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Ma X, Nie Z, Huang H, Yan C, Li S, Hu Z, Wang Y, Yin H. Small RNA profiling reveals that an ovule-specific microRNA, cja-miR5179, targets a B-class MADS-box gene in Camellia japonica. ANNALS OF BOTANY 2023; 132:1007-1020. [PMID: 37831901 PMCID: PMC10808017 DOI: 10.1093/aob/mcad155] [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: 06/27/2023] [Accepted: 10/09/2023] [Indexed: 10/15/2023]
Abstract
BACKGROUND AND AIMS The functional specialization of microRNA and its target genes is often an important factor in the establishment of spatiotemporal patterns of gene expression that are essential to plant development and growth. In different plant lineages, understanding the functional conservation and divergence of microRNAs remains to be explored. METHODS To identify small regulatory RNAs underlying floral patterning, we performed a tissue-specific profiling of small RNAs in various floral organs from single and double flower varieties (flowers characterized by multiple layers of petals) in Camellia japonica. We identified cja-miR5179, which belongs to a deeply conserved microRNA family that is conserved between angiosperms and basal plants but frequently lost in eudicots. We characterized the molecular function of cja-miR5179 and its target - a B-function MADS-box gene - through gene expression analysis and transient expression assays. KEY RESULTS We showed that cja-miR5179 is exclusively expressed in ovule tissues at the early stage of floral development. We found that cja-miR5179 targets the coding sequences of a DEFICIENS-like B-class gene (CjDEF) mRNA, which is located in the K motif of the MADS-box domain; and the target sites of miR5179/MADS-box were consistent in Camellia and orchids. Furthermore, through a petal transient-expression assay, we showed that the BASIC PENTACYSTEINE proteins bind to the GA-rich motifs in the cja-miR5179 promoter region and suppresses its expression. CONCLUSIONS We propose that the regulation between miR5179 and a B-class MADS-box gene in C. japonica has a deep evolutionary origin before the separation of monocots and dicots. During floral development of C. japonica, cja-miR5179 is specifically expressed in the ovule, which may be required for the inhibition of CjDEF function. This work highlights the evolutionary conservation as well as functional divergence of small RNAs in floral development.
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Affiliation(s)
- Xianjin Ma
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, Zhejiang 311400, China
- College of Information Science and Technology, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
- Key Laboratory of Forest Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, Zhejiang 311400, China
| | - Ziyan Nie
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, Zhejiang 311400, China
- College of Information Science and Technology, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
- Key Laboratory of Forest Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, Zhejiang 311400, China
| | - Hu Huang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, Zhejiang 311400, China
- College of Information Science and Technology, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
- Key Laboratory of Forest Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, Zhejiang 311400, China
| | - Chao Yan
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, Zhejiang 311400, China
- Experimental Center for Subtropical Forestry, Chinese Academy of Forestry, Fenyi, Jiangxi 336600, China
| | - Sijia Li
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, Zhejiang 311400, China
- College of Information Science and Technology, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
- Key Laboratory of Forest Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, Zhejiang 311400, China
| | - Zhikang Hu
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, Zhejiang 311400, China
- College of Information Science and Technology, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
- Key Laboratory of Forest Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, Zhejiang 311400, China
| | - Yupeng Wang
- College of Information Science and Technology, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
- Key Laboratory of Forest Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, Zhejiang 311400, China
| | - Hengfu Yin
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, Zhejiang 311400, China
- Key Laboratory of Forest Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, Zhejiang 311400, China
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Tanaka Y, Yokota M, Goto N, Goto T, Yoshida Y, Yasuba KI, Ohno S, Doi M. Morphological and gene expression characterization of maf-1, a floral chili pepper mutant caused by a nonsense mutation in CaLFY. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2022; 42:32. [PMID: 37313508 PMCID: PMC10248606 DOI: 10.1007/s11032-022-01304-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 06/03/2022] [Indexed: 06/15/2023]
Abstract
Chili peppers are important as vegetables and ornamental crops, because of the variety of fruit shapes and colors. Understanding of flower and fruit development in Capsicum is limited compared with closely related Solanaceae crops such as tomato. This study reports a novel malformed fruit mutant named malformed fruit-1 (maf-1), which was isolated from an ethyl methanesulfonate-induced mutant population of chili pepper. maf-1 exhibited homeotic changes in the floral bud, which were characterized by conversion of petals and stamens into sepal-like and carpel-like organs, respectively. In addition, the indeterminate formation of carpel-like tissue was observed. Genetic analysis demonstrated that the causative gene in maf-1 is a nonsense mutation in CaLFY. This is the first characterization of an lfy mutant in Capsicum. Unlike tomatoes, the CaLFY mutation did not affect the architecture of sympodial unit or flowering time but mainly affected the formation of flower organs. Gene expression analysis suggested that a nonsense mutation in CaLFY led to decreased expression of multiple class B genes, resulting in homeotic changes in the flower and fruit. This maf-1 mutant may provide new insights at the molecular level in understanding flower organ formation and the genetic manipulation of fruit shape in chili peppers. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-022-01304-w.
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Affiliation(s)
- Yoshiyuki Tanaka
- Graduate School of Agriculture, Kyoto University, Kitashirakawa-oiwakecho Sakyo-ku, Kyoto, 606-8502 Japan
- Graduate School of Environmental and Life Science, Okayama University, Okayama, 700-8530 Japan
| | - Mizuki Yokota
- Graduate School of Agriculture, Kyoto University, Kitashirakawa-oiwakecho Sakyo-ku, Kyoto, 606-8502 Japan
| | - Naoto Goto
- Graduate School of Environmental and Life Science, Okayama University, Okayama, 700-8530 Japan
| | - Tanjuro Goto
- Graduate School of Environmental and Life Science, Okayama University, Okayama, 700-8530 Japan
| | - Yuichi Yoshida
- Graduate School of Environmental and Life Science, Okayama University, Okayama, 700-8530 Japan
| | - Ken-ichiro Yasuba
- Graduate School of Environmental and Life Science, Okayama University, Okayama, 700-8530 Japan
| | - Sho Ohno
- Graduate School of Agriculture, Kyoto University, Kitashirakawa-oiwakecho Sakyo-ku, Kyoto, 606-8502 Japan
| | - Motoaki Doi
- Graduate School of Agriculture, Kyoto University, Kitashirakawa-oiwakecho Sakyo-ku, Kyoto, 606-8502 Japan
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Qi X, An H, Hall TE, Di C, Blischak PD, McKibben MTW, Hao Y, Conant GC, Pires JC, Barker MS. Genes derived from ancient polyploidy have higher genetic diversity and are associated with domestication in Brassica rapa. THE NEW PHYTOLOGIST 2021; 230:372-386. [PMID: 33452818 DOI: 10.1111/nph.17194] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 11/30/2020] [Indexed: 06/12/2023]
Abstract
Many crops are polyploid or have a polyploid ancestry. Recent phylogenetic analyses have found that polyploidy often preceded the domestication of crop plants. One explanation for this observation is that increased genetic diversity following polyploidy may have been important during the strong artificial selection that occurs during domestication. In order to test the connection between domestication and polyploidy, we identified and examined candidate genes associated with the domestication of the diverse crop varieties of Brassica rapa. Like all 'diploid' flowering plants, B. rapa has a diploidized paleopolyploid genome and experienced many rounds of whole genome duplication (WGD). We analyzed transcriptome data of more than 100 cultivated B. rapa accessions. Using a combination of approaches, we identified > 3000 candidate genes associated with the domestication of four major B. rapa crop varieties. Consistent with our expectation, we found that the candidate genes were significantly enriched with genes derived from the Brassiceae mesohexaploidy. We also observed that paleologs were significantly more diverse than non-paleologs. Our analyses find evidence for that genetic diversity derived from ancient polyploidy played a key role in the domestication of B. rapa and provide support for its importance in the success of modern agriculture.
