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Yang J, Xue H, Li Z, Zhang Y, Shi T, He X, Barrett SCH, Wang Q, Chen J. Haplotype-resolved genome assembly provides insights into the evolution of S-locus supergene in distylous Nymphoides indica. THE NEW PHYTOLOGIST 2023; 240:2058-2071. [PMID: 37717220 DOI: 10.1111/nph.19264] [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: 03/07/2023] [Accepted: 08/30/2023] [Indexed: 09/19/2023]
Abstract
Distyly has evolved independently in numerous animal-pollinated angiosperm lineages. Understanding of its molecular basis has been restricted to a few species, primarily Primula. Here, we investigate the genetic architecture of the single diallelic locus (S-locus) supergene, a linkage group of functionally associated genes, and explore how it may have evolved in distylous Nymphoides indica, a lineage of flowering plants not previously investigated. We assembled haplotype-resolved genomes, used read-coverage-based genome-wide association study (rb-GWAS) to locate the S-locus supergene, co-expression network analysis to explore gene networks underpinning the development of distyly, and comparative genomic analyses to investigate the origins of the S-locus supergene. We identified three linked candidate S-locus genes - NinBAS1, NinKHZ2, and NinS1 - that were only evident in the short-styled morph and were hemizygous. Co-expression network analysis suggested that brassinosteroids contribute to dimorphic sex organs in the short-styled morph. Comparative genomic analyses indicated that the S-locus supergene likely evolved via stepwise duplications and has been affected by transposable element activities. Our study provides novel insight into the structure, regulation, and evolution of the supergene governing distyly in N. indica. It also provides high-quality genomic resources for future research on the molecular mechanisms underlying the striking evolutionary convergence in form and function across heterostylous taxa.
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Affiliation(s)
- Jingshan Yang
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, 430074, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Haoran Xue
- Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcocks St, Toronto, ON, M5S 3B2, Canada
- Institute for Biochemistry and Biology, University of Potsdam, 14476, Potsdam-Golm, Germany
| | - Zhizhong Li
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, 430074, China
| | - Yue Zhang
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, 430074, China
| | - Tao Shi
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, 430074, China
| | - Xiangyan He
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, 430074, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Spencer C H Barrett
- Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcocks St, Toronto, ON, M5S 3B2, Canada
| | - Qingfeng Wang
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, 430074, China
| | - Jinming Chen
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, 430074, China
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Luo Z, Zhao Z, Xu Y, Shi M, Tu T, Pei N, Zhang D. Comprehensive transcriptomic profiling reveals complex molecular mechanisms in the regulation of style-length dimorphism in Guettarda speciosa (Rubiaceae), a species with "anomalous" distyly. FRONTIERS IN PLANT SCIENCE 2023; 14:1116078. [PMID: 37008460 PMCID: PMC10060554 DOI: 10.3389/fpls.2023.1116078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 02/16/2023] [Indexed: 06/19/2023]
Abstract
BACKGROUND The evolution of heterostyly, a genetically controlled floral polymorphism, has been a hotspot of research since the 19th century. In recent years, studies on the molecular mechanism of distyly (the most common form of heterostyly) revealed an evolutionary convergence in genes for brassinosteroids (BR) degradation in different angiosperm groups. This floral polymorphism often exhibits considerable variability that some taxa have significant stylar dimorphism, but anther height differs less. This phenomenon has been termed "anomalous" distyly, which is usually regarded as a transitional stage in evolution. Compared to "typical" distyly, the genetic regulation of "anomalous" distyly is almost unknown, leaving a big gap in our understanding of this special floral adaptation strategy. METHODS Here we performed the first molecular-level study focusing on this floral polymorphism in Guettarda speciosa (Rubiaceae), a tropical tree with "anomalous" distyly. Comprehensive transcriptomic profiling was conducted to examine which genes and metabolic pathways were involved in the genetic control of style dimorphism and if they exhibit similar convergence with "typical" distylous species. RESULTS "Brassinosteroid homeostasis" and "plant hormone signal transduction" was the most significantly enriched GO term and KEGG pathway in the comparisons between L- and S-morph styles, respectively. Interestingly, homologs of all the reported S-locus genes either showed very similar expressions between L- and S-morph styles or no hits were found in G. speciosa. BKI1, a negative regulator of brassinosteroid signaling directly repressing BRI1 signal transduction, was identified as a potential gene regulating style length, which significantly up-regulated in the styles of S-morph. DISCUSSION These findings supported the hypothesis that style length in G. speciosa was regulated through a BR-related signaling network in which BKI1 may be one key gene. Our data suggested, in species with "anomalous" distyly, style length was regulated by gene differential expressions, instead of the "hemizygous" S-locus genes in "typical" distylous flowers such as Primula and Gelsemium, representing an "intermediate" stage in the evolution of distyly. Genome-level analysis and functional studies in more species with "typical" and "anomalous" distyly would further decipher this "most complex marriage arrangement" in angiosperms and improve our knowledge of floral evolution.
