1
|
He J, Van Eck J, Lippman ZB. Blooming balloons: Searching for mechanisms of the inflated calyx. CURRENT OPINION IN PLANT BIOLOGY 2024; 81:102595. [PMID: 38943829 DOI: 10.1016/j.pbi.2024.102595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Revised: 05/31/2024] [Accepted: 06/10/2024] [Indexed: 07/01/2024]
Abstract
Studying morphological novelties offers special insights into developmental biology and evolution. The inflated calyx syndrome (ICS) is a largely unrecognized but fascinating feature of flower development, where sepals form balloon-like husks that encapsulate fruits. Despite its independent emergence in many lineages of flowering plants, the genetic and molecular mechanisms of ICS remain unknown. Early studies in the Solanaceae genus Physalis put forth key roles of MADS-box genes in ICS. However, recent work suggests these classical floral identity transcription factors were false leads. With newfound capabilities that allow rapid development of genetic systems through genomics and genome editing, Physalis has re-emerged as the most tractable model species for dissecting ICS. This review revisits current understanding of ICS and highlights how recent advancements enable a reset in the search for genetic and molecular mechanisms using unbiased, systematic approaches.
Collapse
Affiliation(s)
- Jia He
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA; Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Joyce Van Eck
- Boyce Thompson Institute, Ithaca, NY 14853, USA; Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
| | - Zachary B Lippman
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA; Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA.
| |
Collapse
|
2
|
Jiang Y, Jin Y, Shan Y, Zhong Q, Wang H, Shen C, Feng S. Advances in Physalis molecular research: applications in authentication, genetic diversity, phylogenetics, functional genes, and omics. FRONTIERS IN PLANT SCIENCE 2024; 15:1407625. [PMID: 38993935 PMCID: PMC11236614 DOI: 10.3389/fpls.2024.1407625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Accepted: 06/07/2024] [Indexed: 07/13/2024]
Abstract
The plants of the genus Physalis L. have been extensively utilized in traditional and indigenous Chinese medicinal practices for treating a variety of ailments, including dermatitis, malaria, asthma, hepatitis, and liver disorders. The present review aims to achieve a comprehensive and up-to-date investigation of the genus Physalis, a new model crop, to understand plant diversity and fruit development. Several chloroplast DNA-, nuclear ribosomal DNA-, and genomic DNA-based markers, such as psbA-trnH, internal-transcribed spacer (ITS), simple sequence repeat (SSR), random amplified microsatellites (RAMS), sequence-characterized amplified region (SCAR), and single nucleotide polymorphism (SNP), were developed for molecular identification, genetic diversity, and phylogenetic studies of Physalis species. A large number of functional genes involved in inflated calyx syndrome development (AP2-L, MPF2, MPF3, and MAGO), organ growth (AG1, AG2, POS1, and CNR1), and active ingredient metabolism (24ISO, DHCRT, P450-CPL, SR, DUF538, TAS14, and 3β-HSB) were identified contributing to the breeding of novel Physalis varieties. Various omic studies revealed and functionally identified a series of reproductive organ development-related factors, environmental stress-responsive genes, and active component biosynthesis-related enzymes. The chromosome-level genomes of Physalis floridana Rydb., Physalis grisea (Waterf.) M. Martínez, and Physalis pruinosa L. have been recently published providing a valuable resource for genome editing in Physalis crops. Our review summarizes the recent progress in genetic diversity, molecular identification, phylogenetics, functional genes, and the application of omics in the genus Physalis and accelerates efficient utilization of this traditional herb.
Collapse
Affiliation(s)
- Yan Jiang
- Hangzhou Normal University, Hangzhou, China
| | - Yanyun Jin
- Hangzhou Normal University, Hangzhou, China
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou, China
| | - Yiyi Shan
- Hangzhou Normal University, Hangzhou, China
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou, China
| | - Quanzhou Zhong
- Hangzhou Normal University, Hangzhou, China
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou, China
| | - Huizhong Wang
- Hangzhou Normal University, Hangzhou, China
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou, China
| | - Chenjia Shen
- Hangzhou Normal University, Hangzhou, China
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou, China
| | - Shangguo Feng
- Hangzhou Normal University, Hangzhou, China
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou, China
| |
Collapse
|
3
|
Wang D, Dong X, Zhong MC, Jiang XD, Cui WH, Bendahmane M, Hu JY. Molecular and genetic regulation of petal number variation. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:3233-3247. [PMID: 38546444 DOI: 10.1093/jxb/erae136] [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: 12/14/2023] [Accepted: 03/26/2024] [Indexed: 06/11/2024]
Abstract
Floral forms with an increased number of petals, also known as double-flower phenotypes, have been selected and conserved in many domesticated plants, particularly in ornamentals, because of their great economic value. The molecular and genetic mechanisms that control this trait are therefore of great interest, not only for scientists, but also for breeders. In this review, we summarize current knowledge of the gene regulatory networks of flower initiation and development and known mutations that lead to variation of petal number in many species. In addition to the well-accepted miR172/AP2-like module, for which many questions remain unanswered, we also discuss other pathways in which mutations also lead to the formation of extra petals, such as those involved in meristem maintenance, hormone signalling, epigenetic regulation, and responses to environmental signals. We discuss how the concept of 'natural mutants' and recent advances in genomics and genome editing make it possible to explore the molecular mechanisms underlying double-flower formation, and how such knowledge could contribute to the future breeding and selection of this trait in more crops.
Collapse
Affiliation(s)
- Dan Wang
- Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, 650204 Kunming, Yunnan, China
| | - Xue Dong
- Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, 650201 Kunming, Yunnan, China
| | - Mi-Cai Zhong
- Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Xiao-Dong Jiang
- Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Wei-Hua Cui
- Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Mohammed Bendahmane
- Laboratoire Reproduction et Développement des Plantes, INRAE-CNRS-Lyon1-ENS, Ecole Normale Supérieure de Lyon, Lyon, France
| | - Jin-Yong Hu
- Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| |
Collapse
|
4
|
Zhao JX, Wang S, Liu J, Jiang XD, Wen J, Suo ZQ, Liu J, Zhong MC, Wang Q, Gu Z, Liu C, Deng Y, Hu JY, Li DZ. A comparative full-length transcriptomic resource provides insight into the perennial monocarpic mass flowering. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 116:1842-1855. [PMID: 37665679 DOI: 10.1111/tpj.16452] [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: 07/03/2023] [Revised: 08/21/2023] [Accepted: 08/23/2023] [Indexed: 09/06/2023]
Abstract
Perennial monocarpic mass flowering represents as a key developmental innovation in flowering time diversity in several biological and economical essential families, such as the woody bamboos and the shrubby Strobilanthes. However, molecular and genetic mechanisms underlying this important biodiversity remain poorly investigated. Here, we generated a full-length transcriptome resource incorporated into the BlueOmics database (http://blueomics.iflora.cn) for two Strobilanthes species, which feature contrasting flowering time behaviors. Using about 112 and 104 Gb Iso-seq reads together with ~185 and ~75 Gb strand-specific RNA seq data, we annotated 80 971 and 79 985 non-redundant full-length transcripts for the perennial polycarpic Strobilanthes tetrasperma and the perennial monocarpic Strobilanthes biocullata, respectively. In S. tetrasperma, we identified 8794 transcripts showing spatiotemporal expression in nine tissues. In leaves and shoot apical meristems at two developmental stages, 977 and 1121 transcripts were differentially accumulated in S. tetrasperma and S. biocullata, respectively. Interestingly, among the 33 transcription factors showing differential expression in S. tetrasperma but without differential expression in S. biocullata, three were involved potentially in the photoperiod and circadian-clock pathway of flowering time regulation (FAR1 RELATED SEQUENCE 12, FRS12; NUCLEAR FACTOR Y A1, NFYA1; PSEUDO-RESPONSE REGULATOR 5, PRR5), hence provides an important clue in deciphering the flowering diversity mechanisms. Our data serve as a key resource for further dissection of molecular and genetic mechanisms underpinning key biological innovations, here, the perennial monocarpic mass flowering.