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Affiliation(s)
- Xinshuai Qi
- Department of Ecology & Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA
| | - Hong An
- Division of Biological Sciences, University of Missouri, Columbia, MO, 65211, USA
| | - Tara E Hall
- Department of Ecology & Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA
| | - Chenlu Di
- Department of Ecology & Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA
| | - Paul D Blischak
- Department of Ecology & Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA
| | - Michael T W McKibben
- Department of Ecology & Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA
| | - Yue Hao
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, 27695, USA
| | - Gavin C Conant
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, 27695, USA
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, 27695, USA
| | - J Chris Pires
- Division of Biological Sciences, University of Missouri, Columbia, MO, 65211, USA
| | - Michael S Barker
- Department of Ecology & Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA
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Gu X, Brennan A, Wei W, Guo G, Lindsey K. Vesicle Transport in Plants: A Revised Phylogeny of SNARE Proteins. Evol Bioinform Online 2020; 16:1176934320956575. [PMID: 33116351 PMCID: PMC7573729 DOI: 10.1177/1176934320956575] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 07/21/2020] [Indexed: 12/13/2022] Open
Abstract
Communication systems within and between plant cells involve the transfer of ions and molecules between compartments, and are essential for development and responses to biotic and abiotic stresses. This in turn requires the regulated movement and fusion of membrane systems with their associated cargo. Recent advances in genomics has provided new resources with which to investigate the evolutionary relationships between membrane proteins across plant species. Members of the soluble N-ethylmaleimide-sensitive factor attachment protein receptors (SNAREs) are known to play important roles in vesicle trafficking across plant, animal and microbial species. Using recent public expression and transcriptomic data from 9 representative green plants, we investigated the evolution of the SNARE classes and linked protein changes to functional specialization (expression patterns). We identified an additional 3 putative SNARE genes in the model plant Arabidopsis. We found that all SNARE classes have expanded in number to a greater or lesser degree alongside the evolution of multicellularity, and that within-species expansions are also common. These gene expansions appear to be associated with the accumulation of amino acid changes and with sub-functionalization of SNARE family members to different tissues. These results provide an insight into SNARE protein evolution and functional specialization. The work provides a platform for hypothesis-building and future research into the precise functions of these proteins in plant development and responses to the environment.
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Affiliation(s)
- Xiaoyan Gu
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, China
- Department of Biosciences, Durham University, Durham, UK
| | - Adrian Brennan
- Department of Biosciences, Durham University, Durham, UK
| | - Wenbin Wei
- Department of Biosciences, Durham University, Durham, UK
| | - Guangqin Guo
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Keith Lindsey
- Department of Biosciences, Durham University, Durham, UK
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Xia Y, Shi M, Chen W, Hu R, Jing D, Wu D, Wang S, Li Q, Deng H, Guo Q, Liang G. Expression Pattern and Functional Characterization of PISTILLATA Ortholog Associated With the Formation of Petaloid Sepals in Double-Flower Eriobotrya japonica (Rosaceae). FRONTIERS IN PLANT SCIENCE 2020; 10:1685. [PMID: 32010167 PMCID: PMC6978688 DOI: 10.3389/fpls.2019.01685] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Accepted: 11/29/2019] [Indexed: 06/10/2023]
Abstract
Double-flower Eriobotrya japonica, of which one phenotype is homeotic transformation of sepals into petals, is a new germplasm for revealing the molecular mechanisms underlying the floral organ transformation. Herein, we analyzed the sequence, expression pattern and functional characterization of EjPI, which encoded a B-class floral homeotic protein referred to as PISTILLATA ortholog, from genetically cognate single-flower and double-flower E. japonica. Phylogenetic analysis suggested that the EjPI gene was assigned to the rosids PI/GLO lineage. Analysis of protein sequence alignments showed that EjPI has typical domains of M, I, K, and C, and includes a distinctive PI motif at the C-terminal region. Compared with asterids PI/GLO lineage, the K1 and K3 subdomains of EjPI both contain a single amino acid difference. Subcellular localization of EjPI was determined to be in the nucleus. Expression pattern analysis revealed that EjPI expressed not only in petals, filament, and anther in single-flower E. japonica, but also in petaloid sepals in double-flower E. japonica. Meanwhile, there were high correlation between EjPI transcript level and petaloid area within a sepal. Furthermore, 35S::EjPI transgenic wild-type Arabidopsis caused the homeotic transformation of the first whorl sepals into petaloid sepals. Ectopic expression of EjPI in transgenic pi-1 mutant Arabidopsis rescued normal petals and stamens. These results suggest expression pattern of EjPI is associated with the formation of petaloid sepal. Our study provides the potential application of EjPI for biotechnical engineering to create petaloid sepals or regulate floral organ identity in angiosperms.
