Finally, a small number of plant species have sequences available for multiple accessions or different subspecific taxa including Fragaria vesca L. (Rosaceae, N = 2), Gossypium herbaceum L. (Malvaceae, N = 2), Olea europaea L. (Oleaceae, N = 4), and Oryza sativa L. (Poaceae, N = 3).
In this study, we expanded sampling to include all taxa thought to be related to the reticulate complex based on previous analyses, and we present sequence data from the plastid genome and two nuclear markers, pgiC and gapCp, in most cases for multiple accessions.
This feature of the AFLP technology can be exploited to expedite polymorphism discovery by generating in parallel highly similar genome representations of multiple accessions of crop species for high-throughput sequencing.
While a large proportion of the available herbarium material yielded poor DNA, sequences from multiple accessions were nevertheless obtained for all species except M. ericifolia from East Africa (represented by a single accession).
For those species for which multiple accessions were included, sequences for all accessions fell into the same clade, though in several cases accessions from multiple species grouped together with strong support (e.g. D. clintoniana and D. cristata).
In some cases for which multiple accessions were analysed per genus, the genera were recovered as monophyletic, such as Malephora N.E.Br.
For each species multiple accessions are included.
For species represented by multiple accessions, sequences from all accessions fell into the same clade, and for taxa with multiple copies of pgiC, separate, well-supported clades generally formed that contained the various copies.
For these latter analyses, multiple accessions of the same species were pruned by keeping the most early-branching accession.
Multiple accessions were included for each species.
As with pgiC, sequences of species represented by multiple accessions fell into the same clade, and for taxa with multiple copies of gapCp, separate, well-supported clades generally formed that contained the various copies, though often with additional species present.
