1
|
Chomicki G, Burin G, Busta L, Gozdzik J, Jetter R, Mortimer B, Bauer U. Convergence in carnivorous pitcher plants reveals a mechanism for composite trait evolution. Science 2024; 383:108-113. [PMID: 38175904 DOI: 10.1126/science.ade0529] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 11/07/2023] [Indexed: 01/06/2024]
Abstract
Composite traits involve multiple components that, only when combined, gain a new synergistic function. Thus, how they evolve remains a puzzle. We combined field experiments, microscopy, chemical analyses, and laser Doppler vibrometry with comparative phylogenetic analyses to show that two carnivorous Nepenthes pitcher plant species independently evolved similar adaptations in three distinct traits to acquire a new, composite trapping mechanism. Comparative analyses suggest that this new trait arose convergently through "spontaneous coincidence" of the required trait combination, rather than directional selection in the component traits. Our results indicate a plausible mechanism for composite trait evolution and highlight the importance of stochastic phenotypic variation as a facilitator of evolutionary novelty.
Collapse
Affiliation(s)
- Guillaume Chomicki
- Department of Bioscience, Durham University, South Road, Durham DH1 3LE, UK
| | - Gustavo Burin
- Natural History Museum London, Cromwell Road, London SW7 5BD, UK
| | - Lucas Busta
- Department of Chemistry and Biochemistry, University of Minnesota Duluth, 308 HCAMS, 1038 University Drive, Duluth, MN 55812, USA
| | - Jedrzej Gozdzik
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC V6T 1Z1, Canada
| | - Reinhard Jetter
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC V6T 1Z1, Canada
- Department of Botany, University of British Columbia, 3200-6270 University Boulevard, Vancouver, BC V6T 1Z4, Canada
| | - Beth Mortimer
- Department of Biology, University of Oxford, Mansfield Road, Oxford OX1 3SZ, UK
| | - Ulrike Bauer
- School of Biological Sciences, University of Bristol, 24 Tyndall Avenue, Bristol BS8 1TQ, UK
| |
Collapse
|
2
|
Li Y, Li X, Nie S, Zhang M, Yang Q, Xu W, Duan Y, Wang X. Reticulate evolution of the tertiary relict Osmanthus. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 117:145-160. [PMID: 37837261 DOI: 10.1111/tpj.16480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 09/10/2023] [Accepted: 09/13/2023] [Indexed: 10/15/2023]
Abstract
When interspecific gene flow is common, species relationships are more accurately represented by a phylogenetic network than by a bifurcating tree. This study aimed to uncover the role of introgression in the evolution of Osmanthus, the only genus of the subtribe Oleinae (Oleaceae) with its distribution center in East Asia. We built species trees, detected introgression, and constructed networks using multiple kinds of sequencing data (whole genome resequencing, transcriptome sequencing, and Sanger sequencing of nrDNA) combined with concatenation and coalescence approaches. Then, based on well-understood species relationships, historical biogeographic analyses and diversification rate estimates were employed to reveal the history of Osmanthus. Osmanthus originated in mid-Miocene Europe and dispersed to the eastern Tibetan Plateau in the late Miocene. Thereafter, it continued to spread eastwards. Phylogenetic conflict is common within the 'Core Osmanthus' clade and is seen at both early and late stages of diversification, leading to hypotheses of net-like species relationships. Incomplete lineage sorting proved ineffective in explaining phylogenetic conflicts and thus supported introgression as the main cause of conflicts. This study elucidates the diversification history of a relict genus in the subtropical regions of eastern Asia and reveals that introgression had profound effects on its evolutionary history.
Collapse
Affiliation(s)
- Yongfu Li
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Life Sciences, International Cultivar Registration Center for Osmanthus, Nanjing Forestry University, Nanjing, 210037, Jiangsu, China
| | - Xuan Li
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Life Sciences, International Cultivar Registration Center for Osmanthus, Nanjing Forestry University, Nanjing, 210037, Jiangsu, China
| | - Shuai Nie
- Rice Research Institute, Guangdong Academy of Agricultural Sciences & Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs & Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, Guangdong, China
| | - Min Zhang
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Life Sciences, International Cultivar Registration Center for Osmanthus, Nanjing Forestry University, Nanjing, 210037, Jiangsu, China
| | - Qinghua Yang
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Life Sciences, International Cultivar Registration Center for Osmanthus, Nanjing Forestry University, Nanjing, 210037, Jiangsu, China
| | - Wenbin Xu
- Wuhan Botanical Garden, the Chinese Academy of Sciences, Wuhan, 430074, Hubei, China
| | - Yifan Duan
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Life Sciences, International Cultivar Registration Center for Osmanthus, Nanjing Forestry University, Nanjing, 210037, Jiangsu, China
| | - Xianrong Wang
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Life Sciences, International Cultivar Registration Center for Osmanthus, Nanjing Forestry University, Nanjing, 210037, Jiangsu, China
| |
Collapse
|
3
|
Saul F, Scharmann M, Wakatake T, Rajaraman S, Marques A, Freund M, Bringmann G, Channon L, Becker D, Carroll E, Low YW, Lindqvist C, Gilbert KJ, Renner T, Masuda S, Richter M, Vogg G, Shirasu K, Michael TP, Hedrich R, Albert VA, Fukushima K. Subgenome dominance shapes novel gene evolution in the decaploid pitcher plant Nepenthes gracilis. NATURE PLANTS 2023; 9:2000-2015. [PMID: 37996654 DOI: 10.1038/s41477-023-01562-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 10/09/2023] [Indexed: 11/25/2023]
Abstract
Subgenome dominance after whole-genome duplication generates distinction in gene number and expression at the level of chromosome sets, but it remains unclear how this process may be involved in evolutionary novelty. Here we generated a chromosome-scale genome assembly of the Asian pitcher plant Nepenthes gracilis to analyse how its novel traits (dioecy and carnivorous pitcher leaves) are linked to genomic evolution. We found a decaploid karyotype and a clear indication of subgenome dominance. A male-linked and pericentromerically located region on the putative sex chromosome was identified in a recessive subgenome and was found to harbour three transcription factors involved in flower and pollen development, including a likely neofunctionalized LEAFY duplicate. Transcriptomic and syntenic analyses of carnivory-related genes suggested that the paleopolyploidization events seeded genes that subsequently formed tandem clusters in recessive subgenomes with specific expression in the digestive zone of the pitcher, where specialized cells digest prey and absorb derived nutrients. A genome-scale analysis suggested that subgenome dominance likely contributed to evolutionary innovation by permitting recessive subgenomes to diversify functions of novel tissue-specific duplicates. Our results provide insight into how polyploidy can give rise to novel traits in divergent and successful high-ploidy lineages.