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Affiliation(s)
- Yan Xia
- Key Laboratory of Horticulture Science for Southern Mountains Regions of Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, Chongqing, China
- State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Academy of Agricultural Sciences of Southwest University, Chongqing, China
| | - Min Shi
- Key Laboratory of Horticulture Science for Southern Mountains Regions of Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, Chongqing, China
- State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Academy of Agricultural Sciences of Southwest University, Chongqing, China
| | - Weiwei Chen
- Key Laboratory of Horticulture Science for Southern Mountains Regions of Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, Chongqing, China
- State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Academy of Agricultural Sciences of Southwest University, Chongqing, China
| | - Ruoqian Hu
- State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Academy of Agricultural Sciences of Southwest University, Chongqing, China
| | - Danlong Jing
- Key Laboratory of Horticulture Science for Southern Mountains Regions of Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, Chongqing, China
- State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Academy of Agricultural Sciences of Southwest University, Chongqing, China
| | - Di Wu
- Key Laboratory of Horticulture Science for Southern Mountains Regions of Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, Chongqing, China
- State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Academy of Agricultural Sciences of Southwest University, Chongqing, China
| | - Shuming Wang
- Key Laboratory of Horticulture Science for Southern Mountains Regions of Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, Chongqing, China
- State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Academy of Agricultural Sciences of Southwest University, Chongqing, China
| | - Qingfen Li
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
| | - Honghong Deng
- Key Laboratory of Horticulture Science for Southern Mountains Regions of Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, Chongqing, China
- State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Academy of Agricultural Sciences of Southwest University, Chongqing, China
| | - Qigao Guo
- Key Laboratory of Horticulture Science for Southern Mountains Regions of Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, Chongqing, China
- State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Academy of Agricultural Sciences of Southwest University, Chongqing, China
| | - Guolu Liang
- Key Laboratory of Horticulture Science for Southern Mountains Regions of Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, Chongqing, China
- State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Academy of Agricultural Sciences of Southwest University, Chongqing, China
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Zhou K, Cao QX, Jin CM, Niu YY, Li GL, Zhang JJ. Identification of Two GLOBOSA-Like MADS-Box Genes in Tea Plant (Camellia sinensis [L.] O. Kuntze). Mol Biol 2019. [DOI: 10.1134/s0026893319010199] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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de Bruijn S, Zhao T, Muiño JM, Schranz EM, Angenent GC, Kaufmann K. PISTILLATA paralogs in Tarenaya hassleriana have diverged in interaction specificity. BMC PLANT BIOLOGY 2018; 18:368. [PMID: 30577806 PMCID: PMC6303913 DOI: 10.1186/s12870-018-1574-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Accepted: 11/26/2018] [Indexed: 06/09/2023]
Abstract
BACKGROUND Floral organs are specified by MADS-domain transcription factors that act in a combinatorial manner, as summarized in the (A)BCE model. However, this evolutionarily conserved model is in contrast to a remarkable amount of morphological diversity in flowers. One of the mechanisms suggested to contribute to this diversity is duplication of floral MADS-domain transcription factors. Although gene duplication is often followed by loss of one of the copies, sometimes both copies are retained. If both copies are retained they will initially be redundant, providing freedom for one of the paralogs to change function. Here, we examine the evolutionary fate and functional consequences of a transposition event at the base of the Brassicales that resulted in the duplication of the floral regulator PISTILLATA (PI), using Tarenaya hassleriana (Cleomaceae) as a model system. RESULTS The transposition of a genomic region containing a PI gene led to two paralogs which are located at different positions in the genome. The original PI copy is syntenic in position with most angiosperms, whereas the transposed copy is syntenic with the PI genes in Brassicaceae. The two PI paralogs of T. hassleriana have very similar expression patterns. However, they may have diverged in function, as only one of these PI proteins was able to act heterologously in the first whorl of A. thaliana flowers. We also observed differences in protein complex formation between the two paralogs, and the two paralogs exhibit subtle differences in DNA-binding specificity. Sequence analysis indicates that most of the protein sequence divergence between the two T. hassleriana paralogs emerged in a common ancestor of the Cleomaceae and the Brassicaceae. CONCLUSIONS We found that the PI paralogs in T. hassleriana have similar expression patterns, but may have diverged at the level of protein function. Data suggest that most protein sequence divergence occurred rapidly, prior to the origin of the Brassicaceae and Cleomaceae. It is tempting to speculate that the interaction specificities of the Brassicaceae-specific PI proteins are different compared to the PI found in other angiosperms. This could lead to PI regulating partly different genes in the Brassicaceae, and ultimately might result in change floral in morphology.
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Affiliation(s)
- Suzanne de Bruijn
- Laboratory of Molecular Biology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
- Bioscience, Wageningen Plant Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Tao Zhao
- Biosystematics Group, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Jose M. Muiño
- Institute for Biology, Systems Biology of Gene Regulation, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Eric M. Schranz
- Biosystematics Group, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Gerco C. Angenent
- Laboratory of Molecular Biology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
- Bioscience, Wageningen Plant Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Kerstin Kaufmann
- Institute for Biology, Plant Cell and Molecular Biology, Humboldt-Universität zu Berlin, Philippstraße 13, 10115 Berlin, Germany
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Block PD, Rakotonasolo F, Ntore S, Sylvain G. Razafimandimbison, Janssens S. Four new endemic genera of Rubiaceae (Pavetteae) from Madagascar represent multiple radiations into drylands. PHYTOKEYS 2018; 99:1-66. [PMID: 29861651 PMCID: PMC5972148 DOI: 10.3897/phytokeys.99.23713] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Accepted: 04/24/2018] [Indexed: 10/29/2023]
Abstract
The taxonomic positions and phylogenetic relationships of six Pavetteae species endemic to Madagascar were tested with a phylogenetic study of the Afro-Madagascan representatives of the tribe Pavetteae based on sequence data from six markers rps16, trnT-F, petD, accD-psa1, PI and ITS. The six species were resolved into four well-supported and morphologically distinct clades which we here formally recognise at generic level. The new genera are the monospecific Exallosperma and Pseudocoptosperma, each with a single species, and Helictosperma and Tulearia, each with two species. Each genus is characterised by one or more autapomorphies or by a unique combination of plesiomorphic characters. Mostly, the distinguishing characters are found in fruit and seed; Exallosperma differs from all other Pavetteae genera by the fruit consisting of two stony pyrenes, each with a single laterally flattened seed with irregularly distributed ridges on the surface; Helictosperma is unique by its single spherical seed rolled-in on itself in the shape of a giant pill-millipede. Pseudocoptosperma is characterised by the combination of three ovules pendulous from a small placenta and triangular stipules with a strongly developed awn, whereas Tulearia is characterised by robust sericeous flowers, small leaves, uni- or pauciflorous inflorescences and fruits with two pyrenes, each with a single ruminate seed. The four new genera show marked adaptations to the dry habitats in which they grow. They represent multiple radiations into drylands and highlight the importance of the dry forest and scrub vegetation in western, southern and northern Madagascar for plant biodiversity. The description of the four new genera shows that the tribe Pavetteae exhibits the same pattern as many plant groups in Madagascar, which are characterised by a high proportion of endemic genera comprising a single or a few species. In the four new genera, five new species are described and one new combination is made: Exallosperma longiflora De Block; Helictosperma malacophylla (Drake) De Block, Helictosperma poissoniana De Block, Pseudocoptosperma menabense Capuron ex De Block; Tulearia capsaintemariensis De Block and Tulearia splendida De Block.