Collapse
Affiliation(s)
- Jiu-Xia Zhao
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shu Wang
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Jiazhi Liu
- University of Chinese Academy of Sciences, Beijing, 100049, China
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Yunnan Key Laboratory of Crop Wild Relatives Omics, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, 650223, China
| | - Xiao-Dong Jiang
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Jing Wen
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhi-Quan Suo
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Jie Liu
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Mi-Cai Zhong
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Qin Wang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Zhirong Gu
- Administration of National Nature Reserve of Badagongshan, Sangzhi, 427000, Hunan, China
| | - Changning Liu
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Yunnan Key Laboratory of Crop Wild Relatives Omics, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, 650223, China
| | - Yunfei Deng
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Jin-Yong Hu
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - De-Zhu Li
- Germplasm Bank of Wild Species, Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
| |
Collapse
|
5
|
Mamut J, Chen K, Baskin CC, Tan D. Inflated Ovary May Increase the Dispersal Ability of Three Species in the Cold Deserts of Central Asia. PLANTS (BASEL, SWITZERLAND) 2023; 12:1950. [PMID: 37653867 PMCID: PMC10223576 DOI: 10.3390/plants12101950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 04/08/2023] [Accepted: 05/09/2023] [Indexed: 09/02/2023]
Abstract
Among the diaspores of angiosperms an inflated ovary (IO) is a novel morphological trait, but no studies have evaluated its effects on dispersal. The primary aim of this study was to determine the effect of the IO on diaspore dispersal in three cold desert species (Carex physodes, Calligonum junceum, and Sphaerophysa salsula). Various morphological features and the mass of fruits and seeds of each species were measured. The role of an IO in diaspore dispersal by wind and water was determined by comparing responses of intact (inflated) IOs and flattened fruits and seeds. Mature diaspores of three species were dispersed by wind, and the IO significantly increased dispersal distance in the field and at different wind speeds in the laboratory. The floating time on water was greater for inflated fruits than flattened fruits and seeds. Since the seed remains inside the IO until after dispersal is completed, the IO of the three species enhances diaspore dispersal. This is the first detailed study on how an IO increases diaspore/seed dispersal. Furthermore, after primary dispersal by wind, secondary dispersal can occur via wind or surface runoff of water, and each method is enhanced by the presence of an IO.
Collapse
Affiliation(s)
- Jannathan Mamut
- College of Life Science, Xinjiang Agricultural University, Ürümqi 830052, China; (J.M.); (K.C.); (C.C.B.)
- Key Laboratory of Ministry of Education for Western Arid Region Grassland Resources and Ecology, College of Grassland Sciences, Xinjiang Agricultural University, Ürümqi 830052, China
| | - Kewei Chen
- College of Life Science, Xinjiang Agricultural University, Ürümqi 830052, China; (J.M.); (K.C.); (C.C.B.)
| | - Carol C. Baskin
- College of Life Science, Xinjiang Agricultural University, Ürümqi 830052, China; (J.M.); (K.C.); (C.C.B.)
- Department of Biology, University of Kentucky, Lexington, KY 40506, USA
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY 40546, USA
| | - Dunyan Tan
- College of Life Science, Xinjiang Agricultural University, Ürümqi 830052, China; (J.M.); (K.C.); (C.C.B.)
- Key Laboratory of Ministry of Education for Western Arid Region Grassland Resources and Ecology, College of Grassland Sciences, Xinjiang Agricultural University, Ürümqi 830052, China
| |
Collapse
|
6
|
He J, Alonge M, Ramakrishnan S, Benoit M, Soyk S, Reem NT, Hendelman A, Van Eck J, Schatz MC, Lippman ZB. Establishing Physalis as a Solanaceae model system enables genetic reevaluation of the inflated calyx syndrome. THE PLANT CELL 2023; 35:351-368. [PMID: 36268892 PMCID: PMC9806562 DOI: 10.1093/plcell/koac305] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 09/22/2022] [Indexed: 06/16/2023]
Abstract
The highly diverse Solanaceae family contains several widely studied models and crop species. Fully exploring, appreciating, and exploiting this diversity requires additional model systems. Particularly promising are orphan fruit crops in the genus Physalis, which occupy a key evolutionary position in the Solanaceae and capture understudied variation in traits such as inflorescence complexity, fruit ripening and metabolites, disease and insect resistance, self-compatibility, and most notable, the striking inflated calyx syndrome (ICS), an evolutionary novelty found across angiosperms where sepals grow exceptionally large to encapsulate fruits in a protective husk. We recently developed transformation and genome editing in Physalis grisea (groundcherry). However, to systematically explore and unlock the potential of this and related Physalis as genetic systems, high-quality genome assemblies are needed. Here, we present chromosome-scale references for P. grisea and its close relative Physalis pruinosa and use these resources to study natural and engineered variations in floral traits. We first rapidly identified a natural structural variant in a bHLH gene that causes petal color variation. Further, and against expectations, we found that CRISPR-Cas9-targeted mutagenesis of 11 MADS-box genes, including purported essential regulators of ICS, had no effect on inflation. In a forward genetics screen, we identified huskless, which lacks ICS due to mutation of an AP2-like gene that causes sepals and petals to merge into a single whorl of mixed identity. These resources and findings elevate Physalis to a new Solanaceae model system and establish a paradigm in the search for factors driving ICS.
Collapse
Affiliation(s)
- Jia He
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | | | - Srividya Ramakrishnan
- Department of Computer Science, Johns Hopkins University, Baltimore, Maryland 21218, USA
| | | | | | | | - Anat Hendelman
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Joyce Van Eck
- Boyce Thompson Institute, Ithaca, New York 14853, USA
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, New York 14853, USA
| | - Michael C Schatz
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
- Department of Computer Science, Johns Hopkins University, Baltimore, Maryland 21218, USA
- Department of Biology, Johns Hopkins University, Baltimore, Maryland 21218, USA
| | | |
Collapse
|
7
|
de Souza AX, Riederer M, Leide J. Multifunctional Contribution of the Inflated Fruiting Calyx: Implication for Cuticular Barrier Profiles of the Solanaceous Genera Physalis, Alkekengi, and Nicandra. FRONTIERS IN PLANT SCIENCE 2022; 13:888930. [PMID: 35874003 PMCID: PMC9298275 DOI: 10.3389/fpls.2022.888930] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 06/10/2022] [Indexed: 06/15/2023]
Abstract
Pivotal barrier properties of the hydrophobic plant cuticle covering aerial plant surfaces depend on its physicochemical composition. Among plant species and organs, compounds of this boundary layer between the plant interior and the environment vary considerably but cuticle-related studies comparing different organs from the same plant species are still scarce. Thus, this study focused on the cuticle profiles of Physalis peruviana, Physalis ixocarpa, Alkekengi officinarum, and Nicandra physalodes species. Inflated fruiting calyces enveloping fruits make Physalis, Alkekengi, and Nicandra highly recognizable genera among the Solanoideae subfamily. Although the inflation of fruiting calyces is well discussed in the literature still little is known about their post-floral functionalities. Cuticular composition, surface structure, and barrier function were examined and compared in fully expanded amphistomatous leaves, ripe astomatous fruits, and fully inflated hypostomatous fruiting calyces. Species- and organ-specific abundances of non-glandular and glandular trichomes revealed high structural diversity, covering not only abaxial and adaxial leaf surfaces but also fruiting calyx surfaces, whereas fruits were glabrous. Cuticular waxes, which limit non-stomatal transpiration, ranged from <1 μg cm-2 on P. peruviana fruiting calyces and N. physalodes fruits to 22 μg cm-2 on P. peruviana fruits. Very-long-chain aliphatic compounds, notably n-alkanes, iso-, and anteiso-branched alkanes, alkanols, alkanoic acids, and alkyl esters, dominated the cuticular wax coverages (≥86%). Diversity of cuticular wax patterns rose from leaves to fruiting calyces and peaked in fruits. The polymeric cutin matrix providing the structural framework for cuticular waxes was determined to range from 81 μg cm-2 for N. physalodes to 571 μg cm-2 for A. officinarum fruits. Cuticular transpiration barriers were highly efficient, with water permeabilities being ≤5 × 10-5 m s-1. Only the cuticular water permeability of N. physalodes fruits was 10 × 10-5 m s-1 leading to their early desiccation and fruits that easily split, whereas P. peruviana, P. ixocarpa, and A. officinarum bore fleshy fruits for extended periods after maturation. Regarding the functional significance, fruiting calyces establish a physicochemical shield that reduces water loss and enables fruit maturation within a protective microclimate, and promotes different seed dispersal strategies among plant species investigated.
