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Tribble CM, Alzate-Guarín F, Gándara E, Vartoumian A, Burleigh JG, Zenil-Ferguson R, Specht CD, Rothfels CJ. The rapid radiation of Bomarea (Alstroemeriaceae: Liliales), driven by the rise of the Andes. Evolution 2024; 78:221-236. [PMID: 37831628 DOI: 10.1093/evolut/qpad184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 09/09/2023] [Accepted: 10/03/2023] [Indexed: 10/15/2023]
Abstract
Geological events such as mountain uplift affect how, when, and where species diversify, but measuring those effects is a longstanding challenge. Andean orogeny impacted the evolution of regional biota by creating barriers to gene flow, opening new habitats, and changing local climate. Bomarea (Alstroemeriaceae) are tropical plants with (often) small, isolated ranges; in total, Bomarea species occur from central Mexico to central Chile. This genus appears to have evolved rapidly and quite recently, and rapid radiations are often challenging to resolve with traditional phylogenetic inference. In this study, we apply phylogenomics-with hundreds of loci, gene-tree-based data curation, and a multispecies-coalescent approach-to infer the phylogeny of Bomarea. We use this phylogeny to untangle the potential drivers of diversification and biogeographic history. In particular, we test if Andean orogeny contributed to the diversification of Bomarea. We find that Bomarea originated in the central Andes during the mid-Miocene, then spread north, following the trajectory of mountain uplift. Furthermore, Andean lineages diversified faster than non-Andean relatives. Bomarea thus demonstrates that-at least in some cases-geological change rather than environmental stability has driven high species diversity in a tropical biodiversity hotspot. These results also demonstrate the utility (and danger) of genome-scale data for making macroevolutionary inferences.
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Affiliation(s)
- Carrie M Tribble
- School of Life Sciences, University of Hawai'i at Mānoa, Honolulu, HI, United States
- Department of Integrative Biology and University Herbarium, University of California, Berkeley, Berkeley, CA, United States
| | - Fernando Alzate-Guarín
- Grupo de Estudios Botánicos (GEOBOTA) and Herbario Universidad de Antioquia (HUA), Instituto de Biología, Facultad de Ciencias Exactas y Naturales, Universidad de Antioquia, Medellín, Colombia
| | - Etelvina Gándara
- Facultad de Ciencias Biológicas, Benemérita Universidad Autónoma de Puebla, Puebla, Puebla, Mexico
| | - Araz Vartoumian
- School of Life Sciences, University of Hawai'i at Mānoa, Honolulu, HI, United States
- Department of Oral Biology, University of California, Los Angeles, Los Angeles, CA, United States
| | | | | | - Chelsea D Specht
- Section of Plant Biology and the L.H. Bailey Hortorium, School of Integrative Plant Science, Cornell University, Ithaca, NY, United States
| | - Carl J Rothfels
- Department of Integrative Biology and University Herbarium, University of California, Berkeley, Berkeley, CA, United States
- Intermountain Herbarium, Department of Biology, and Ecology Center, Utah State University, Logan, UT, United States
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Tsuchida CA, Zhang S, Doost MS, Zhao Y, Wang J, O'Brien E, Fang H, Li CP, Li D, Hai ZY, Chuck J, Brötzmann J, Vartoumian A, Burstein D, Chen XW, Nogales E, Doudna JA, Liu JJG. Chimeric CRISPR-CasX enzymes and guide RNAs for improved genome editing activity. Mol Cell 2022; 82:1199-1209.e6. [PMID: 35219382 PMCID: PMC9189900 DOI: 10.1016/j.molcel.2022.02.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 12/25/2021] [Accepted: 01/28/2022] [Indexed: 12/14/2022]
Abstract
A compact protein with a size of <1,000 amino acids, the CRISPR-associated protein CasX is a fundamentally distinct RNA-guided nuclease when compared to Cas9 and Cas12a. Although it can induce RNA-guided genome editing in mammalian cells, the activity of CasX is less robust than that of the widely used S. pyogenes Cas9. Here, we show that structural features of two CasX homologs and their guide RNAs affect the R-loop complex assembly and DNA cleavage activity. Cryo-EM-based structural engineering of either the CasX protein or the guide RNA produced two new CasX genome editors (DpbCasX-R3-v2 and PlmCasX-R1-v2) with significantly improved DNA manipulation efficacy. These results advance both the mechanistic understanding of CasX and its application as a genome-editing tool.
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Affiliation(s)
- Connor A Tsuchida
- University of California, Berkeley-University of California, San Francisco Graduate Program in Bioengineering, University of California, Berkeley, California 94720, USA; Innovative Genomics Institute, University of California, Berkeley, California 94720, USA
| | - Shouyue Zhang
- Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Mohammad Saffari Doost
- Innovative Genomics Institute, University of California, Berkeley, California 94720, USA; California Institute for Quantitative Biosciences, University of California, Berkeley, California 94720, USA
| | - Yuqian Zhao
- Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Jia Wang
- Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Elizabeth O'Brien
- Innovative Genomics Institute, University of California, Berkeley, California 94720, USA; California Institute for Quantitative Biosciences, University of California, Berkeley, California 94720, USA
| | - Huan Fang
- Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing 100871, China
| | - Cheng-Ping Li
- Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Danyuan Li
- Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Zhuo-Yan Hai
- Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Jonathan Chuck
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, Jupiter, Florida 33458, USA
| | - Julian Brötzmann
- Department of Structural Cell Biology, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Araz Vartoumian
- Innovative Genomics Institute, University of California, Berkeley, California 94720, USA; California Institute for Quantitative Biosciences, University of California, Berkeley, California 94720, USA
| | - David Burstein
- School of Molecular Cell Biology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Xiao-Wei Chen
- Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing 100871, China
| | - Eva Nogales
- California Institute for Quantitative Biosciences, University of California, Berkeley, California 94720, USA; Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, USA; Molecular Biophysics & Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA; Howard Hughes Medical Institute, University of California, Berkeley, California 94720, USA
| | - Jennifer A Doudna
- University of California, Berkeley-University of California, San Francisco Graduate Program in Bioengineering, University of California, Berkeley, California 94720, USA; Innovative Genomics Institute, University of California, Berkeley, California 94720, USA; California Institute for Quantitative Biosciences, University of California, Berkeley, California 94720, USA; Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, USA; Molecular Biophysics & Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA; Howard Hughes Medical Institute, University of California, Berkeley, California 94720, USA; Department of Chemistry, University of California, Berkeley, California 94720, USA; Gladstone Institute of Data Science and Biotechnology. Gladstone Institutes, San Francisco, California 94158, USA.
| | - Jun-Jie Gogo Liu
- Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China.
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