McKain, M. R., Wickett, N., Zhang, Y., Ayyampalayam, S., McCombie, W. R., Chase, M. W., Pires, J. C., dePamphilis, C. W., Leebens-Mack, J. (February 2012) Phylogenomic analysis of transcriptome data elucidates co-occurrence of a paleopolyploid event and the origin of bimodal karyotypes in Agavoideae (Asparagaceae). American Journal of Botany, 99 (2). pp. 397-406. ISSN 0002-9122
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Abstract
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 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. Key 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.
| Item Type: | Paper |
|---|---|
| Uncontrolled Keywords: | Agavoideae bimodal karyotype next generation sequencing paleopolyploidy genome size dna-sequences flowering plants chromosome evolution group classification maximum-likelihood chloroplast dna duplicate genes agavaceae speciation |
| Subjects: | bioinformatics > genomics and proteomics > genetics & nucleic acid processing bioinformatics > genomics and proteomics organism description > plant bioinformatics > genomics and proteomics > genetics & nucleic acid processing > transcriptomes |
| CSHL Authors: | |
| Communities: | CSHL labs > McCombie lab |
| Depositing User: | Matt Covey |
| Date: | February 2012 |
| Date Deposited: | 30 Jan 2013 15:00 |
| Last Modified: | 25 Oct 2018 16:13 |
| Related URLs: | |
| URI: | https://repository.cshl.edu/id/eprint/27000 |
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