Collapse
|
8
|
Lu J, Luo M, Wang L, Li K, Yu Y, Yang W, Gong P, Gao H, Li Q, Zhao J, Wu L, Zhang M, Liu X, Zhang X, Zhang X, Kang J, Yu T, Li Z, Jiao Y, Wang H, He C. The Physalis floridana genome provides insights into the biochemical and morphological evolution of Physalis fruits. HORTICULTURE RESEARCH 2021; 8:244. [PMID: 34795210 PMCID: PMC8602270 DOI: 10.1038/s41438-021-00705-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 09/13/2021] [Accepted: 09/15/2021] [Indexed: 05/04/2023]
Abstract
The fruits of Physalis (Solanaceae) have a unique structure, a lantern-like fruiting calyx known as inflated calyx syndrome (ICS) or the Chinese lantern, and are rich in steroid-related compounds. However, the genetic variations underlying the origin of these characteristic traits and diversity in Physalis remain largely unknown. Here, we present a high-quality chromosome-level reference genome assembly of Physalis floridana (~1.40 Gb in size) with a contig N50 of ~4.87 Mb. Through evolutionary genomics and experimental approaches, we found that the loss of the SEP-like MADS-box gene MBP21 subclade is likely a key mutation that, together with the previously revealed mutation affecting floral MPF2 expression, might have contributed to the origination of ICS in Physaleae, suggesting that the origination of a morphological novelty may have resulted from an evolutionary scenario in which one mutation compensated for another deleterious mutation. Moreover, the significant expansion of squalene epoxidase genes is potentially associated with the natural variation of steroid-related compounds in Physalis fruits. The results reveal the importance of gene gains (duplication) and/or subsequent losses as genetic bases of the evolution of distinct fruit traits, and the data serve as a valuable resource for the evolutionary genetics and breeding of solanaceous crops.
Collapse
Affiliation(s)
- Jiangjie Lu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, 100093, Xiangshan, Beijing, China
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Science, Hangzhou Normal University, 310036, Hangzhou, China
| | - Meifang Luo
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, 100093, Xiangshan, Beijing, China
- University of Chinese Academy of Sciences, Yuquan Road 19, 100049, Beijing, China
| | - Li Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, 100093, Xiangshan, Beijing, China
| | - Kunpeng Li
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, 100093, Xiangshan, Beijing, China
- University of Chinese Academy of Sciences, Yuquan Road 19, 100049, Beijing, China
| | - Yongyi Yu
- Annoroad Gene Technology (Beijing) Co, Ltd, 100176, Beijing, China
| | - Weifei Yang
- Annoroad Gene Technology (Beijing) Co, Ltd, 100176, Beijing, China
| | - Pichang Gong
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, 100093, Xiangshan, Beijing, China
| | - Huihui Gao
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, 100093, Xiangshan, Beijing, China
- University of Chinese Academy of Sciences, Yuquan Road 19, 100049, Beijing, China
| | - Qiaoru Li
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, 100093, Xiangshan, Beijing, China
- University of Chinese Academy of Sciences, Yuquan Road 19, 100049, Beijing, China
| | - Jing Zhao
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, 100093, Xiangshan, Beijing, China
- University of Chinese Academy of Sciences, Yuquan Road 19, 100049, Beijing, China
| | - Lanfeng Wu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, 100093, Xiangshan, Beijing, China
- University of Chinese Academy of Sciences, Yuquan Road 19, 100049, Beijing, China
| | - Mingshu Zhang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, 100093, Xiangshan, Beijing, China
- University of Chinese Academy of Sciences, Yuquan Road 19, 100049, Beijing, China
| | - Xueyang Liu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, 100093, Xiangshan, Beijing, China
- University of Chinese Academy of Sciences, Yuquan Road 19, 100049, Beijing, China
| | - Xuemei Zhang
- Annoroad Gene Technology (Beijing) Co, Ltd, 100176, Beijing, China
| | - Xian Zhang
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Science, Hangzhou Normal University, 310036, Hangzhou, China
| | - Jieyu Kang
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Science, Hangzhou Normal University, 310036, Hangzhou, China
| | - Tongyuan Yu
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Science, Hangzhou Normal University, 310036, Hangzhou, China
| | - Zhimin Li
- Annoroad Gene Technology (Beijing) Co, Ltd, 100176, Beijing, China
| | - Yuannian Jiao
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, 100093, Xiangshan, Beijing, China.
- University of Chinese Academy of Sciences, Yuquan Road 19, 100049, Beijing, China.
| | - Huizhong Wang
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Science, Hangzhou Normal University, 310036, Hangzhou, China.
| | - Chaoying He
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, 100093, Xiangshan, Beijing, China.
- University of Chinese Academy of Sciences, Yuquan Road 19, 100049, Beijing, China.
- The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China.
| |
Collapse
|
9
|
Deanna R, Wilf P, Gandolfo MA. New physaloid fruit-fossil species from early Eocene South America. AMERICAN JOURNAL OF BOTANY 2020; 107:1749-1762. [PMID: 33247843 DOI: 10.1002/ajb2.1565] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 08/19/2020] [Indexed: 06/12/2023]
Abstract
PREMISE Solanaceae is a scientifically and economically important angiosperm family with a minimal fossil record and an intriguing early evolutionary history. Here, we report a newly discovered fossil lantern fruit with a suite of features characteristic of Physalideae within Solanaceae. The fossil comes from the early Eocene Laguna del Hunco site (ca. 52 Ma) in Chubut, Argentina, which previously yielded the only other physaloid fruit fossil, Physalis infinemundi. METHODS The fruit morphology and calyx venation pattern of the new fossil were compared with P. infinemundi and extant species of Solanaceae. RESULTS Physalis hunickenii sp. nov. is clearly distinct from P. infinemundi in its fruiting calyx with wider primary veins, longer and thinner lobes, and especially in its venation pattern with high density, transverse tertiary veins; these features support its placement in a new species. In comparison with extant physaloid genera, the calyx venation pattern and other diagnostic traits reinforce placement of the new fossil, like P. infinemundi, within the tribe Physalideae of Solanaceae. CONCLUSIONS Both species of fossil nightshades from Laguna del Hunco represent crown-group Solanaceae but are older than all prior age estimates of the family. Although at least 20 transoceanic dispersals have been proposed as the driver of range expansion of Solanaceae, the Patagonian fossils push back the diversification of the family to Gondwanan times. Thus, overland dispersal across Gondwana is now a likely scenario for at least some biogeographic patterns, in light of the ancient trans-Antarctic land connections between South America and Australia.
Collapse
Affiliation(s)
- Rocío Deanna
- Instituto Multidisciplinario de Biología Vegetal, IMBIV (CONICET-UNC), CC 495, Córdoba, 5000, Argentina
- Departamento de Ciencias Farmacéuticas, Facultad de Ciencias Químicas (FCQ, UNC), Medina Allende s.n., Córdoba, 5000, Argentina
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado, 80305, USA
| | - Peter Wilf
- Department of Geosciences and Earth and Environmental Systems Institute, Pennsylvania State University, University Park, Pennsylvania, 16802, USA
| | - Maria A Gandolfo
- L.H. Bailey Hortorium, Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, New York, 14853, USA
| |
Collapse
|
10
|
Enciso-Rodríguez FE, Osorio-Guarín JA, Garzón-Martínez GA, Delgadillo-Duran P, Barrero LS. Optimization of the genotyping-by-sequencing SNP calling for diversity analysis in cape gooseberry (Physalis peruviana L.) and related taxa. PLoS One 2020; 15:e0238383. [PMID: 32845934 PMCID: PMC7449456 DOI: 10.1371/journal.pone.0238383] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 08/14/2020] [Indexed: 12/03/2022] Open
Abstract
A robust Genotyping-By-Sequencing (GBS) pipeline platform was examined to provide accurate discovery of Single Nucleotide Polymorphisms (SNPs) in a cape gooseberry (Physalis peruviana L.) and related taxa germplasm collection. A total of 176 accessions representing, wild, weedy, and commercial cultivars as well as related taxa from the Colombian germplasm bank and other world repositories were screened using GBS. The pipeline parameters mnLCov of 0.5 and a mnScov of 0.7, tomato and potato genomes, and cape gooseberry transcriptome for read alignments, were selected to better assess diversity and population structure in cape gooseberry and related taxa. A total of 7,425 SNPs, derived from P. peruviana common tags (unique 64 bp sequences shared between selected species), were used. Within P. peruviana, five subpopulations with a high genetic diversity and allele fixation (HE: 0.35 to 0.36 and FIS: -0.11 to -0.01, respectively) were detected. Conversely, low genetic differentiation (FST: 0.01 to 0.05) was also observed, indicating a high gene flow among subpopulations. These results contribute to the establishment of adequate conservation and breeding strategies for Cape gooseberry and closely related Physalis species.
