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Phylogeny and multiple independent whole-genome duplication events in the Brassicales.
Am J Bot. 2020 08; 107(8):1148-1164.AJ

Abstract

PREMISE

Whole-genome duplications (WGDs) are prevalent throughout the evolutionary history of plants. For example, dozens of WGDs have been phylogenetically localized across the order Brassicales, specifically, within the family Brassicaceae. A WGD event has also been identified in the Cleomaceae, the sister family to Brassicaceae, yet its placement, as well as that of WGDs in other families in the order, remains unclear.

METHODS

Phylo-transcriptomic data were generated and used to infer a nuclear phylogeny for 74 Brassicales taxa. Genome survey sequencing was also performed on 66 of those taxa to infer a chloroplast phylogeny. These phylogenies were used to assess and confirm relationships among the major families of the Brassicales and within Brassicaceae. Multiple WGD inference methods were then used to assess the placement of WGDs on the nuclear phylogeny.

RESULTS

Well-supported chloroplast and nuclear phylogenies for the Brassicales and the putative placement of the Cleomaceae-specific WGD event Th-ɑ are presented. This work also provides evidence for previously hypothesized WGDs, including a well-supported event shared by at least two members of the Resedaceae family, and a possible event within the Capparaceae.

CONCLUSIONS

Phylogenetics and the placement of WGDs within highly polyploid lineages continues to be a major challenge. This study adds to the conversation on WGD inference difficulties by demonstrating that sampling is especially important for WGD identification and phylogenetic placement. Given its economic importance and genomic resources, the Brassicales continues to be an ideal group for assessing WGD inference methods.

Authors+Show Affiliations

Division of Biological Sciences and Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, Missouri, 65211, USA.Division of Biological Sciences and Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, Missouri, 65211, USA.Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona, 85719, USA.Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona, 85719, USA.Division of Biological Sciences and Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, Missouri, 65211, USA.Informatics Research Core Facility and Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, Missouri, 65211, USA.Department of Horticulture, Michigan State University, East Lansing, Michigan, 48824, USA.Plant Genetics Research Unit, USDA-ARS, Columbia, Missouri, 65211, USA.Division of Biological Sciences and Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, Missouri, 65211, USA.Department of Biological Sciences, University of Alberta, Edmonton, T6G 2E9, Canada.Department of Biological Sciences, The University of Alabama, Tuscaloosa, Alabama, 35401, USA.Missouri Botanical Garden, St. Louis, Missouri, 63110, USA.Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona, 85719, USA.Wageningen University and Research, Wageningen, The Netherlands.Bioinformatics Research Center, Program in Genetics and Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina, 27695, USA.Division of Biological Sciences and Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, Missouri, 65211, USA.

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

32830865

Citation

Mabry, Makenzie E., et al. "Phylogeny and Multiple Independent Whole-genome Duplication Events in the Brassicales." American Journal of Botany, vol. 107, no. 8, 2020, pp. 1148-1164.
Mabry ME, Brose JM, Blischak PD, et al. Phylogeny and multiple independent whole-genome duplication events in the Brassicales. Am J Bot. 2020;107(8):1148-1164.
Mabry, M. E., Brose, J. M., Blischak, P. D., Sutherland, B., Dismukes, W. T., Bottoms, C. A., Edger, P. P., Washburn, J. D., An, H., Hall, J. C., McKain, M. R., Al-Shehbaz, I., Barker, M. S., Schranz, M. E., Conant, G. C., & Pires, J. C. (2020). Phylogeny and multiple independent whole-genome duplication events in the Brassicales. American Journal of Botany, 107(8), 1148-1164. https://doi.org/10.1002/ajb2.1514
Mabry ME, et al. Phylogeny and Multiple Independent Whole-genome Duplication Events in the Brassicales. Am J Bot. 2020;107(8):1148-1164. PubMed PMID: 32830865.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Phylogeny and multiple independent whole-genome duplication events in the Brassicales. AU - Mabry,Makenzie E, AU - Brose,Julia M, AU - Blischak,Paul D, AU - Sutherland,Brittany, AU - Dismukes,Wade T, AU - Bottoms,Christopher A, AU - Edger,Patrick P, AU - Washburn,Jacob D, AU - An,Hong, AU - Hall,Jocelyn C, AU - McKain,Michael R, AU - Al-Shehbaz,Ihsan, AU - Barker,Michael S, AU - Schranz,M Eric, AU - Conant,Gavin C, AU - Pires,J Chris, Y1 - 2020/08/24/ PY - 2019/12/10/received PY - 2020/05/05/accepted PY - 2020/8/25/pubmed PY - 2020/10/6/medline PY - 2020/8/25/entrez KW - Brassicales KW - Capparaceae KW - Cleomaceae KW - Resedaceae KW - phylo-transcriptomics KW - phylogeny KW - whole-genome duplication SP - 1148 EP - 1164 JF - American journal of botany JO - Am J Bot VL - 107 IS - 8 N2 - PREMISE: Whole-genome duplications (WGDs) are prevalent throughout the evolutionary history of plants. For example, dozens of WGDs have been phylogenetically localized across the order Brassicales, specifically, within the family Brassicaceae. A WGD event has also been identified in the Cleomaceae, the sister family to Brassicaceae, yet its placement, as well as that of WGDs in other families in the order, remains unclear. METHODS: Phylo-transcriptomic data were generated and used to infer a nuclear phylogeny for 74 Brassicales taxa. Genome survey sequencing was also performed on 66 of those taxa to infer a chloroplast phylogeny. These phylogenies were used to assess and confirm relationships among the major families of the Brassicales and within Brassicaceae. Multiple WGD inference methods were then used to assess the placement of WGDs on the nuclear phylogeny. RESULTS: Well-supported chloroplast and nuclear phylogenies for the Brassicales and the putative placement of the Cleomaceae-specific WGD event Th-ɑ are presented. This work also provides evidence for previously hypothesized WGDs, including a well-supported event shared by at least two members of the Resedaceae family, and a possible event within the Capparaceae. CONCLUSIONS: Phylogenetics and the placement of WGDs within highly polyploid lineages continues to be a major challenge. This study adds to the conversation on WGD inference difficulties by demonstrating that sampling is especially important for WGD identification and phylogenetic placement. Given its economic importance and genomic resources, the Brassicales continues to be an ideal group for assessing WGD inference methods. SN - 1537-2197 UR - https://www.unboundmedicine.com/medline/citation/32830865/Phylogeny_and_multiple_independent_whole_genome_duplication_events_in_the_Brassicales_ L2 - https://doi.org/10.1002/ajb2.1514 DB - PRIME DP - Unbound Medicine ER -