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Affiliation(s)
- Petra De Block
- Botanic Garden Meise, Nieuwelaan 38, 1860 Meise, Belgium
| | - Franck Rakotonasolo
- Kew Madagascar Conservation Centre, Lot II J 131 Ambodivoanjo, Ivandry, Antananarivo, Madagascar
- Parc Botanique et Zoologique de Tsimbazaza, Antananarivo-101, Madagascar
| | - Salvator Ntore
- Botanic Garden Meise, Nieuwelaan 38, 1860 Meise, Belgium
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Roque E, Gómez-Mena C, Ferrándiz C, Beltrán JP, Cañas LA. Functional Genomics and Genetic Control of Flower and Fruit Development in Medicago truncatula: An Overview. Methods Mol Biol 2018; 1822:273-290. [PMID: 30043310 DOI: 10.1007/978-1-4939-8633-0_18] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
A-, B-, and C-class genes code for MADS-box transcription factors required for floral organ identity in angiosperms. Other members of the family are also crucial to ensure proper carpel and fruit development. Development of genetic and genomic tools for Medicago truncatula has allowed its use as model system to study the genetic control of flower and fruit development in legumes. M. truncatula contains a single A-class gene, four B-function genes, and three C-class genes in its genome. This has made possible to do extensive functional characterization of these MADS-box transcription factors using gene expression analyses, protein-protein interactions, and forward and reverse genetic approaches. We have demonstrated the functions of these MADS-box transcription factors and the respective contributions of paralogous gene pairs to M. truncatula floral development. We have also defined the evolutionary outcomes of each duplicated pairs thus testing theoretical framework of several models about the evolution by gene duplication. Moreover, we have also studied the function of MADS-box fruit genes and how they may have contributed to the diversification of pod morphology within the Medicago genus. Our findings not only have contributed to increase knowledge in the field of the genetic control of flower and fruit development but also have provided a more complete understanding of the complexity of evolution by gene duplication and protein sequence diversification.
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Affiliation(s)
- Edelín Roque
- Instituto de Biología Molecular y Celular de Plantas (CSIC-UPV), Ciudad Politécnica de la Innovación Edf. 8E, C/ Ingeniero Fausto Elio s.n., Valencia, E-46011, Spain
| | - Concepción Gómez-Mena
- Instituto de Biología Molecular y Celular de Plantas (CSIC-UPV), Ciudad Politécnica de la Innovación Edf. 8E, C/ Ingeniero Fausto Elio s.n., Valencia, E-46011, Spain
| | - Cristina Ferrándiz
- Instituto de Biología Molecular y Celular de Plantas (CSIC-UPV), Ciudad Politécnica de la Innovación Edf. 8E, C/ Ingeniero Fausto Elio s.n., Valencia, E-46011, Spain
| | - José Pío Beltrán
- CSIC-UPV, Institute for Plant Cell and Molecular Biology(IBMCP), Valencia, Spain.
| | - Luis A Cañas
- CSIC-UPV, Institute for Plant Cell and Molecular Biology(IBMCP), Valencia, Spain.
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Li J, Cocker JM, Wright J, Webster MA, McMullan M, Dyer S, Swarbreck D, Caccamo M, Oosterhout CV, Gilmartin PM. Genetic architecture and evolution of the S locus supergene in Primula vulgaris. NATURE PLANTS 2016; 2:16188. [PMID: 27909301 DOI: 10.1038/nplants.2016.188] [Citation(s) in RCA: 90] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Accepted: 10/31/2016] [Indexed: 06/06/2023]
Abstract
Darwin's studies on heterostyly in Primula described two floral morphs, pin and thrum, with reciprocal anther and stigma heights that promote insect-mediated cross-pollination. This key innovation evolved independently in several angiosperm families. Subsequent studies on heterostyly in Primula contributed to the foundation of modern genetic theory and the neo-Darwinian synthesis. The established genetic model for Primula heterostyly involves a diallelic S locus comprising several genes, with rare recombination events that result in self-fertile homostyle flowers with anthers and stigma at the same height. Here we reveal the S locus supergene as a tightly linked cluster of thrum-specific genes that are absent in pins. We show that thrums are hemizygous not heterozygous for the S locus, which suggests that homostyles do not arise by recombination between S locus haplotypes as previously proposed. Duplication of a floral homeotic gene 51.7 million years (Myr) ago, followed by its neofunctionalization, created the current S locus assemblage which led to floral heteromorphy in Primula. Our findings provide new insights into the structure, function and evolution of this archetypal supergene.
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Affiliation(s)
- Jinhong Li
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
- John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Jonathan M Cocker
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
- John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Jonathan Wright
- The Earlham Institute, Norwich Research Park, Norwich NR4 7UH, UK
| | - Margaret A Webster
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
- John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Mark McMullan
- The Earlham Institute, Norwich Research Park, Norwich NR4 7UH, UK
| | - Sarah Dyer
- The Earlham Institute, Norwich Research Park, Norwich NR4 7UH, UK
| | - David Swarbreck
- The Earlham Institute, Norwich Research Park, Norwich NR4 7UH, UK
| | - Mario Caccamo
- The Earlham Institute, Norwich Research Park, Norwich NR4 7UH, UK
| | - Cock van Oosterhout
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
| | - Philip M Gilmartin
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
- John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
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11
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Roque E, Fares MA, Yenush L, Rochina MC, Wen J, Mysore KS, Gómez-Mena C, Beltrán JP, Cañas LA. Evolution by gene duplication of Medicago truncatula PISTILLATA-like transcription factors. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:1805-1817. [PMID: 26773809 PMCID: PMC4783364 DOI: 10.1093/jxb/erv571] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
PISTILLATA (PI) is a member of the B-function MADS-box gene family, which controls the identity of both petals and stamens in Arabidopsis thaliana. In Medicago truncatula (Mt), there are two PI-like paralogs, known as MtPI and MtNGL9. These genes differ in their expression patterns, but it is not known whether their functions have also diverged. Describing the evolution of certain duplicated genes, such as transcription factors, remains a challenge owing to the complex expression patterns and functional divergence between the gene copies. Here, we report a number of functional studies, including analyses of gene expression, protein-protein interactions, and reverse genetic approaches designed to demonstrate the respective contributions of each M. truncatula PI-like paralog to the B-function in this species. Also, we have integrated molecular evolution approaches to determine the mode of evolution of Mt PI-like genes after duplication. Our results demonstrate that MtPI functions as a master regulator of B-function in M. truncatula, maintaining the overall ancestral function, while MtNGL9 does not seem to have a role in this regard, suggesting that the pseudogenization could be the functional evolutionary fate for this gene. However, we provide evidence that purifying selection is the primary evolutionary force acting on this paralog, pinpointing the conservation of its biochemical function and, alternatively, the acquisition of a new role for this gene.