Collapse
Affiliation(s)
- Felix E. Enciso-Rodríguez
- Centro de Investigación Tibaitatá, Corporación Colombiana de Investigación Agropecuaria–Agrosavia, Mosquera, Cundinamarca, Colombia
| | - Jaime A. Osorio-Guarín
- Centro de Investigación Tibaitatá, Corporación Colombiana de Investigación Agropecuaria–Agrosavia, Mosquera, Cundinamarca, Colombia
| | - Gina A. Garzón-Martínez
- Centro de Investigación Tibaitatá, Corporación Colombiana de Investigación Agropecuaria–Agrosavia, Mosquera, Cundinamarca, Colombia
| | - Paola Delgadillo-Duran
- Centro de Investigación Tibaitatá, Corporación Colombiana de Investigación Agropecuaria–Agrosavia, Mosquera, Cundinamarca, Colombia
| | - Luz Stella Barrero
- Centro de Investigación Tibaitatá, Corporación Colombiana de Investigación Agropecuaria–Agrosavia, Mosquera, Cundinamarca, Colombia
- * E-mail:
| |
Collapse
|
11
|
Guo ZH, Ma PF, Yang GQ, Hu JY, Liu YL, Xia EH, Zhong MC, Zhao L, Sun GL, Xu YX, Zhao YJ, Zhang YC, Zhang YX, Zhang XM, Zhou MY, Guo Y, Guo C, Liu JX, Ye XY, Chen YM, Yang Y, Han B, Lin CS, Lu Y, Li DZ. Genome Sequences Provide Insights into the Reticulate Origin and Unique Traits of Woody Bamboos. MOLECULAR PLANT 2019; 12:1353-1365. [PMID: 31145999 DOI: 10.1016/j.molp.2019.05.009] [Citation(s) in RCA: 81] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2019] [Revised: 05/01/2019] [Accepted: 05/20/2019] [Indexed: 05/15/2023]
Abstract
Polyploidization is a major driver of speciation and its importance to plant evolution has been well recognized. Bamboos comprise one diploid herbaceous and three polyploid woody lineages, and are members of the only major subfamily in grasses that diversified in forests, with the woody members having a tree-like lignified culm. In this study, we generated four draft genome assemblies of major bamboo lineages with three different ploidy levels (diploid, tetraploid, and hexaploid). We also constructed a high-density genetic linkage map for a hexaploid species of bamboo, and used a linkage-map-based strategy for genome assembly and identification of subgenomes in polyploids. Further phylogenomic analyses using a large dataset of syntenic genes with expected copies based on ploidy levels revealed that woody bamboos originated subsequent to the divergence of the herbaceous bamboo lineage, and experienced complex reticulate evolution through three independent allopolyploid events involving four extinct diploid ancestors. A shared but distinct subgenome was identified in all polyploid forms, and the progenitor of this subgenome could have been critical in ancient polyploidizations and the origin of woody bamboos. Important genetic clues to the unique flowering behavior and woody trait in bamboos were also found. Taken together, our study provides significant insights into ancient reticulate evolution at the subgenome level in the absence of extant donor species, and offers a potential model scenario for broad-scale study of angiosperm origination by allopolyploidization.
Collapse
Affiliation(s)
- Zhen-Hua Guo
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Peng-Fei Ma
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Guo-Qian Yang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Jin-Yong Hu
- Key Laboratory for Plant Diversity and Biogeography in East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Yun-Long Liu
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - En-Hua Xia
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Mi-Cai Zhong
- Key Laboratory for Plant Diversity and Biogeography in East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Lei Zhao
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Gui-Ling Sun
- Institute of Plant Stress Biology, State Key Laboratory of Cotton Biology, Department of Biology, Henan University, Kaifeng, Henan 475001, China
| | - Yu-Xing Xu
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - You-Jie Zhao
- College of Big Data and Intelligent Engineering, Southwest Forestry University, Kunming, Yunnan 650224, China
| | - Yi-Chi Zhang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Yu-Xiao Zhang
- Yunnan Academy of Biodiversity, Southwest Forestry University, Kunming, Yunnan 650224, China
| | - Xue-Mei Zhang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Meng-Yuan Zhou
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Ying Guo
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Cen Guo
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Jing-Xia Liu
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Xia-Ying Ye
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Yun-Mei Chen
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Yang Yang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Bin Han
- National Center for Gene Research, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Choun-Sea Lin
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei.
| | - Ying Lu
- College of Fisheries and Life Science, Shanghai Ocean University, Shanghai 201306, China.
| | - De-Zhu Li
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China.
| |
Collapse
|
12
|
Deanna R, Larter MD, Barboza GE, Smith SD. Repeated evolution of a morphological novelty: a phylogenetic analysis of the inflated fruiting calyx in the Physalideae tribe (Solanaceae). AMERICAN JOURNAL OF BOTANY 2019; 106:270-279. [PMID: 30779447 DOI: 10.1002/ajb2.1242] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Accepted: 11/27/2018] [Indexed: 06/09/2023]
Abstract
PREMISE OF THE STUDY The evolution of novel fruit morphologies has been integral to the success of angiosperms. The inflated fruiting calyx, in which the balloon-like calyx swells to completely surround the fruit, has evolved repeatedly across angiosperms and is postulated to aid in protection and dispersal. We investigated the evolution of this trait in the tomatillos and their allies (Physalideae, Solanaceae). METHODS The Physalideae phylogeny was estimated using four regions (ITS, LEAFY, trnL-F, waxy) with maximum likelihood (ML) and Bayesian inference. Under the best-fitting ML model of trait evolution, we estimated ancestral states along with the numbers of gains and losses of fruiting calyx accrescence and inflation with Bayesian stochastic mapping. Also, phylogenetic signal in calyx morphology was examined with two metrics (parsimony score and Fritz and Purvis's D). KEY RESULTS Based on our well-resolved and densely sampled phylogeny, we infer that calyx evolution has proceeded in a stepwise and directional fashion, from non-accrescent to accrescent to inflated. In total, we inferred 24 gains of accrescence, 24 subsequent transitions to a fully inflated calyx, and only two reversals. Despite this lability, fruiting calyx accrescence and inflation showed strong phylogenetic signal. CONCLUSIONS Our phylogeny greatly improves the resolution of Physalideae and highlights the need for taxonomic work. The comparative analyses reveal that the inflated fruiting calyx has evolved many times and that the trajectory toward this phenotype is generally stepwise and irreversible. These results provide a strong foundation for studying the genetic and developmental mechanisms responsible for the repeated origins of this charismatic fruit trait.
Collapse
Affiliation(s)
- Rocío Deanna
- Instituto Multidisciplinario de Biología Vegetal, IMBIV (CONICET-UNC), CC 495, Córdoba, 5000, Argentina
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado, 80305, USA
- Departamento de Ciencias Farmacéuticas, Facultad de Ciencias Químicas (FCQ, UNC), Medina Allende s.n., Córdoba, 5000, Argentina
| | - Maximilian D Larter
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado, 80305, USA
| | - Gloria E Barboza
- Instituto Multidisciplinario de Biología Vegetal, IMBIV (CONICET-UNC), CC 495, Córdoba, 5000, Argentina
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado, 80305, USA
- Departamento de Ciencias Farmacéuticas, Facultad de Ciencias Químicas (FCQ, UNC), Medina Allende s.n., Córdoba, 5000, Argentina
| | - Stacey D Smith
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado, 80305, USA
| |
Collapse
|
13
|
Chinese lantern in Physalis is an advantageous morphological novelty and improves plant fitness. Sci Rep 2019; 9:596. [PMID: 30679462 PMCID: PMC6345875 DOI: 10.1038/s41598-018-36436-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Accepted: 11/22/2018] [Indexed: 01/04/2023] Open
Abstract
The origin of morphological novelties is an important but neglected issue of evolutionary biology. The fruit of the genus Physalis, a berry, is encapsulated by a novel morphological feature of the post-floral, accrescent calyx that is referred to as a Chinese lantern. The evolutionary developmental genetics of the Chinese lantern have been investigated in the last decade; however, the selective values of the morphological novelty remain elusive. Here, we measured the photosynthetic parameters of the fruiting calyces, monitored microclimatic variation within the Chinese lanterns during fruit development, performed floral-calyx-removal experiments, and recorded the fitness-related traits in Physalis floridana. Ultimately, we show that the green-fruiting calyx of Physalis has photosynthetic capabilities, thus serving as an energy source for fruit development. Moreover, the developing Chinese lantern provides a microclimate that benefits the development and maturation of berry and seed, and it improves plant fitness in terms of fruit/seed weight and number, and fruit maturation under low-temperature environments. Furthermore, the lantern structure facilitates the dispersal of fruits and seeds by water and wind. Our results suggest that the Chinese lantern morphology of Physalis is an evolutionary adaptive trait and improves plant fitness, thus providing new insight into the origin of morphological novelties.