Collapse
Affiliation(s)
- Franziska Saul
- Institute for Molecular Plant Physiology and Biophysics, University of Würzburg, Würzburg, Germany
| | - Mathias Scharmann
- Institute for Biochemistry and Biology (IBB), University of Potsdam, Potsdam, Germany
| | - Takanori Wakatake
- Institute for Molecular Plant Physiology and Biophysics, University of Würzburg, Würzburg, Germany
| | - Sitaram Rajaraman
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - André Marques
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Matthias Freund
- Institute for Molecular Plant Physiology and Biophysics, University of Würzburg, Würzburg, Germany
| | - Gerhard Bringmann
- Institute of Organic Chemistry, University of Würzburg, Am Hubland, Würzburg, Germany
| | - Louisa Channon
- Institute for Molecular Plant Physiology and Biophysics, University of Würzburg, Würzburg, Germany
| | - Dirk Becker
- Institute for Molecular Plant Physiology and Biophysics, University of Würzburg, Würzburg, Germany
| | - Emily Carroll
- Department of Biological Sciences, University at Buffalo, Buffalo, NY, USA
| | - Yee Wen Low
- Singapore Botanic Gardens, National Parks Board, Singapore, Singapore
| | | | - Kadeem J Gilbert
- Department of Plant Biology & W.K. Kellogg Biological Station & Program in Ecology, Evolution, and Behavior, Michigan State University, Hickory Corners, MI, USA
| | - Tanya Renner
- Department of Entomology, The Pennsylvania State University, University Park, PA, USA
| | - Sachiko Masuda
- Riken Center for Sustainable Resource Science, Yokohama, Japan
| | - Michaela Richter
- Department of Biological Sciences, University at Buffalo, Buffalo, NY, USA
| | - Gerd Vogg
- Botanical Garden, University of Würzburg, Würzburg, Germany
| | - Ken Shirasu
- Riken Center for Sustainable Resource Science, Yokohama, Japan
| | - Todd P Michael
- Plant Molecular and Cellular Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Rainer Hedrich
- Institute for Molecular Plant Physiology and Biophysics, University of Würzburg, Würzburg, Germany
| | - Victor A Albert
- Department of Biological Sciences, University at Buffalo, Buffalo, NY, USA.
| | - Kenji Fukushima
- Institute for Molecular Plant Physiology and Biophysics, University of Würzburg, Würzburg, Germany.
| |
Collapse
|
4
|
Baharin A, Ting TY, Goh HH. Omics Approaches in Uncovering Molecular Evolution and Physiology of Botanical Carnivory. PLANTS (BASEL, SWITZERLAND) 2023; 12:408. [PMID: 36679121 PMCID: PMC9867145 DOI: 10.3390/plants12020408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 01/09/2023] [Accepted: 01/09/2023] [Indexed: 06/17/2023]
Abstract
Systems biology has been increasingly applied with multiple omics for a holistic comprehension of complex biological systems beyond the reductionist approach that focuses on individual molecules. Different high-throughput omics approaches, including genomics, transcriptomics, metagenomics, proteomics, and metabolomics have been implemented to study the molecular mechanisms of botanical carnivory. This covers almost all orders of carnivorous plants, namely Caryophyllales, Ericales, Lamiales, and Oxalidales, except Poales. Studies using single-omics or integrated multi-omics elucidate the compositional changes in nucleic acids, proteins, and metabolites. The omics studies on carnivorous plants have led to insights into the carnivory origin and evolution, such as prey capture and digestion as well as the physiological adaptations of trap organ formation. Our understandings of botanical carnivory are further enhanced by the discoveries of digestive enzymes and transporter proteins that aid in efficient nutrient sequestration alongside dynamic molecular responses to prey. Metagenomics studies revealed the mutualistic relationships between microbes and carnivorous plants. Lastly, in silico analysis accelerated the functional characterization of new molecules from carnivorous plants. These studies have provided invaluable molecular data for systems understanding of carnivorous plants. More studies are needed to cover the diverse species with convergent evolution of botanical carnivory.
Collapse
|