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Affiliation(s)
- Zhonglai Luo
- School of Life Sciences and Medicine, Shandong University of Technology, Zibo, China
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Zhongtao Zhao
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Yuanqing Xu
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Miaomiao Shi
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Tieyao Tu
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Nancai Pei
- Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou, China
| | - Dianxiang Zhang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
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Henning PM, Shore JS, McCubbin AG. The S-Gene YUC6 Pleiotropically Determines Male Mating Type and Pollen Size in Heterostylous Turnera (Passifloraceae): A Novel Neofunctionalization of the YUCCA Gene Family. PLANTS (BASEL, SWITZERLAND) 2022; 11:2640. [PMID: 36235506 PMCID: PMC9572539 DOI: 10.3390/plants11192640] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 09/27/2022] [Accepted: 10/05/2022] [Indexed: 06/16/2023]
Abstract
In heterostylous, self-incompatible Turnera species, a member of the YUCCA gene family, YUC6, resides at the S-locus and has been hypothesized to determine the male mating type. YUCCA gene family members synthesize the auxin, indole-3-acetic acid, via a two-step process involving the TAA gene family. Consequently, it has been speculated that differences in auxin concentration in developing anthers are the biochemical basis underlying the male mating type. Here, we provide empirical evidence that supports this hypothesis. Using a transgenic knockdown approach, we show that YUC6 acts pleiotropically to control both the male physiological mating type and pollen size, but not the filament length dimorphism associated with heterostyly in Turnera. Using qPCR to assess YUC6 expression in different transgenic lines, we demonstrate that the level of YUC6 knockdown correlates with the degree of change observed in the male mating type. Further assessment of YUC6 expression through anther development, in the knockdown lines, suggests that the male mating type is irreversibly determined during a specific developmental window prior to microsporogenesis, which is consistent with the genetically sporophytic nature of this self-incompatibility system. These results represent the first gene controlling male mating type to be characterized in any species with heterostyly.