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Affiliation(s)
- Edelín Roque
- Instituto de Biología Molecular y Celular de Plantas Consejo Superior de Investigaciones Científicas & Universidad Politécnica de Valencia (CSIC-UPV), Ciudad Politécnica de la Innovación, Edf. 8E, C/ Ingeniero Fausto Elio s/n, E-46011 Valencia, Spain
| | - Mario A Fares
- Instituto de Biología Molecular y Celular de Plantas Consejo Superior de Investigaciones Científicas & Universidad Politécnica de Valencia (CSIC-UPV), Ciudad Politécnica de la Innovación, Edf. 8E, C/ Ingeniero Fausto Elio s/n, E-46011 Valencia, Spain
| | - Lynne Yenush
- Instituto de Biología Molecular y Celular de Plantas Consejo Superior de Investigaciones Científicas & Universidad Politécnica de Valencia (CSIC-UPV), Ciudad Politécnica de la Innovación, Edf. 8E, C/ Ingeniero Fausto Elio s/n, E-46011 Valencia, Spain
| | - Mari Cruz Rochina
- Instituto de Biología Molecular y Celular de Plantas Consejo Superior de Investigaciones Científicas & Universidad Politécnica de Valencia (CSIC-UPV), Ciudad Politécnica de la Innovación, Edf. 8E, C/ Ingeniero Fausto Elio s/n, E-46011 Valencia, Spain
| | - Jiangqi Wen
- Plant Biology Division, The Samuel Roberts Noble Foundation, 2510 Sam Noble Parkway, Ardmore, OK 73401, USA
| | - Kirankumar S Mysore
- Plant Biology Division, The Samuel Roberts Noble Foundation, 2510 Sam Noble Parkway, Ardmore, OK 73401, USA
| | - Concepción Gómez-Mena
- Instituto de Biología Molecular y Celular de Plantas Consejo Superior de Investigaciones Científicas & Universidad Politécnica de Valencia (CSIC-UPV), Ciudad Politécnica de la Innovación, Edf. 8E, C/ Ingeniero Fausto Elio s/n, E-46011 Valencia, Spain
| | - José Pío Beltrán
- Instituto de Biología Molecular y Celular de Plantas Consejo Superior de Investigaciones Científicas & Universidad Politécnica de Valencia (CSIC-UPV), Ciudad Politécnica de la Innovación, Edf. 8E, C/ Ingeniero Fausto Elio s/n, E-46011 Valencia, Spain
| | - Luis A Cañas
- Instituto de Biología Molecular y Celular de Plantas Consejo Superior de Investigaciones Científicas & Universidad Politécnica de Valencia (CSIC-UPV), Ciudad Politécnica de la Innovación, Edf. 8E, C/ Ingeniero Fausto Elio s/n, E-46011 Valencia, Spain
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12
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Zhang S, Zhang JS, Zhao J, He C. Distinct subfunctionalization and neofunctionalization of the B-class MADS-box genes in Physalis floridana. PLANTA 2015; 241:387-402. [PMID: 25326772 DOI: 10.1007/s00425-014-2190-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Accepted: 10/02/2014] [Indexed: 05/24/2023]
Abstract
This work suggested that in Physalis PFGLO1-PFDEF primarily determined corolla and androecium identity, and acquired a novel role in gynoecia functionality, while PFGLO2-PFTM6 functioned in pollen maturation only. The B-class MADS-box genes play a crucial role in determining the organ identity of the corolla and androecium. Two GLOBOSA-like (GLO-like) PFGLO1 and PFGLO2 and two DEFICIENS-like (DEF-like) PFDEF and PFTM6 genes were present in Physalis floridana. However, the double-layered-lantern1 (doll1) mutant is the result of a single recessive mutation in PFGLO1, hinting a distinct divergent pattern of B-class genes. In this work, we utilized the tobacco rattle virus (TRV)-mediated gene silencing approach to further verify this assumption in P. floridana. Silencing of PFGLO1 or/and PFDEF demonstrated their primary role in determining corolla and androecium identity. However, specific PFGLO2 or/and PFTM6 silencing did not affect any organ identity but showed a reduction in mature pollen. These results suggested that both PFGLO2 and PFTM6 had lost their role in organ identity determination but functioned in pollen maturation. Evaluation of fruit setting in reciprocal crosses suggested that both PFGLO1 and PFDEF might have acquired an essential and novel role in the functionality of gynoecia. Such a divergence of the duplicated GLO-DEF heterodimer genes in floral development is different from the existing observations within Solanaceae. Therefore, our research sheds new light on the functional evolution of the duplicated B-class MADS-box genes in angiosperms.
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Affiliation(s)
- Shaohua Zhang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Xiangshan, Beijing, 100093, China
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13
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Jing D, Xia Y, Chen F, Wang Z, Zhang S, Wang J. Ectopic expression of a Catalpa bungei (Bignoniaceae) PISTILLATA homologue rescues the petal and stamen identities in Arabidopsis pi-1 mutant. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2015; 231:40-51. [PMID: 25575990 DOI: 10.1016/j.plantsci.2014.11.004] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2014] [Revised: 11/02/2014] [Accepted: 11/17/2014] [Indexed: 05/11/2023]
Abstract
PISTILLATA (PI) plays crucial roles in Arabidopsis flower development by specifying petal and stamen identities. To investigate the molecular mechanisms underlying organ development of woody angiosperm in Catalpa, we isolated and identified a PI homologue, referred to as CabuPI (C. bungei PISTILLATA), from two genetically cognate C. bungei (Bignoniaceae) bearing single and double flowers. Sequence and phylogenetic analyses revealed that the gene is closest related to the eudicot PI homologues. Moreover, a highly conserved PI-motif is found in the C-terminal regions of CabuPI. Semi-quantitative and quantitative real time PCR analyses showed that the expression of CabuPI was restricted to petals and stamens. However, CabuPI expression in the petals and stamens persisted throughout all floral development stages, but the expression levels were different. In 35S::CabuPI transgenic homozygous pi-1 mutant Arabidopsis, the second and the third whorl floral organs produced normal petals and a different number of stamens, respectively. Furthermore, ectopic expression of the CabuPI in transgenic wild-type or heterozygote pi-1 mutant Arabidopsis caused the first whorl sepal partially converted into a petal-like structure. These results clearly reveal the functional conservation of PI homologues between C. bungei and Arabidopsis.
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Affiliation(s)
- Danlong Jing
- State Key Laboratory of Forest Genetics and Tree Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, PR China.
| | - Yan Xia
- State Key Laboratory of Forest Genetics and Tree Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, PR China.
| | - Faju Chen
- Biotechnology Research Center, China Three Gorges University, Yichang City 443002, Hubei Province, PR China.
| | - Zhi Wang
- State Key Laboratory of Forest Genetics and Tree Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, PR China.
| | - Shougong Zhang
- State Key Laboratory of Forest Genetics and Tree Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, PR China.
| | - Junhui Wang
- State Key Laboratory of Forest Genetics and Tree Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, PR China.
