Abstract

Phylogenetic methods that rely on information from multiple, unlinked genes have recently been developed for resolving complex situations where evolutionary relationships do not conform to bifurcated trees and are more adequately depicted by networks. Such situations arise when successive interspecific hybridizations in combination with genome duplications have shaped species phylogenies. Several processes such as homoeolog loss and deep coalescence can potentially hamper our ability to recover the historical signal correctly. Consequently the prospect of reconstructing accurate phylogenies lies in the combination of several low-copy nuclear markers that when used in concert can provide homoeologs for all the ancestral genomes and help to disentangle gene tree incongruence due to deep coalescence events. The genus Silene L. is a prime example of a plant group whose evolutionary history involves numerous events of hybridization and polyploidization. As for many groups there is currently a shortage of low-copy nuclear markers, for which phylogenetic usefulness has been demonstrated. Here, we present two Expressed Sequence Tag (EST) libraries for two species of Silene that belong to large phylogenetic groups not previously investigated with next generation technologies. The assembled and annotated transcriptomes are used for identifying low copy number nuclear regions, suitable for sequencing.