Phylogenomic analysis of transcriptome data elucidates co-occurrence of a paleopolyploid event and the origin of bimodal karyotypes in Agavoideae (Asparagaceae).
OBJECTIVE
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 RNA-seq data were generated for phylogenetically strategic species in Agavoideae. Paleopolyploidy was inferred in analyses of frequency plots for synonymous substitutions per synonymous site (K(s)) 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 to place inferred paleopolyploid events on a species tree.


RESULTS
K(s) 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 polyploidy 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 nonmodel species.
Department of Plant Biology, University of Georgia, Athens, Georgia 30602, USA.
Michael R
MR
McKain
Norman
N
Wickett
Yeting
Y
Zhang
Saravanaraj
S
Ayyampalayam
W Richard
WR
McCombie
Mark W
MW
Chase
J Chris
JC
Pires
Claude W
CW
dePamphilis
Jim
J
Leebens-Mack
D001483:Base Sequence; D032461:Chromosomes, Plant / Q000235:genetics; D019143:Evolution, Molecular; D020440:Gene Duplication; D017343:Genes, Plant; D007621:Karyotyping; D019668:Liliaceae / Q000145:classification / Q000235:genetics*; D005810:Multigene Family; D010802:Phylogeny; D011123:Polyploidy; D018749:RNA, Plant / Q000235:genetics; D017423:Sequence Analysis, RNA; D013045:Species Specificity; D059467:Transcriptome
D018749:RNA, Plant