Data from: Phylogenomic analysis of transcriptome data elucidates co-occurrence of a paleopolyploid event and the origin of bimodal karyotypes in Agavoideae (Asparagaceae)
McKain, Michael R., University of Georgia
Wickett, Norman, Pennsylvania State University
Zhang, Yeting, Pennsylvania State University
Ayyampalayam, Saravanaraj, University of Georgia
McCombie, W. Richard, Cold Spring Harbor Laboratory
Chase, Mark W., Royal Botanic Gardens
Pires, J. Chris, University of Missouri
dePamphilis, Claude W.
Leebens-Mack, Jim, University of Georgia
de Pamphilis, Claude W., Pennsylvania State University
Published Mar 28, 2012 on Dryad.
Cite this dataset
McKain, Michael R. et al. (2012). Data from: Phylogenomic analysis of transcriptome data elucidates co-occurrence of a paleopolyploid event and the origin of bimodal karyotypes in Agavoideae (Asparagaceae) [Dataset]. Dryad. https://doi.org/10.5061/dryad.7pg045t2
PREMISE OF THE STUDY: The stability of the bimodal karyotype found in Agave and closely related species has long interested botanists. The origin of the bimodal karyotype has been attributed to allopolyploidy, but this hypothesis has not been tested. Next Generation transcriptome sequence data were used to test whether a paleopolyploid event occurred on the same branch of the Agavoideae phylogenetic tree as the origin of the Yucca-Agave bimodal karyotype. METHODS: Illumina RNAseq data were generated for phylogenetically strategic species in Agavoideae. Paleopolyploidy was inferred in analyses of frequency plots for synonymous substitutions per synonymous site (Ks) between Hosta, Agave and Chlorophytum paralogous and orthologous gene pairs. Phylogenies of gene families including paralogous genes for these species and outgroup species were estimated in order to place inferred paleopolyploid events on a species tree. KEY RESULTS: Ks frequency plots suggested paleopolyploid events in the history of the genera Agave, Hosta and Chlorophytum. Phylogenetic analyses of gene families estimated from transcriptome data revealed two polyploid events: one predating the last common ancestor of Agave and Hosta and one within the lineage leading to Chlorophytum. CONCLUSIONS: We found that allopolyoidy and the origin of the Yucca-Agave bimodal karyotype co-occur on the same lineage consistent with the hypothesis that the bimodal karyotype is a consequence of allopolyploidy. We discuss this and alternative mechanisms for the formation of the Yucca-Agave bimodal karyotype. More generally, we illustrate how the use of next generation sequencing technology is a cost-efficient means for assessing genome evolution in non-model species.