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Affiliation(s)
- Paige M. Henning
- School of Biological Sciences, Washington State University, Pullman, WA 99164-4236, USA
| | - Joel S. Shore
- Department of Biology, York University, Toronto, ON M3J 1P3, Canada
| | - Andrew G. McCubbin
- School of Biological Sciences, Washington State University, Pullman, WA 99164-4236, USA
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Takeshima R, Nishio T, Komatsu S, Kurauchi N, Matsui K. Identification of a gene encoding polygalacturonase expressed specifically in short styles in distylous common buckwheat (Fagopyrum esculentum). Heredity (Edinb) 2019; 123:492-502. [PMID: 31076649 PMCID: PMC6781162 DOI: 10.1038/s41437-019-0227-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 04/11/2019] [Indexed: 11/09/2022] Open
Abstract
Common buckwheat (Fagopyrum esculentum) is a heteromorphic self-incompatible (SI) species with two types of floral architecture: thrum (short style) and pin (long style). The floral morphology and intra-morph incompatibility are controlled by a single genetic locus, S. However, the molecular mechanisms underlying the heteromorphic self-incompatibility of common buckwheat remain unclear. To identify these mechanisms, we performed proteomic, quantitative reverse-transcription PCR, and linkage analyses. Comparison of protein profiles between the long and short styles revealed a protein unique to the short style. Amino-acid sequencing revealed that it was a truncated form of polygalacturonase (PG); we designated the gene encoding this protein FePG1. Phylogenetic analysis classified FePG1 into the same clade as PGs that function in pollen development and floral morphology. FePG1 expression was significantly higher in short styles than in long styles. It was expressed in flowers of a short-homostyle line but not in flowers of a long-homostyle line. Linkage analysis indicated that FePG1 was not linked to the S locus; it could be a factor downstream of this locus. Our finding of a gene putatively working under the regulation of the S locus provides useful information for elucidation of the mechanism of heteromorphic self-incompatibility.
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Affiliation(s)
- Ryoma Takeshima
- Institute of Crop Science, National Agriculture and Food Research Organization (NARO), Kannondai 2-1-2, Tsukuba, Ibaraki, 305-8518, Japan
| | | | - Setsuko Komatsu
- Institute of Crop Science, National Agriculture and Food Research Organization (NARO), Kannondai 2-1-2, Tsukuba, Ibaraki, 305-8518, Japan
- Department of Environmental and Food Sciences, Fukui University of Technology, Gakuen 3-6-1, Fukui, 910-8505, Japan
| | - Nobuyuki Kurauchi
- College of Bioresource Sciences, Nihon University, 1866, Kameino, Fujisawa, Kanagawa, 252-0880, Japan
| | - Katsuhiro Matsui
- Institute of Crop Science, National Agriculture and Food Research Organization (NARO), Kannondai 2-1-2, Tsukuba, Ibaraki, 305-8518, Japan.
- Graduate School of Life and Environmental Science, University of Tsukuba, Kannondai 2-1-2, Tsukuba, Ibaraki, 305-8518, Japan.
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Global transcriptome and gene co-expression network analyses on the development of distyly in Primula oreodoxa. Heredity (Edinb) 2019; 123:784-794. [PMID: 31308492 DOI: 10.1038/s41437-019-0250-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 06/27/2019] [Accepted: 06/27/2019] [Indexed: 12/14/2022] Open
Abstract
Distyly is a genetically controlled flower polymorphism that has intrigued both botanists and evolutionary biologists ever since Darwin's time. Despite extensive reports on the pollination and evolution of distylous systems, the genetic basis and mechanism of molecular regulation remain unclear. In the present study, comparative transcriptome profiling was conducted in primrose (Primula oreodoxa), the prime research model for heterostyly. Thirty-six transcriptomes were sequenced for styles at different stages and corolla tube in the three morphs of P. oreodoxa. Large numbers of differentially expressed genes (DEGs) were detected in the transcriptomes of styles across different morphs. Several transcription factors (TFs) and phytohormone metabolism-related genes were highlighted in S-morphs. A growing number of genes showed differential expression patterns along with the development of styles, suggesting that the genetic control of distyly may be more complicated than ever expected. Analysis of co-expression networks and module-trait relationships identified modules significantly associated with style development. CYP734A50, a key S-locus gene whose products degrade brassinosteroids, was co-expressed with many genes in the module and showed significant negative association with style length. In addition, crucial TFs involved in phytohormone signaling pathways were found to be connected with CYP734A50 in the co-expression module. Our global transcriptomic analysis has identified DEGs that are potentially involved in regulation of style length in P. oreodoxa, and may shed light on the evolution and broad biological processes of heterostyly.
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