Collapse
|
14
|
Wang P, Moore BM, Panchy NL, Meng F, Lehti-Shiu MD, Shiu SH. Factors Influencing Gene Family Size Variation Among Related Species in a Plant Family, Solanaceae. Genome Biol Evol 2018; 10:2596-2613. [PMID: 30239695 PMCID: PMC6171734 DOI: 10.1093/gbe/evy193] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/29/2018] [Indexed: 12/13/2022] Open
Abstract
Gene duplication and loss contribute to gene content differences as well as phenotypic divergence across species. However, the extent to which gene content varies among closely related plant species and the factors responsible for such variation remain unclear. Here, using the Solanaceae family as a model and Pfam domain families as a proxy for gene families, we investigated variation in gene family sizes across species and the likely factors contributing to the variation. We found that genes in highly variable families have high turnover rates and tend to be involved in processes that have diverged between Solanaceae species, whereas genes in low-variability families tend to have housekeeping roles. In addition, genes in high- and low-variability gene families tend to be duplicated by tandem and whole genome duplication, respectively. This finding together with the observation that genes duplicated by different mechanisms experience different selection pressures suggest that duplication mechanism impacts gene family turnover. We explored using pseudogene number as a proxy for gene loss but discovered that a substantial number of pseudogenes are actually products of pseudogene duplication, contrary to the expectation that most plant pseudogenes are remnants of once-functional duplicates. Our findings reveal complex relationships between variation in gene family size, gene functions, duplication mechanism, and evolutionary rate. The patterns of lineage-specific gene family expansion within the Solanaceae provide the foundation for a better understanding of the genetic basis underlying phenotypic diversity in this economically important family.
Collapse
Affiliation(s)
- Peipei Wang
- Department of Plant Biology, Michigan State University
| | - Bethany M Moore
- Department of Plant Biology, Michigan State University.,Ecology, Evolutionary Biology, and Behavior Program, Michigan State University
| | - Nicholas L Panchy
- National Institute for Mathematical and Biological Synthesis, University of Tennessee
| | - Fanrui Meng
- Department of Plant Biology, Michigan State University
| | | | - Shin-Han Shiu
- Department of Plant Biology, Michigan State University.,Ecology, Evolutionary Biology, and Behavior Program, Michigan State University.,Department of Computational Mathematics, Science, and Engineering, Michigan State University
| |
Collapse
|
15
|
Abstract
The angiosperm flower develops through a modular programme which, although ancient and conserved, provides the flexibility that has allowed an almost infinite variety of floral forms to emerge. In this review, we explore the evolution of floral diversity, focusing on our recent understanding of the mechanistic basis of evolutionary change. We discuss the various ways in which flower size and floral organ size can be modified, the means by which flower shape and symmetry can change, and the ways in which floral organ position can be varied. We conclude that many challenges remain before we fully understand the ecological and molecular processes that facilitate the diversification of flower structure.
Collapse
|
16
|
Phylogenetic relationships of Deprea: New insights into the evolutionary history of physaloid groups. Mol Phylogenet Evol 2017; 119:71-80. [PMID: 29108936 DOI: 10.1016/j.ympev.2017.11.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 10/31/2017] [Accepted: 11/01/2017] [Indexed: 01/29/2023]
Abstract
Deprea is the genus with the second highest species richness in tribe Physalideae (Solanaceae) and comprises 50 species that are mainly distributed in the Andes of South America. The taxonomy of Deprea has been unstable after controversial hypotheses about its position and circumscription. Additionally, biogeographical inferences are only based on observations of the restricted area of distribution of some species and no ancestral area estimation have been performed. Here, we present a phylogenetic analysis and an ancestral area reconstruction of Deprea in order to establish its circumscription, resolve its position within Physalideae, and reconstruct its biogeographical history. Phylogenetic analyses were conducted using Maximum Likelihood and Bayesian approaches. Forty-three Deprea species and 26 related taxa were sampled for three DNA markers (psbA-trnH, ITS, and waxy). A Bayesian binary MCMC model was applied in order to infer ancestral areas. Deprea is resolved as a strongly supported monophyletic group according to its current circumscription and is placed within subtribe Withaninae of Physalideae. The phylogenetic relationships enabled us to solve taxonomic problems including the rejection and acceptance of previous synonyms. The most probable ancestral area for Deprea is the Northern Andes of South America and the Amotape-Huancabamba zone. Our phylogeny provides increased resolution and support for the current position and circumscription of Deprea. Better resolution of interspecific relationships was also obtained, although some affinities remain unclear. The phylogenetic and ancestral area reconstructions provide a framework for addressing taxonomic problems and investigating new evolutionary questions.
Collapse
|
17
|
Wilf P, Carvalho MR, Gandolfo MA, Cúneo NR. Eocene lantern fruits from Gondwanan Patagonia and the early origins of Solanaceae. Science 2017; 355:71-75. [PMID: 28059765 DOI: 10.1126/science.aag2737] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Revised: 10/15/2016] [Accepted: 11/18/2016] [Indexed: 11/02/2022]
Abstract
The nightshade family Solanaceae holds exceptional economic and cultural importance. The early diversification of Solanaceae is thought to have occurred in South America during its separation from Gondwana, but the family's sparse fossil record provides few insights. We report 52.2-million-year-old lantern fruits from terminal-Gondwanan Patagonia, featuring highly inflated, five-lobed calyces, as a newly identified species of the derived, diverse New World genus Physalis (e.g., groundcherries and tomatillos). The fossils are considerably older than corresponding molecular divergence dates and demonstrate an ancient history for the inflated calyx syndrome. The derived position of these early Eocene fossils shows that Solanaceae were well diversified long before final Gondwanan breakup.
Collapse
Affiliation(s)
- Peter Wilf
- Department of Geosciences, Pennsylvania State University, University Park, PA 16802, USA.
| | - Mónica R Carvalho
- L. H. Bailey Hortorium, Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
| | - María A Gandolfo
- L. H. Bailey Hortorium, Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
| | - N Rubén Cúneo
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Museo Paleontológico Egidio Feruglio, 9100 Trelew, Chubut, Argentina
| |
Collapse
|
18
|
Lisa De-Silva D, Mota LL, Chazot N, Mallarino R, Silva-Brandão KL, Piñerez LMG, Freitas AV, Lamas G, Joron M, Mallet J, Giraldo CE, Uribe S, Särkinen T, Knapp S, Jiggins CD, Willmott KR, Elias M. North Andean origin and diversification of the largest ithomiine butterfly genus. Sci Rep 2017; 7:45966. [PMID: 28387233 PMCID: PMC5384087 DOI: 10.1038/srep45966] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Accepted: 02/22/2017] [Indexed: 01/01/2023] Open
Abstract
The Neotropics harbour the most diverse flora and fauna on Earth. The Andes are a major centre of diversification and source of diversity for adjacent areas in plants and vertebrates, but studies on insects remain scarce, even though they constitute the largest fraction of terrestrial biodiversity. Here, we combine molecular and morphological characters to generate a dated phylogeny of the butterfly genus Pteronymia (Nymphalidae: Danainae), which we use to infer spatial, elevational and temporal diversification patterns. We first propose six taxonomic changes that raise the generic species total to 53, making Pteronymia the most diverse genus of the tribe Ithomiini. Our biogeographic reconstruction shows that Pteronymia originated in the Northern Andes, where it diversified extensively. Some lineages colonized lowlands and adjacent montane areas, but diversification in those areas remained scarce. The recent colonization of lowland areas was reflected by an increase in the rate of evolution of species' elevational ranges towards present. By contrast, speciation rate decelerated with time, with no extinction. The geological history of the Andes and adjacent regions have likely contributed to Pteronymia diversification by providing compartmentalized habitats and an array of biotic and abiotic conditions, and by limiting dispersal between some areas while promoting interchange across others.
