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A genome triplication associated with early diversification of the core eudicots.
Genome Biol. 2012 Jan 26; 13(1):R3.GB

Abstract

BACKGROUND

Although it is agreed that a major polyploidy event, gamma, occurred within the eudicots, the phylogenetic placement of the event remains unclear.

RESULTS

To determine when this polyploidization occurred relative to speciation events in angiosperm history, we employed a phylogenomic approach to investigate the timing of gene set duplications located on syntenic gamma blocks. We populated 769 putative gene families with large sets of homologs obtained from public transcriptomes of basal angiosperms, magnoliids, asterids, and more than 91.8 gigabases of new next-generation transcriptome sequences of non-grass monocots and basal eudicots. The overwhelming majority (95%) of well-resolved gamma duplications was placed before the separation of rosids and asterids and after the split of monocots and eudicots, providing strong evidence that the gamma polyploidy event occurred early in eudicot evolution. Further, the majority of gene duplications was placed after the divergence of the Ranunculales and core eudicots, indicating that the gamma appears to be restricted to core eudicots. Molecular dating estimates indicate that the duplication events were intensely concentrated around 117 million years ago.

CONCLUSIONS

The rapid radiation of core eudicot lineages that gave rise to nearly 75% of angiosperm species appears to have occurred coincidentally or shortly following the gamma triplication event. Reconciliation of gene trees with a species phylogeny can elucidate the timing of major events in genome evolution, even when genome sequences are only available for a subset of species represented in the gene trees. Comprehensive transcriptome datasets are valuable complements to genome sequences for high-resolution phylogenomic analysis.

Authors+Show Affiliations

Intercollege Graduate Degree Program in Plant Biology, The Pennsylvania State University, University Park, PA 16802, USA.No affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info available

Pub Type(s)

Journal Article
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.

Language

eng

PubMed ID

22280555

Citation

Jiao, Yuannian, et al. "A Genome Triplication Associated With Early Diversification of the Core Eudicots." Genome Biology, vol. 13, no. 1, 2012, pp. R3.
Jiao Y, Leebens-Mack J, Ayyampalayam S, et al. A genome triplication associated with early diversification of the core eudicots. Genome Biol. 2012;13(1):R3.
Jiao, Y., Leebens-Mack, J., Ayyampalayam, S., Bowers, J. E., McKain, M. R., McNeal, J., Rolf, M., Ruzicka, D. R., Wafula, E., Wickett, N. J., Wu, X., Zhang, Y., Wang, J., Zhang, Y., Carpenter, E. J., Deyholos, M. K., Kutchan, T. M., Chanderbali, A. S., Soltis, P. S., ... Depamphilis, C. W. (2012). A genome triplication associated with early diversification of the core eudicots. Genome Biology, 13(1), R3. https://doi.org/10.1186/gb-2012-13-1-r3
Jiao Y, et al. A Genome Triplication Associated With Early Diversification of the Core Eudicots. Genome Biol. 2012 Jan 26;13(1):R3. PubMed PMID: 22280555.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - A genome triplication associated with early diversification of the core eudicots. AU - Jiao,Yuannian, AU - Leebens-Mack,Jim, AU - Ayyampalayam,Saravanaraj, AU - Bowers,John E, AU - McKain,Michael R, AU - McNeal,Joel, AU - Rolf,Megan, AU - Ruzicka,Daniel R, AU - Wafula,Eric, AU - Wickett,Norman J, AU - Wu,Xiaolei, AU - Zhang,Yong, AU - Wang,Jun, AU - Zhang,Yeting, AU - Carpenter,Eric J, AU - Deyholos,Michael K, AU - Kutchan,Toni M, AU - Chanderbali,Andre S, AU - Soltis,Pamela S, AU - Stevenson,Dennis W, AU - McCombie,Richard, AU - Pires,J Chris, AU - Wong,Gane Ka-Shu, AU - Soltis,Douglas E, AU - Depamphilis,Claude W, Y1 - 2012/01/26/ PY - 2011/11/03/received PY - 2012/01/26/accepted PY - 2012/1/28/entrez PY - 2012/1/28/pubmed PY - 2013/1/1/medline SP - R3 EP - R3 JF - Genome biology JO - Genome Biol. VL - 13 IS - 1 N2 - BACKGROUND: Although it is agreed that a major polyploidy event, gamma, occurred within the eudicots, the phylogenetic placement of the event remains unclear. RESULTS: To determine when this polyploidization occurred relative to speciation events in angiosperm history, we employed a phylogenomic approach to investigate the timing of gene set duplications located on syntenic gamma blocks. We populated 769 putative gene families with large sets of homologs obtained from public transcriptomes of basal angiosperms, magnoliids, asterids, and more than 91.8 gigabases of new next-generation transcriptome sequences of non-grass monocots and basal eudicots. The overwhelming majority (95%) of well-resolved gamma duplications was placed before the separation of rosids and asterids and after the split of monocots and eudicots, providing strong evidence that the gamma polyploidy event occurred early in eudicot evolution. Further, the majority of gene duplications was placed after the divergence of the Ranunculales and core eudicots, indicating that the gamma appears to be restricted to core eudicots. Molecular dating estimates indicate that the duplication events were intensely concentrated around 117 million years ago. CONCLUSIONS: The rapid radiation of core eudicot lineages that gave rise to nearly 75% of angiosperm species appears to have occurred coincidentally or shortly following the gamma triplication event. Reconciliation of gene trees with a species phylogeny can elucidate the timing of major events in genome evolution, even when genome sequences are only available for a subset of species represented in the gene trees. Comprehensive transcriptome datasets are valuable complements to genome sequences for high-resolution phylogenomic analysis. SN - 1474-760X UR - https://www.unboundmedicine.com/medline/citation/22280555/A_genome_triplication_associated_with_early_diversification_of_the_core_eudicots_ L2 - https://genomebiology.biomedcentral.com/articles/10.1186/gb-2012-13-1-r3 DB - PRIME DP - Unbound Medicine ER -