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14
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Nowak MD, Russo G, Schlapbach R, Huu CN, Lenhard M, Conti E. The draft genome of Primula veris yields insights into the molecular basis of heterostyly. Genome Biol 2015; 16:12. [PMID: 25651398 PMCID: PMC4305239 DOI: 10.1186/s13059-014-0567-z] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2014] [Accepted: 12/11/2014] [Indexed: 12/04/2022] Open
Abstract
Background The flowering plant Primula veris is a common spring blooming perennial that is widely cultivated throughout Europe. This species is an established model system in the study of the genetics, evolution, and ecology of heterostylous floral polymorphisms. Despite the long history of research focused on this and related species, the continued development of this system has been restricted due the absence of genomic and transcriptomic resources. Results We present here a de novo draft genome assembly of P. veris covering 301.8 Mb, or approximately 63% of the estimated 479.22 Mb genome, with an N50 contig size of 9.5 Kb, an N50 scaffold size of 164 Kb, and containing an estimated 19,507 genes. The results of a RADseq bulk segregant analysis allow for the confident identification of four genome scaffolds that are linked to the P. veris S-locus. RNAseq data from both P. veris and the closely related species P. vulgaris allow for the characterization of 113 candidate heterostyly genes that show significant floral morph-specific differential expression. One candidate gene of particular interest is a duplicated GLOBOSA homolog that may be unique to Primula (PveGLO2), and is completely silenced in L-morph flowers. Conclusions The P. veris genome represents the first genome assembled from a heterostylous species, and thus provides an immensely important resource for future studies focused on the evolution and genetic dissection of heterostyly. As the first genome assembled from the Primulaceae, the P. veris genome will also facilitate the expanded application of phylogenomic methods in this diverse family and the eudicots as a whole. Electronic supplementary material The online version of this article (doi:10.1186/s13059-014-0567-z) contains supplementary material, which is available to authorized users.
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15
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Sun Y, Fan Z, Li X, Liu Z, Li J, Yin H. Distinct double flower varieties in Camellia japonica exhibit both expansion and contraction of C-class gene expression. BMC PLANT BIOLOGY 2014; 14:288. [PMID: 25344122 PMCID: PMC4219040 DOI: 10.1186/s12870-014-0288-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2014] [Accepted: 10/15/2014] [Indexed: 05/27/2023]
Abstract
BACKGROUND Double flower domestication is of great value in ornamental plants and presents an excellent system to study the mechanism of morphological alterations by human selection. The classic ABC model provides a genetic framework underlying the control of floral organ identity and organogenesis from which key regulators have been identified and evaluated in many plant species. Recent molecular studies have underscored the importance of C-class homeotic genes, whose functional attenuation contributed to the floral diversity in various species. Cultivated Camellia japonica L. possesses several types of double flowers, however the molecular mechanism underlying their floral morphological diversification remains unclear. RESULTS In this study, we cloned the C-class orthologous gene CjAG in C. japonica. We analyzed the expression patterns of CjAG in wild C. japonica, and performed ectopic expression in Arabidopsis. These results revealed that CjAG shared conserved C-class function that controls stamen and carpel development. Further we analyzed the expression pattern of CjAG in two different C. japonica double-flower varieties, 'Shibaxueshi' and 'Jinpanlizhi', and showed that expression of CjAG was highly contracted in 'Shibaxueshi' but expanded in inner petals of 'Jinpanlizhi'. Moreover, detailed expression analyses of B- and C-class genes have uncovered differential patterns of B-class genes in the inner organs of 'Jinpanlizhi'. CONCLUSIONS These results demonstrated that the contraction and expansion of CjAG expression were associated with the formation of different types of double flowers. Our studies have manifested two different trajectories of double flower domestication regarding the C-class gene expression in C. japonica.
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Affiliation(s)
- Yingkun Sun
- />Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Fuyang, 311400 Zhejiang China
- />College of Landscape Architecture and Forestry, Qingdao Agricultural University, Qingdao, 266109 Shandong China
| | - Zhengqi Fan
- />Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Fuyang, 311400 Zhejiang China
| | - Xinlei Li
- />Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Fuyang, 311400 Zhejiang China
| | - Zhongchi Liu
- />Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, ᅟᅟ Maryland USA
| | - Jiyuan Li
- />Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Fuyang, 311400 Zhejiang China
- />ᅟᅟ, Zhejiang Provincial Key Laboratory of Forest genetics and breeding, ᅟᅟ, ᅟᅟ Zhejiang China
| | - Hengfu Yin
- />Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Fuyang, 311400 Zhejiang China
- />ᅟᅟ, Zhejiang Provincial Key Laboratory of Forest genetics and breeding, ᅟᅟ, ᅟᅟ Zhejiang China
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16
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Cheng S, van den Bergh E, Zeng P, Zhong X, Xu J, Liu X, Hofberger J, de Bruijn S, Bhide AS, Kuelahoglu C, Bian C, Chen J, Fan G, Kaufmann K, Hall JC, Becker A, Bräutigam A, Weber AP, Shi C, Zheng Z, Li W, Lv M, Tao Y, Wang J, Zou H, Quan Z, Hibberd JM, Zhang G, Zhu XG, Xu X, Schranz ME. The Tarenaya hassleriana genome provides insight into reproductive trait and genome evolution of crucifers. THE PLANT CELL 2013; 25:2813-30. [PMID: 23983221 PMCID: PMC3784582 DOI: 10.1105/tpc.113.113480] [Citation(s) in RCA: 71] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2013] [Revised: 07/06/2013] [Accepted: 08/06/2013] [Indexed: 05/18/2023]
Abstract
The Brassicaceae, including Arabidopsis thaliana and Brassica crops, is unmatched among plants in its wealth of genomic and functional molecular data and has long served as a model for understanding gene, genome, and trait evolution. However, genome information from a phylogenetic outgroup that is essential for inferring directionality of evolutionary change has been lacking. We therefore sequenced the genome of the spider flower (Tarenaya hassleriana) from the Brassicaceae sister family, the Cleomaceae. By comparative analysis of the two lineages, we show that genome evolution following ancient polyploidy and gene duplication events affect reproductively important traits. We found an ancient genome triplication in Tarenaya (Th-α) that is independent of the Brassicaceae-specific duplication (At-α) and nested Brassica (Br-α) triplication. To showcase the potential of sister lineage genome analysis, we investigated the state of floral developmental genes and show Brassica retains twice as many floral MADS (for minichromosome maintenance1, AGAMOUS, DEFICIENS and serum response factor) genes as Tarenaya that likely contribute to morphological diversity in Brassica. We also performed synteny analysis of gene families that confer self-incompatibility in Brassicaceae and found that the critical serine receptor kinase receptor gene is derived from a lineage-specific tandem duplication. The T. hassleriana genome will facilitate future research toward elucidating the evolutionary history of Brassicaceae genomes.