Collapse
Affiliation(s)
- Donna Lisa De-Silva
- Institut de Systématique, Évolution, Biodiversité, ISYEB - UMR 7205–CNRS MNHN UPMC EPHE, Muséum National d’Histoire Naturelle, Sorbonne Universités, 57 rue Cuvier CP50 F-75005, Paris, France
| | - Luísa L. Mota
- Departamento de Zoologia and Museu de Zoologia, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, São Paulo, Brazil
| | - Nicolas Chazot
- Institut de Systématique, Évolution, Biodiversité, ISYEB - UMR 7205–CNRS MNHN UPMC EPHE, Muséum National d’Histoire Naturelle, Sorbonne Universités, 57 rue Cuvier CP50 F-75005, Paris, France
- Department of Biology, Lunds Universitet, Lund, Sweden
| | - Ricardo Mallarino
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Karina L. Silva-Brandão
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Campinas, São Paulo, Brazil
| | - Luz Miryam Gómez Piñerez
- Universidad Nacional de Colombia, sede Medellín, Medellín, Colombia
- Grupo de investigación Ciencias Forenses y Salud, Tecnológico de Antioquia, Medellin, Colombia
| | - André V.L. Freitas
- Departamento de Zoologia and Museu de Zoologia, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, São Paulo, Brazil
| | - Gerardo Lamas
- Museo de Historia Natural, Universidad Nacional Mayor de San Marcos, Lima, Peru
| | - Mathieu Joron
- Centre d’Ecologie Fonctionnelle et Evolutive, CEFE, UMR 5175 CNRS - EPHE - Université de Montpellier - Université Paul Valéry Montpellier, 34293 Montpellier 5, France
| | - James Mallet
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Carlos E. Giraldo
- Universidad Nacional de Colombia, sede Medellín, Medellín, Colombia
- Grupo de Investigación de Sanidad Vegetal, Universidad Católica de Oriente, Rionegro, Antioquia, Colombia
| | - Sandra Uribe
- Universidad Nacional de Colombia, sede Medellín, Medellín, Colombia
| | - Tiina Särkinen
- Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh EH3 5LR, UK
| | - Sandra Knapp
- Department of Life Sciences, Natural History Museum, Cromwell Road, London SW7 5BD, UK
| | - Chris D. Jiggins
- Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK
| | - Keith R. Willmott
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, Florida 32611, USA
| | - Marianne Elias
- Institut de Systématique, Évolution, Biodiversité, ISYEB - UMR 7205–CNRS MNHN UPMC EPHE, Muséum National d’Histoire Naturelle, Sorbonne Universités, 57 rue Cuvier CP50 F-75005, Paris, France
| |
Collapse
|
19
|
Zamora-Tavares MDP, Martínez M, Magallón S, Guzmán-Dávalos L, Vargas-Ponce O. Physalis and physaloids: A recent and complex evolutionary history. Mol Phylogenet Evol 2016; 100:41-50. [DOI: 10.1016/j.ympev.2016.03.032] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2015] [Revised: 03/23/2016] [Accepted: 03/31/2016] [Indexed: 10/22/2022]
|
20
|
Wang L, Li J, Zhao J, He C. Evolutionary developmental genetics of fruit morphological variation within the Solanaceae. FRONTIERS IN PLANT SCIENCE 2015; 6:248. [PMID: 25918515 PMCID: PMC4394660 DOI: 10.3389/fpls.2015.00248] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Accepted: 03/27/2015] [Indexed: 05/20/2023]
Abstract
Morphological variations of fruits such as shape and size, and color are a result of adaptive evolution. The evolution of morphological novelties is particularly intriguing. An understanding of these evolutionary processes calls for the elucidation of the developmental and genetic mechanisms that result in particular fruit morphological characteristics, which determine seed dispersal. The genetic and developmental basis for fruit morphological variation was established at a microevolutionary time scale. Here, we summarize the progress on the evolutionary developmental genetics of fruit size, shape and color in the Solanaceae. Studies suggest that the recruitment of a pre-existing gene and subsequent modification of its interaction and regulatory networks are frequently involved in the evolution of morphological diversity. The basic mechanisms underlying changes in plant morphology are alterations in gene expression and/or gene function. We also deliberate on the future direction in evolutionary developmental genetics of fruit morphological variation such as fruit type. These studies will provide insights into plant developmental processes and will help to improve the productivity and fruit quality of crops.
Collapse
Affiliation(s)
- Li Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany – Chinese Academy of Sciences, BeijingChina
| | - Jing Li
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany – Chinese Academy of Sciences, BeijingChina
- Graduate University of Chinese Academy of Sciences, BeijingChina
| | - Jing Zhao
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany – Chinese Academy of Sciences, BeijingChina
- Graduate University of Chinese Academy of Sciences, BeijingChina
| | - Chaoying He
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany – Chinese Academy of Sciences, BeijingChina
- *Correspondence: Chaoying He, State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany – Chinese Academy of Sciences, Nanxincun 20, Xiangshan, 100093 Beijing, China
| |
Collapse
|
21
|
Theißen G. My favourite flowering image: a cob of pod corn. JOURNAL OF EXPERIMENTAL BOTANY 2014; 65:6751-6754. [PMID: 24980907 DOI: 10.1093/jxb/ert461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
For good reasons scientists usually do not report the personal circumstances of their work when publishing their results. This means, however, that the scientific facts being reported may not accurately reflect the personal importance of the respective work for the individual scientists. Pictures of pod corn (or Tunicate maize) have been on my mind for much of my life, through good and through bad times. This is why...
Collapse
Affiliation(s)
- Günter Theißen
- Department of Genetics, Friedrich Schiller University Jena, Philosophenweg 12, D-07743 Jena, Germany
| |
Collapse
|
22
|
Hu JY, Zhou Y, He F, Dong X, Liu LY, Coupland G, Turck F, de Meaux J. miR824-Regulated AGAMOUS-LIKE16 Contributes to Flowering Time Repression in Arabidopsis. THE PLANT CELL 2014; 26:2024-2037. [PMID: 24876250 PMCID: PMC4079366 DOI: 10.1105/tpc.114.124685] [Citation(s) in RCA: 76] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2014] [Revised: 04/22/2014] [Accepted: 05/05/2014] [Indexed: 05/18/2023]
Abstract
The timing of flowering is pivotal for maximizing reproductive success under fluctuating environmental conditions. Flowering time is tightly controlled by complex genetic networks that integrate endogenous and exogenous cues, such as light, temperature, photoperiod, and hormones. Here, we show that AGAMOUS-LIKE16 (AGL16) and its negative regulator microRNA824 (miR824) control flowering time in Arabidopsis thaliana. Knockout of AGL16 effectively accelerates flowering in nonvernalized Col-FRI, in which the floral inhibitor FLOWERING LOCUS C (FLC) is strongly expressed, but shows no effect if plants are vernalized or grown in short days. Alteration of AGL16 expression levels by manipulating miR824 abundance influences the timing of flowering quantitatively, depending on the expression level and number of functional FLC alleles. The effect of AGL16 is fully dependent on the presence of FLOWERING LOCUS T (FT). Further experiments show that AGL16 can interact directly with SHORT VEGETATIVE PHASE and indirectly with FLC, two proteins that form a complex to repress expression of FT. Our data reveal that miR824 and AGL16 modulate the extent of flowering time repression in a long-day photoperiod.
