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Thureborn O, Wikström N, Razafimandimbison SG, Rydin C. Plastid phylogenomics and cytonuclear discordance in Rubioideae, Rubiaceae. PLoS One 2024; 19:e0302365. [PMID: 38768140 PMCID: PMC11104678 DOI: 10.1371/journal.pone.0302365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 04/03/2024] [Indexed: 05/22/2024] Open
Abstract
In this study of evolutionary relationships in the subfamily Rubioideae (Rubiaceae), we take advantage of the off-target proportion of reads generated via previous target capture sequencing projects based on nuclear genomic data to build a plastome phylogeny and investigate cytonuclear discordance. The assembly of off-target reads resulted in a comprehensive plastome dataset and robust inference of phylogenetic relationships, where most intratribal and intertribal relationships are resolved with strong support. While the phylogenetic results were mostly in agreement with previous studies based on plastome data, novel relationships in the plastid perspective were also detected. For example, our analyses of plastome data provide strong support for the SCOUT clade and its sister relationship to the remaining members of the subfamily, which differs from previous results based on plastid data but agrees with recent results based on nuclear genomic data. However, several instances of highly supported cytonuclear discordance were identified across the Rubioideae phylogeny. Coalescent simulation analysis indicates that while ILS could, by itself, explain the majority of the discordant relationships, plastome introgression may be the better explanation in some cases. Our study further indicates that plastomes across the Rubioideae are, with few exceptions, highly conserved and mainly conform to the structure, gene content, and gene order present in the majority of the flowering plants.
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Affiliation(s)
- Olle Thureborn
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
| | - Niklas Wikström
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
- The Bergius Foundation, The Royal Academy of Sciences, Stockholm, Sweden
| | | | - Catarina Rydin
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
- The Bergius Foundation, The Royal Academy of Sciences, Stockholm, Sweden
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Wu H, Li DZ, Ma PF. Unprecedented variation pattern of plastid genomes and the potential role in adaptive evolution in Poales. BMC Biol 2024; 22:97. [PMID: 38679718 PMCID: PMC11057118 DOI: 10.1186/s12915-024-01890-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 04/16/2024] [Indexed: 05/01/2024] Open
Abstract
BACKGROUND The plastid is the photosynthetic organelle in plant cell, and the plastid genomes (plastomes) are generally conserved in evolution. As one of the most economically and ecologically important order of angiosperms, Poales was previously documented to exhibit great plastomic variation as an order of photoautotrophic plants. RESULTS We acquired 93 plastomes, representing all the 16 families and 5 major clades of Poales to reveal the extent of their variation and evolutionary pattern. Extensive variation including the largest one in monocots with 225,293 bp in size, heterogeneous GC content, and a wide variety of gene duplication and loss were revealed. Moreover, rare occurrences of three inverted repeat (IR) copies in angiosperms and one IR loss were observed, accompanied by short IR (sIR) and small direct repeat (DR). Widespread structural heteroplasmy, diversified inversions, and unusual genomic rearrangements all appeared in Poales, occasionally within a single species. Extensive repeats in the plastomes were found to be positively correlated with the observed inversions and rearrangements. The variation all showed a "small-large-moderate" trend along the evolution of Poales, as well as for the sequence substitution rate. Finally, we found some positively selected genes, mainly in C4 lineages, while the closely related lineages of those experiencing gene loss tended to have undergone more relaxed purifying selection. CONCLUSIONS The variation of plastomes in Poales may be related to its successful diversification into diverse habitats and multiple photosynthetic pathway transitions. Our order-scale analyses revealed unusual evolutionary scenarios for plastomes in the photoautotrophic order of Poales and provided new insights into the plastome evolution in angiosperms as a whole.