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Affiliation(s)
| | - Erik van den Bergh
- Biosystematics Group, Wageningen University, 6708 PB Wageningen, The Netherlands
| | - Peng Zeng
- Beijing Genomics Institute, 518083 Shenzhen, China
| | - Xiao Zhong
- Beijing Genomics Institute, 518083 Shenzhen, China
| | - Jiajia Xu
- Plant Systems Biology Group, Partner Institute of Computational Biology, Chinese Academy of Sciences/Max Planck Society, Shanghai 200031, China
| | - Xin Liu
- Beijing Genomics Institute, 518083 Shenzhen, China
| | - Johannes Hofberger
- Biosystematics Group, Wageningen University, 6708 PB Wageningen, The Netherlands
| | - Suzanne de Bruijn
- Molecular Biology Group, Wageningen University, 6708 PB Wageningen, The Netherlands
- Institute for Biochemistry and Biology, University of Potsdam, 14476 Potsdam, Germany
| | - Amey S. Bhide
- Plant Developmental Biology Group, Institute of Botany, Justus-Liebig-University, 35392 Giessen, Germany
| | - Canan Kuelahoglu
- Institute of Plant Biochemistry, Center of Excellence on Plant Sciences, Heinrich-Heine-University, D-40225 Duesseldorf, Germany
| | - Chao Bian
- Beijing Genomics Institute, 518083 Shenzhen, China
| | - Jing Chen
- Beijing Genomics Institute, 518083 Shenzhen, China
| | - Guangyi Fan
- Beijing Genomics Institute, 518083 Shenzhen, China
| | - Kerstin Kaufmann
- Institute for Biochemistry and Biology, University of Potsdam, 14476 Potsdam, Germany
| | - Jocelyn C. Hall
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada T6G 2E9
| | - Annette Becker
- Plant Developmental Biology Group, Institute of Botany, Justus-Liebig-University, 35392 Giessen, Germany
| | - Andrea Bräutigam
- Institute of Plant Biochemistry, Center of Excellence on Plant Sciences, Heinrich-Heine-University, D-40225 Duesseldorf, Germany
| | - Andreas P.M. Weber
- Institute of Plant Biochemistry, Center of Excellence on Plant Sciences, Heinrich-Heine-University, D-40225 Duesseldorf, Germany
| | | | - Zhijun Zheng
- Beijing Genomics Institute, 518083 Shenzhen, China
| | - Wujiao Li
- Beijing Genomics Institute, 518083 Shenzhen, China
| | - Mingju Lv
- Plant Systems Biology Group, Partner Institute of Computational Biology, Chinese Academy of Sciences/Max Planck Society, Shanghai 200031, China
| | - Yimin Tao
- Plant Systems Biology Group, Partner Institute of Computational Biology, Chinese Academy of Sciences/Max Planck Society, Shanghai 200031, China
| | - Junyi Wang
- Beijing Genomics Institute, 518083 Shenzhen, China
| | - Hongfeng Zou
- Beijing Genomics Institute, 518083 Shenzhen, China
- State Key Laboratory of Agricultural Genomics, Beijing Genomics Institute, 518083 Shenzhen, China
- Key Laboratory of Genomics, Ministry of Agriculture, Beijing Genomics Institute, 518083 Shenzhen, China
| | - Zhiwu Quan
- Beijing Genomics Institute, 518083 Shenzhen, China
- State Key Laboratory of Agricultural Genomics, Beijing Genomics Institute, 518083 Shenzhen, China
- Key Laboratory of Genomics, Ministry of Agriculture, Beijing Genomics Institute, 518083 Shenzhen, China
| | - Julian M. Hibberd
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom
| | - Gengyun Zhang
- Beijing Genomics Institute, 518083 Shenzhen, China
- State Key Laboratory of Agricultural Genomics, Beijing Genomics Institute, 518083 Shenzhen, China
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom
| | - Xin-Guang Zhu
- Plant Systems Biology Group, Partner Institute of Computational Biology, Chinese Academy of Sciences/Max Planck Society, Shanghai 200031, China
| | - Xun Xu
- Beijing Genomics Institute, 518083 Shenzhen, China
| | - M. Eric Schranz
- Biosystematics Group, Wageningen University, 6708 PB Wageningen, The Netherlands
- Address correspondence to
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Vekemans D, Viaene T, Caris P, Geuten K. Transference of function shapes organ identity in the dove tree inflorescence. THE NEW PHYTOLOGIST 2012; 193:216-228. [PMID: 21992614 DOI: 10.1111/j.1469-8137.2011.03915.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
• An important evolutionary mechanism shaping the biodiversity of flowering plants is the transfer of function from one plant organ to another. To investigate whether and how transference of function is associated with the remodeling of the floral organ identity program we studied Davidia involucrata, a species with conspicuous, petaloid bracts subtending a contracted inflorescence with reduced flowers. • A detailed ontogeny enabled the interpretation of expression patterns of B-, C- and E-class homeotic MADS-box genes using qRT-PCR and in situ hybridization techniques. We investigated protein-protein interactions using yeast two-hybrid assays. • Although loss of organs does not appear to have affected organ identity in the retained organs of the reduced flowers of D. involucrata, the bracts express the B-class TM6 (Tomato MADS box gene 6) and GLOBOSA homologs, but not DEFICIENS, and the C-class AGAMOUS homolog, representing a subset of genes also involved in stamen identity. • Our results may illustrate how petal identity can be partially transferred outside the flower by expressing a subset of stamen identity genes. This adds to the molecular mechanisms explaining the diversity of plant reproductive morphology.
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Affiliation(s)
- Dries Vekemans
- Department of Biology, Katholieke Universiteit Leuven (K.U.Leuven), Kasteelpark Arenberg 31, 3001 Leuven, Belgium
| | - Tom Viaene
- VIB Department of Plant Systems Biology, Universiteit Gent (UGent), Technologiepark 927, 9052 Gent, Belgium
| | - Pieter Caris
- Department of Biology, Katholieke Universiteit Leuven (K.U.Leuven), Kasteelpark Arenberg 31, 3001 Leuven, Belgium
| | - Koen Geuten
- Department of Biology, Katholieke Universiteit Leuven (K.U.Leuven), Kasteelpark Arenberg 31, 3001 Leuven, Belgium
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Lee HL, Irish VF. Gene duplication and loss in a MADS box gene transcription factor circuit. Mol Biol Evol 2011; 28:3367-80. [PMID: 21712469 DOI: 10.1093/molbev/msr169] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Although many models have been proposed that could lead to the maintenance of gene duplicates, the ways in which interacting gene duplicates influence each other's evolution and function remain poorly understood. Here, we focus on duplication and loss of the B class MADS box transcription factor genes in the euasterids I and the ramifications of such changes on paralog evolution and their encoded functions. In core eudicots, the B class genes belong to two paralogous lineages whose products form obligate heterodimers. Based on comparative genomic and phylogenetic analyses, we show that five stepwise B class MADS box gene gain or loss events occurred during the radiation of the euasterids I within core eudicots. Gene loss in one sublineage was correlated with a deficit of other sublineage genes. We also show that the gain or loss of B class MADS box gene paralogs were associated with altered protein-protein interactions among the remaining copies. These altered protein interactions were correlated with asymmetric patterns of sequence diversification and selection, suggesting that compensatory changes were driving the evolution of such genes. Furthermore, these B class MADS box gene gain or loss events were associated with the evolutionary divergence of floral morphology in the euasterids I. Together, these observations point to a cooperative strategy by which gene networks evolve, with selection maintaining the overall logic of a network despite changes in individual components.