Collapse
Affiliation(s)
- Jin-Yong Hu
- Department of Plant Breeding and Genetics, Max-Planck-Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Yue Zhou
- Department of Plant Development, Max-Planck-Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Fei He
- Molecular Evolutionary Biology, Institute for Evolution and Biodiversity, Westfalische Wilhelms-Universitat, 48149 Munster, Germany
| | - Xue Dong
- Department of Plant Development, Max-Planck-Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Liang-Yu Liu
- Department of Plant Development, Max-Planck-Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - George Coupland
- Department of Plant Development, Max-Planck-Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Franziska Turck
- Department of Plant Development, Max-Planck-Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Juliette de Meaux
- Molecular Evolutionary Biology, Institute for Evolution and Biodiversity, Westfalische Wilhelms-Universitat, 48149 Munster, Germany
| |
Collapse
|
23
|
Zhang JS, Zhao J, Zhang S, He C. Efficient gene silencing mediated by tobacco rattle virus in an emerging model plant physalis. PLoS One 2014; 9:e85534. [PMID: 24454885 PMCID: PMC3891815 DOI: 10.1371/journal.pone.0085534] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2013] [Accepted: 11/28/2013] [Indexed: 12/30/2022] Open
Abstract
The fruit of Physalis has a berry and a novelty called inflated calyx syndrome (ICS, also named the 'Chinese lantern'). Elucidation of the underlying developmental mechanisms of fruit diversity demands an efficient gene functional inference platform. Here, we tested the application of the tobacco rattle virus (TRV)-mediated gene-silencing system in Physalis floridana. First, we characterized the putative gene of a phytoene desaturase in P. floridana (PfPDS). Infecting the leaves of the Physalis seedlings with the PfPDS-TRV vector resulted in a bleached plant, including the developing leaves, floral organs, ICS, berry, and seed. These results indicated that a local VIGS treatment can efficiently induce a systemic mutated phenotype. qRT-PCR analyses revealed that the bleaching extent correlated to the mRNA reduction of the endogenous PfPDS. Detailed comparisons of multiple infiltration and growth protocols allowed us to determine the optimal methodologies for VIGS manipulation in Physalis. We subsequently utilized this optimized VIGS methodology to downregulate the expression of two MADS-box genes, MPF2 and MPF3, and compared the resulting effects with gene-downregulation mediated by RNA interference (RNAi) methods. The VIGS-mediated gene knockdown plants were found to resemble the mutated phenotypes of floral calyx, fruiting calyx and pollen maturation of the RNAi transgenic plants for both MPF2 and MPF3. Moreover, the two MADS-box genes were appeared to have a novel role in the pedicel development in P. floridana. The major advantage of VIGS-based gene knockdown lies in practical aspects of saving time and easy manipulation as compared to the RNAi. Despite the lack of heritability and mosaic mutation phenotypes observed in some organs, the TRV-mediated gene silencing system provides an alternative efficient way to infer gene function in various developmental processes in Physalis, thus facilitating understanding of the genetic basis of the evolution and development of the morphological diversities within the Solanaceae.
Collapse
Affiliation(s)
- Ji-Si Zhang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jing Zhao
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Shaohua Zhang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Chaoying He
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- * E-mail:
| |
Collapse
|
24
|
Khan MR, Ali GM. Functional evolution of cis-regulatory modules of STMADS11 superclade MADS-box genes. PLANT MOLECULAR BIOLOGY 2013; 83:489-506. [PMID: 23860795 DOI: 10.1007/s11103-013-0105-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2012] [Accepted: 07/03/2013] [Indexed: 06/02/2023]
Abstract
Evolution of phenotypic morphologies is closely associated with modular organization of cis-regulatory elements underlying expression divergence. The MADS-box gene family is the subject of extensive studies that try to unscramble the structural complexity of flowering plants. This study is envisaged to explore the potential of CRMs in highly constrained non-coding elements of STMADS11superclade MADS-box genes in expression divergence. Phylogenetic reconstruction differentiated the STMADS11 genes into SVP-like, ZMM19-like, MPF1-like and MPF2-like clades. Differential gene expression in vegetative and floral organs was evident within the clades as well as at inter-clade level. The genomic DNA search for clusters of short motifs and sequence conservation of the -2 kb promoter region of particularly, MPF2-like clade permitted to establish three well defined CRMs where transcription factors bind, being CRM1 the activator, CRM2 the repressor, and CRM3 the enhancer element. Similar clusters were also mapped in the large 1st introns in the coding region. Within these CRMs many transcription factor-binding sites, particularly the hotspots for MADS-domain TF binding elements--CArG-boxes, directing sepal specific expression in Arabidopsis--were accrued in the CRM1 of MPF2-like promoters. Site-directed mutagenesis and motif swapping through reporter assays allude towards their implication as functionally active elements. In terms of directional evolution of MPF2-like promoters, CRMs are significantly more conserved than flanking regions, hence, bearing the signatures for purifying selection. Thus, CRMs are the pervasive feature of STMADS11 genes and mutations and/or appearance of new transcription factor binding sites and position of the CRMs are responsible for the divergence in expression patterns in this clade. These results have implications in understanding functional evolution of cis-regulatory modules in plants.
Collapse
Affiliation(s)
- Muhammad Ramzan Khan
- National Institute for Genomics and Advanced Biotechnology (NIGAB), National Agricultural Research Centre, Park Road, Islamabad, Pakistan,
| | | |
Collapse
|
25
|
Khan MR, Khan IU, Ali GM. MPF2-like MADS-box genes affecting expression of SOC1 and MAF1 are recruited to control flowering time. Mol Biotechnol 2013; 54:25-36. [PMID: 22539207 DOI: 10.1007/s12033-012-9540-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
A complex and intricate network of genes responding to various developmental and environmental signals control floral transition in plants. MADS-box genes are the key regulators and major contributors with regard to flowering time determination. Previously, MPF2-like genes belonging to the STMADS11 superclade were duplicated into MPF2-like-A and MPF2-like-B in Withania (WSA206 and WSB206) and Tubocapsicum (TAB 201). The present study was conducted to determine the effect of MPF2-like genes on flowering time by analyzing 35S:MPF2-like transgenic Arabidopsis plants as well as to probe their effects on the expression of SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1 (SOC1, a floral promoter) and MADS AFFECTING FLOWERING 1 (MAF1, a floral repressor) genes. The overexpression of WSA206 (35S:MPF2-like-A) moderately promoted flowering, while that of WSB206 and TAB 201 (35S:MPF2-like-B) exhibited no effects on floral transition. Concomitantly, an elevation in SOC1 transcript abundance and a reduction for MAF1 transcript levels were observed in 35S:WSA206 transgenic plants. Nucleotide diversity analysis indicated an extraordinary 8 aa extension at the C-terminus of the WSA206 protein. Ectopic expression of a truncated WSA206-version without these 8 aa (WSA206ΔC246) and of MPF2-like-B-versions elongated by these 8 aa (WSB206∇C257 and TAB 201∇C257) in Arabidopsis revealed an ambiguous role of the 8 aa signature in floral transition. It may influence a protein's ability to modulate flowering time but is neither sufficient nor strictly necessary for early flowering. Nevertheless, the 8 aa extension influences the expression of SOC1 and MAF1 in MPF2-like derivative constructs. Our studies provide insight into the role of MPF2-like genes in phase transition by interacting with SOC1 and MAF1 genes, thereby also pointing to their significance as potential candidates for modifying flowering in crop plants in the future.
Collapse
Affiliation(s)
- Muhammad Ramzan Khan
- National Institute for Genomics and Advanced Biotechnology, National Agricultural Research Center, Park Road, Islamabad, Pakistan.
| | | | | |
Collapse
|
26
|
Plastid trnF pseudogenes are present in Jaltomata, the sister genus of Solanum (Solanaceae): molecular evolution of tandemly repeated structural mutations. Gene 2013; 530:143-50. [PMID: 23962687 DOI: 10.1016/j.gene.2013.08.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2013] [Revised: 08/05/2013] [Accepted: 08/06/2013] [Indexed: 11/24/2022]
Abstract
Extensive gene duplication arranged in a tandem array is rare in the plastome of embryophytes. Interestingly, we found pseudogene copies of the trnF gene in the genus Jaltomata, the sister genus of Solanum where such gene duplication has been previously reported. In each Jaltomata sequence available we found two pseudogene copies in close 5'-proximity to the original functional gene. The size of each pseudogene copy ranged between 17 and 48 bp and the anticodon domain was identified as the most conserved element. A common ATT(G)n motif is particularly interesting and its modifications were found to border the 3' of the duplicated regions. Other motifs were partial residues, or entire parts of the T- and D-domains, and both domains proved to be variable in length among the pseudogenes identified. The residues of the 3' and 5' acceptor stem were not found among the copies. We further compared the newly discovered copies of Jaltomata with those ones previously described from Solanum and inferred phylogenetic relationships of the copies aligned. The evolution of Solanum copies, in contrast to Jaltomata, is hard to explain as resulting only in parsimonious changes since reticulate evolutionary patterns were detected among the copies. The dynamic evolutionary patterns of Solanum might be explained by possible inter- or intrachromosomal recombination.