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Affiliation(s)
- Hong Wu
- Germplasm Bank of Wild Species and Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - De-Zhu Li
- Germplasm Bank of Wild Species and Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Peng-Fei Ma
- Germplasm Bank of Wild Species and Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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Yang Z, Guo Z, Gong C, Xia J, Hu Y, Zhong J, Yang X, Xie W, Wang S, Wu Q, Ye W, Liu B, Zhou X, Turlings TCJ, Zhang Y. Two horizontally acquired bacterial genes steer the exceptionally efficient and flexible nitrogenous waste cycling in whiteflies. SCIENCE ADVANCES 2024; 10:eadi3105. [PMID: 38306427 PMCID: PMC10836729 DOI: 10.1126/sciadv.adi3105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 01/03/2024] [Indexed: 02/04/2024]
Abstract
Nitrogen is an essential element for all life on earth. Nitrogen metabolism, including excretion, is essential for growth, development, and survival of plants and animals alike. Several nitrogen metabolic processes have been described, but the underlying molecular mechanisms are unclear. Here, we reveal a unique process of nitrogen metabolism in the whitefly Bemisia tabaci, a global pest. We show that it has acquired two bacterial uricolytic enzyme genes, B. tabaci urea carboxylase (BtUCA) and B. tabaci allophanate hydrolase (BtAtzF), through horizontal gene transfer. These genes operate in conjunction to not only coordinate an efficient way of metabolizing nitrogenous waste but also control B. tabaci's exceptionally flexible nitrogen recycling capacity. Its efficient nitrogen processing explains how this important pest can feed on a vast spectrum of plants. This finding provides insight into how the hijacking of microbial genes has allowed whiteflies to develop a highly economic and stable nitrogen metabolism network and offers clues for pest management strategies.
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Affiliation(s)
- Zezhong Yang
- State Key Laboratory of Vegetable Biobreeding, Department of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- Institute of Plant Protection, Tianjin Academy of Agricultural Sciences, Tianjin 300381, China
| | - Zhaojiang Guo
- State Key Laboratory of Vegetable Biobreeding, Department of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Cheng Gong
- State Key Laboratory of Vegetable Biobreeding, Department of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jixing Xia
- State Key Laboratory of Vegetable Biobreeding, Department of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yuan Hu
- State Key Laboratory of Vegetable Biobreeding, Department of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jie Zhong
- State Key Laboratory of Vegetable Biobreeding, Department of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xin Yang
- State Key Laboratory of Vegetable Biobreeding, Department of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Wen Xie
- State Key Laboratory of Vegetable Biobreeding, Department of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Shaoli Wang
- State Key Laboratory of Vegetable Biobreeding, Department of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Qingjun Wu
- State Key Laboratory of Vegetable Biobreeding, Department of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Wenfeng Ye
- Laboratory of Fundamental and Applied Research in Chemical Ecology, Institute of Biology, University of Neuchâtel, CH-2000 Neuchâtel, Switzerland
| | - Baiming Liu
- Institute of Plant Protection, Tianjin Academy of Agricultural Sciences, Tianjin 300381, China
| | - Xuguo Zhou
- Department of Entomology, University of Kentucky, Lexington, KY 40546-0091, USA
| | - Ted C J Turlings
- Laboratory of Fundamental and Applied Research in Chemical Ecology, Institute of Biology, University of Neuchâtel, CH-2000 Neuchâtel, Switzerland
| | - Youjun Zhang
- State Key Laboratory of Vegetable Biobreeding, Department of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
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Pavlovič A, Koller J, Vrobel O, Chamrád I, Lenobel R, Tarkowski P. Is the co-option of jasmonate signalling for botanical carnivory a universal trait for all carnivorous plants? JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:334-349. [PMID: 37708289 PMCID: PMC10735409 DOI: 10.1093/jxb/erad359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 09/13/2023] [Indexed: 09/16/2023]
Abstract
The carnivorous plants in the order Caryophyllales co-opted jasmonate signalling from plant defence to botanical carnivory. However, carnivorous plants have at least 11 independent origins, and here we ask whether jasmonate signalling has been co-opted repeatedly in different evolutionary lineages. We experimentally wounded and fed the carnivorous plants Sarracenia purpurea (order Ericales), Cephalotus follicularis (order Oxalidales), Drosophyllum lusitanicum (order Caryophyllales), and measured electrical signals, phytohormone tissue level, and digestive enzymes activity. Coronatine was added exogenously to confirm the role of jasmonates in the induction of digestive process. Immunodetection of aspartic protease and proteomic analysis of digestive fluid was also performed. We found that prey capture induced accumulation of endogenous jasmonates only in D. lusitanicum, in accordance with increased enzyme activity after insect prey or coronatine application. In C. follicularis, the enzyme activity was constitutive while in S. purpurea was regulated by multiple factors. Several classes of digestive enzymes were identified in the digestive fluid of D. lusitanicum. Although carnivorous plants from different evolutionary lineages use the same digestive enzymes, the mechanism of their regulation differs. All investigated genera use jasmonates for their ancient role, defence, but jasmonate signalling has been co-opted for botanical carnivory only in some of them.