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Affiliation(s)
- Hae-Lim Lee
- Department of Molecular, Cellular and Developmental Biology, Yale University, USA
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19
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Geuten K, Viaene T, Irish VF. Robustness and evolvability in the B-system of flower development. ANNALS OF BOTANY 2011; 107:1545-56. [PMID: 21441246 PMCID: PMC3108807 DOI: 10.1093/aob/mcr061] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2010] [Revised: 12/17/2010] [Accepted: 01/24/2011] [Indexed: 05/23/2023]
Abstract
BACKGROUND Gene duplication has often been invoked as a key mechanism responsible for evolution of new morphologies. The floral homeotic B-group gene family has undergone a number of gene duplication events, and yet the functions of these genes appear to be largely conserved. However, detailed comparative analysis has indicated that such duplicate genes have considerable cryptic variability in their functions. In the Solanaceae, two duplicate B-group gene lineages have been retained in three subfamilies. Comparisons of orthologous genes across members of the Solanaceae have demonstrated that the combined function of all four B-gene members is to establish petal and stamen identity, but that this function was partitioned differently in each species. These observations emphasize both the robustness and the evolvability of the B-system. SCOPE We provide an overview of how the B-function genes can robustly specify petal and stamen identity and at the same time evolve through changes in protein-protein interaction, gene expression patterns, copy number variation or alterations in the downstream genes they control. By using mathematical models we explore regulatory differences between species and how these impose constraints on downstream gene regulation. CONCLUSIONS Evolvability of the B-genes can be understood through the multiple ways in which the B-system can be robust. Quantitative approaches should allow for the incorporation of more biological realism in the representations of these regulatory systems and this should contribute to understanding the constraints under which different B-systems can function and evolve. This, in turn, can provide a better understanding of the ways in which B-genes have contributed to flower diversity.
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Affiliation(s)
- K Geuten
- Department of Biology, K.U. Leuven, Kasteelpark Arenberg 31, 3001 Heverlee, Belgium.
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Dynamic programming procedure for searching optimal models to estimate substitution rates based on the maximum-likelihood method. Proc Natl Acad Sci U S A 2011; 108:7860-5. [PMID: 21521791 DOI: 10.1073/pnas.1018621108] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The substitution rate in a gene can provide valuable information for understanding its functionality and evolution. A widely used method to estimate substitution rates is the maximum-likelihood method implemented in the CODEML program in the PAML package. A limited number of branch models, chosen based on a priori information or an interest in a particular lineage(s), are tested, whereas a large number of potential models are neglected. A complementary approach is also needed to test all or a large number of possible models to search for the globally optional model(s) of maximum likelihood. However, the computational time for this search even in a small number of sequences becomes impractically long. Thus, it is desirable to explore the most probable spaces to search for the optimal models. Using dynamic programming techniques, we developed a simple computational method for searching the most probable optimal branch-specific models in a practically feasible computational time. We propose three search methods to find the optimal models, which explored O(n) (method 1) to O(n(2)) (method 2 and method 3) models when the given phylogeny has n branches. In addition, we derived a formula to calculate the number of all possible models, revealing the complexity of finding the optimal branch-specific model. We show that in a reanalysis of over 50 previously published studies, the vast majority obtained better models with significantly higher likelihoods than the conventional hypothesis model methods.
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Shi T, Huang H, Barker MS. Ancient genome duplications during the evolution of kiwifruit (Actinidia) and related Ericales. ANNALS OF BOTANY 2010; 106:497-504. [PMID: 20576738 PMCID: PMC2924827 DOI: 10.1093/aob/mcq129] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2010] [Revised: 04/20/2010] [Accepted: 05/20/2010] [Indexed: 05/21/2023]
Abstract
BACKGROUND AND AIMS To assess the number and phylogenetic distribution of large-scale genome duplications in the ancestry of Actinidia, publicly available expressed sequenced tags (ESTs) for members of the Actinidiaceae and related Ericales, including tea (Camellia sinensis), were analysed. METHODS Synonymous divergences (K(s)) were calculated for all duplications within gene families and examined for evidence of large-scale duplication events. Phylogenetic comparisons for a selection of orthologues among several related species in Ericales and two outgroups permitted placement of duplication events in relation to lineage divergences. Gene ontology (GO) categories were analysed for each whole-genome duplication (WGD) and the whole transcriptome. KEY RESULTS Evidence for three ancient WGDs in Actinidia was found. Analyses of paleologue GO categories indicated a different pattern of retained genes for each genome duplication, but a pattern consistent with the dosage-balance hypothesis among all retained paleologues. CONCLUSIONS This study provides evidence for one independent WGD in the ancestry of Actinidia (Ad-alpha), a WGD shared by Actinidia and Camellia (Ad-beta), and the well-established At-gamma WGD that occurred prior to the divergence of all taxa examined. More ESTs in other taxa are needed to elucidate which groups in Ericales share the Ad-beta or Ad-alpha duplications and their impact on diversification.
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Affiliation(s)
- Tao Shi
- Key Laboratory of Plant Germplasm Enhancement and Speciality Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, Hubei, China
| | - Hongwen Huang
- Key Laboratory of Plant Germplasm Enhancement and Speciality Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, Hubei, China
- South China Botanical Garden/South China Institute of Botany, Chinese Academy of Sciences, Guangzhou, Guangdong, China
| | - Michael S. Barker
- South China Botanical Garden/South China Institute of Botany, Chinese Academy of Sciences, Guangzhou, Guangdong, China
- The Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada V6T 1Z4
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
- For correspondence. E-mail
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Geuten K, Irish V. Hidden variability of floral homeotic B genes in Solanaceae provides a molecular basis for the evolution of novel functions. THE PLANT CELL 2010; 22:2562-78. [PMID: 20807882 PMCID: PMC2947177 DOI: 10.1105/tpc.110.076026] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2010] [Revised: 06/18/2010] [Accepted: 08/09/2010] [Indexed: 05/08/2023]
Abstract
B-class MADS box genes specify petal and stamen identities in several core eudicot species. Members of the Solanaceae possess duplicate copies of these genes, allowing for diversification of function. To examine the changing roles of such duplicate orthologs, we assessed the functions of B-class genes in Nicotiana benthamiana and tomato (Solanum lycopersicum) using virus-induced gene silencing and RNA interference approaches. Loss of function of individual duplicates can have distinct phenotypes, yet complete loss of B-class gene function results in extreme homeotic transformations of petal and stamen identities. We also show that these duplicate gene products have qualitatively different protein-protein interaction capabilities and different regulatory roles. Thus, compensatory changes in B-class MADS box gene duplicate function have occurred in the Solanaceae, in that individual gene roles are distinct, but their combined functions are equivalent. Furthermore, we show that species-specific differences in the stamen regulatory network are associated with differences in the expression of the microRNA miR169. Whereas there is considerable plasticity in individual B-class MADS box transcription factor function, there is overall conservation in the roles of the multimeric MADS box B-class protein complexes, providing robustness in the specification of petal and stamen identities. Such hidden variability in gene function as we observe for individual B-class genes can provide a molecular basis for the evolution of regulatory functions that result in novel morphologies.
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Affiliation(s)
- Koen Geuten
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Conecticut 06520, USA.
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