Collapse
|
27
|
Zhang J, Khan MR, Tian Y, Li Z, Riss S, He C. Divergences of MPF2-like MADS-domain proteins have an association with the evolution of the inflated calyx syndrome within Solanaceae. PLANTA 2012; 236:1247-1260. [PMID: 22711285 DOI: 10.1007/s00425-012-1684-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2012] [Accepted: 05/31/2012] [Indexed: 06/01/2023]
Abstract
The inflated calyx syndrome (ICS) is a post-floral novelty within Solanaceae. Previous work has shown that MPF2-like MADS-box genes have been recruited for the development and evolution of ICS through heterotopic expression from vegetative to floral organs. ICS seems to be a plesiomorphic trait in Physaleae, but it has been secondarily lost in some lineages during evolution. We hypothesized that molecular and functional divergences of MPF2-like proteins might play a role in the loss of ICS. In this study we analyzed the phylogeny, selection and various functions of MPF2-like proteins with respect to the evolution of ICS. Directional selection of MPF2-like orthologs toward evolution of ICS was detected. While auto-activation capacity between proteins varies in yeast, MPF2-like interaction with floral MADS-domain proteins is robustly detected, hence substantiating their integration into the floral developmental programs. Dimerization with A- (MPF3) and E-function (PFSEP1/3) proteins seems to be essential for ICS development within Solanaceae. Moreover, the occurrence of the enlarged sepals, reminiscent of ICS, and MPF2-like interactions with these specific partners were observed in transgenic Arabidopsis. The interaction spectrum relevant to ICS seems to be plesiomorphic, reinforcing the plesiomorphy of this trait. The inability of some MPF2-like to interact with either the A-function or any of the E-function partners characterized is correlated with the loss of ICS in the lineages that showed a MPF2-like expression in the calyx. Our findings suggest that, after recruitment of MPF2-like genes for floral development, diversification in their coding region due to directional selection leads to a modification of the MADS-domain protein interacting spectrum, which might serve as a constraint for the evolution of ICS within Solanaceae.
Collapse
Affiliation(s)
- Jisi Zhang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Xiangshan, Beijing 100093, China
| | | | | | | | | | | |
Collapse
|
28
|
Khan MR, Hu J, He C. Plant hormones including ethylene are recruited in calyx inflation in Solanaceous plants. JOURNAL OF PLANT PHYSIOLOGY 2012; 169:940-948. [PMID: 22551956 DOI: 10.1016/j.jplph.2012.02.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2011] [Revised: 02/04/2012] [Accepted: 02/07/2012] [Indexed: 05/31/2023]
Abstract
Plant hormones direct many processes of floral and post-floral morphogenesis in Angiosperms. However, their role in shaping floral morphological novelties, such as inflated calyx syndrome (ICS) exhibited by a few genera of the Solanaceae, remains unknown. In Withania and Physalis, sepals resume growth after pollination and encapsulate the mature fruit to form a balloon-like structure, i.e. ICS. The epidermal cells of calyx show enlargement and lobation post-fertilization. Application of hormones to depistillated flower buds of Withania revealed that cytokinins and gibberellins mimic fertilization signals. The ICS development is a synchronous step with fruit development; both processes are under the control of more or less the same set of hormones, including cytokinins and gibberellic acids. Interestingly, inhibition of ethylene in the system is sufficient to yield inflated calyx in Withania. In contrast, Tubocapsicum, a closely related species and an evolutionary natural loss mutant of ICS - showed no response to applied hormones, and ethylene led to inflation of the receptacle indirectly. In addition to hormones, the expression of an MPF2-like MADS-box transcription factor in sepals is essential for ICS formation. Nevertheless, the interactions between MPF2-like genes and hormones are barely detectable at the transcript level. Our data provide insight into the role of hormones in generating floral morphological diversity during evolution.
Collapse
Affiliation(s)
- Muhammad Ramzan Khan
- Department of Molecular Plant Genetics, Max-Planck-Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829 Cologne, Germany.
| | | | | |
Collapse
|
29
|
Garzón-Martínez GA, Zhu ZI, Landsman D, Barrero LS, Mariño-Ramírez L. The Physalis peruviana leaf transcriptome: assembly, annotation and gene model prediction. BMC Genomics 2012; 13:151. [PMID: 22533342 PMCID: PMC3488962 DOI: 10.1186/1471-2164-13-151] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2011] [Accepted: 04/25/2012] [Indexed: 11/16/2022] Open
Abstract
Background Physalis peruviana commonly known as Cape gooseberry is a member of the Solanaceae family that has an increasing popularity due to its nutritional and medicinal values. A broad range of genomic tools is available for other Solanaceae, including tomato and potato. However, limited genomic resources are currently available for Cape gooseberry. Results We report the generation of a total of 652,614 P. peruviana Expressed Sequence Tags (ESTs), using 454 GS FLX Titanium technology. ESTs, with an average length of 371 bp, were obtained from a normalized leaf cDNA library prepared using a Colombian commercial variety. De novo assembling was performed to generate a collection of 24,014 isotigs and 110,921 singletons, with an average length of 1,638 bp and 354 bp, respectively. Functional annotation was performed using NCBI’s BLAST tools and Blast2GO, which identified putative functions for 21,191 assembled sequences, including gene families involved in all the major biological processes and molecular functions as well as defense response and amino acid metabolism pathways. Gene model predictions in P. peruviana were obtained by using the genomes of Solanum lycopersicum (tomato) and Solanum tuberosum (potato). We predict 9,436 P. peruviana sequences with multiple-exon models and conserved intron positions with respect to the potato and tomato genomes. Additionally, to study species diversity we developed 5,971 SSR markers from assembled ESTs. Conclusions We present the first comprehensive analysis of the Physalis peruviana leaf transcriptome, which will provide valuable resources for development of genetic tools in the species. Assembled transcripts with gene models could serve as potential candidates for marker discovery with a variety of applications including: functional diversity, conservation and improvement to increase productivity and fruit quality. P. peruviana was estimated to be phylogenetically branched out before the divergence of five other Solanaceae family members, S. lycopersicum, S. tuberosum, Capsicum spp, S. melongena and Petunia spp.
Collapse
Affiliation(s)
- Gina A Garzón-Martínez
- Plant Molecular Genetics Laboratory, Center of Biotechnology and Bioindustry (CBB), Colombian Corporation for Agricultural Research (CORPOICA), Bogota, Colombia
| | | | | | | | | |
Collapse
|
30
|
Viaene T, Vekemans D, Irish VF, Geeraerts A, Huysmans S, Janssens S, Smets E, Geuten K. Pistillata--duplications as a mode for floral diversification in (Basal) asterids. Mol Biol Evol 2009; 26:2627-45. [PMID: 19679752 DOI: 10.1093/molbev/msp181] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Basal asterid families, and to a lesser extent the asterids as a whole, are characterized by a high variation in petal and stamen morphology. Moreover, the stamen number, the adnation of stamens to petals, and the degree of sympetaly vary considerably among basal asterid taxa. The B group genes, members of the APETALA3 (AP3) and PISTILLATA (PI) gene lineages, have been shown to specify petal and stamen identities in several core eudicot species. Duplicate genes in these lineages have been shown in some cases to have diversified in their function; for instance in Petunia, a PI paralog is required for the fusion of stamens to the corolla tube, illustrating that such genes belonging to this lineage are not just involved in specifying the identity of the stamens and petals but can also specify novel floral morphologies. This motivated us to study the duplication history of class B genes throughout asterid lineages, which comprise approximately one-third of all flowering plants. The evolutionary history of the PI gene subfamily indicates that the two genes in Petunia result from an ancient duplication event, coinciding with the origin of core asterids. A second duplication event occurred before the speciation of basal asterid Ericales families. These and other duplications in the PI lineage are not correlated with duplications in the AP3 lineage. To understand the molecular evolution of the Ericales PI genes after duplication, we have described their expression patterns using reverse transcription polymerase chain reaction and in situ hybridization, reconstructed how selection shaped their protein sequences and tested their protein interaction specificity with other class B proteins. We find that after duplication, PI paralogs have acquired multiple different expression patterns and negative selective pressure on their codons is relaxed, whereas substitutions in sites putatively involved in protein-protein interactions show positive selection, allowing for a change in the interaction behavior of the PI paralogs after duplication. Together, these observations suggest that the asterids have preferentially recruited PI duplicate genes to diverse and potentially novel roles in asterid flower development.
Collapse
Affiliation(s)
- Tom Viaene
- Laboratory of Plant Systematics, Institute of Botany and Microbiology, P.O. Box 2437, Leuven, Belgium.
| | | | | | | | | | | | | | | |
Collapse
|
31
|
Khan MR, Hu JY, Riss S, He C, saedler H. MPF2-Like-A MADS-Box Genes Control the Inflated Calyx Syndrome in Withania (Solanaceae): Roles of Darwinian Selection. Mol Biol Evol 2009; 26:2463-73. [DOI: 10.1093/molbev/msp159] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
|