Next Generation Sequencing (NGS)

Using large datasets to understand patterns of chromosome divergence

We are using large NGS data sets to study patterns of repeat divergence in plant chromosomes. Of particular importance in that study is RepeatExplorer and genome skimming approaches.  We have used the approaches to show that repeat copy numbers can diverge rapidly with polyploidy, and that patterns of repeat abundance can be used to develop phylogenetic hypotheses of species relationships (Dodsworth et al 2014).
phylogeny
We are also exploiting transcriptome datasets to dissect epigenetic pathways associated with genome size divergence and polyploidy.
454 Roche data sets

N. tabacum comprising 5% of the genome is obtained here
N. tomentosiformis comprising 5% of the genome is obtained here
N. sylvestris comprising 5% of the genome is obtained here

NGS programmes