elements were found in the comparative clustering of 21 samples, notwithstanding the close relationship of the genera. The repetitive sequence landscape was characterised among three apple cultivars. Repetitive DNA represents some 45 % of the apple genome. Graph-based sequence-read clustering showed the amount and genome composition of TEs with genome-wide dispersal was similar in various apple cultivars. LTR-retrotransposons were the most abundant, and similar Ty1-copia and Ty3-gypsy proportions. Analysis of in situ hybridisation to chromosomes was used for localisation of the various repetitive elements (including the 5S and 45S rDNA loci) and comparing abundance and organisation with published genome assemblies and unassembled raw sequence reads. In apple fruit, sectors of different colours are occasionally observed, just in the skin (peel) of the apple. The colour sectors arise from movement of TEs around the MYB transcription factor, giving rise to different expression of anthocyanin genes and hence pigmentation. Genomic DNA (c. 12-fold genome coverage) from the skin sectors was analysed. Notably, Gala is heterozygous for a key MYB gene. Insertional polymorphisms were identified in or around the MYB genes between the sectors and rest of the fruit, showing that DNA sequence movement was likely to cause the colour differences.