Nuclear and chloroplast genome diversity in apomictic microspecies of Taraxacum

Whole genomic survey sequences were obtained for Taraxacum obtusifrons Markl. (O978); T. stridulum Trávniček ined. (S3); and T. amplum Markl. (A978), three apomictic triploid (2n=3x=24) dandelions from the T. officinale agg. (Asteraceae) Retroelement-based markers and chloroplast data showed that S3 and O978 are genetically the most similar microspecies. Genomic diversity in Taraxacum and also Hieracium was high, discriminating species but not showing phylogeny; major groups of retroelements were abundant in both genera. The chloroplast genomes of accessions O978 and S3 were identical. Repetitive DNA including transposable elements (TEs) are dynamically evolving in genomes, but their variability and abundance make them challenging to study using molecular biology. In the current study, we used the whole genomic sequences to investigate the repetitive structure, diversity and components of the three closely related Taraxacum accessions. Analysis of about 45Gb sequence (10x to 20× genome coverage) of three closely related Taraxacum microspecies, were analysed by graph-based clustering of the raw reads (using the program RepeatExplorer) and frequency analysis of all DNA motifs possible for various motif lengths (k-mer analysis). Different DNA motif lengths were evaluated and complemented the graph-based results. Graph-based clustering showed that many of the Taraxacum microspecies repeats consist of Ty1-copia (13-16%) and Ty3-gypsy (10-14%) family retroelements, while DNA transposons were rare. Unclassified repetitive DNA sequence clusters were investigated. In situ hybridization was used to localize major repetitive DNA families on chromosomes. Apart from 5S and 45S rDNA and telomere sequences, few tandemly repeated DNA motifs were found, although a 49bp repeat was found at some centromeres. There were differences between the three Taraxacum microspecies in genomic proportions and locations for repetitive DNA types suggesting many sequence motifs are evolving rapidly with increasing or decreasing copy numbers. A class of repetitive DNA has been recognized as Passively Amplified DNA Sequences, PADS.