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Affiliation(s)
- Andrej Pavlovič
- Department of Biophysics, Faculty of Science, Palacký University, Šlechtitelů 27, CZ-783 71, Olomouc, Czech Republic
| | - Jana Koller
- Department of Biophysics, Faculty of Science, Palacký University, Šlechtitelů 27, CZ-783 71, Olomouc, Czech Republic
| | - Ondřej Vrobel
- Czech Advanced Technology and Research Institute, Palacký University, Šlechtitelů 27, CZ-783 71, Olomouc, Czech Republic
- Center of the Region Haná for Biotechnological and Agricultural Research, Department of Genetic Resources for Vegetables, Medicinal and Special Plants, Crop Research Institute, Šlechtitelů 29, CZ-783 71 Olomouc, Czech Republic
| | - Ivo Chamrád
- Laboratory of Growth Regulators, Faculty of Science, Palacký University and Institute of Experimental Botany of the Czech Academy of Sciences, Šlechtitelů 27, CZ-783 71, Olomouc, Czech Republic
| | - René Lenobel
- Laboratory of Growth Regulators, Faculty of Science, Palacký University and Institute of Experimental Botany of the Czech Academy of Sciences, Šlechtitelů 27, CZ-783 71, Olomouc, Czech Republic
| | - Petr Tarkowski
- Czech Advanced Technology and Research Institute, Palacký University, Šlechtitelů 27, CZ-783 71, Olomouc, Czech Republic
- Center of the Region Haná for Biotechnological and Agricultural Research, Department of Genetic Resources for Vegetables, Medicinal and Special Plants, Crop Research Institute, Šlechtitelů 29, CZ-783 71 Olomouc, Czech Republic
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Procko C, Chory J. Carnivorous plant evolution: is a killer defense always the best option? JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:9-12. [PMID: 38128899 PMCID: PMC10735428 DOI: 10.1093/jxb/erad431] [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] [Indexed: 12/23/2023]
Abstract
This article comments on:Pavlovič A, Koller J, Vrobel O, Chamrád I, Lenobel R, and Tarkowski P. 2024. Is the co-option of jasmonate signalling for botanical carnivory a universal trait for all carnivorous plants? Journal of Experimental Botany 75, 334–349.
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Affiliation(s)
- Carl Procko
- Plant Biology Laboratory, Salk Institute for Biological Studies, 10010 N. Torrey Pines Rd, La Jolla, CA 92037, USA
| | - Joanne Chory
- Plant Biology Laboratory, Salk Institute for Biological Studies, 10010 N. Torrey Pines Rd, La Jolla, CA 92037, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
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Fu CN, Wicke S, Zhu AD, Li DZ, Gao LM. Distinctive plastome evolution in carnivorous angiosperms. BMC PLANT BIOLOGY 2023; 23:660. [PMID: 38124058 PMCID: PMC10731798 DOI: 10.1186/s12870-023-04682-1] [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: 07/14/2023] [Accepted: 12/11/2023] [Indexed: 12/23/2023]
Abstract
BACKGROUND Independent origins of carnivory in multiple angiosperm families are fabulous examples of convergent evolution using a diverse array of life forms and habitats. Previous studies have indicated that carnivorous plants have distinct evolutionary trajectories of plastid genome (plastome) compared to their non-carnivorous relatives, yet the extent and general characteristics remain elusive. RESULTS We compared plastomes from 9 out of 13 carnivorous families and their non-carnivorous relatives to assess carnivory-associated evolutionary patterns. We identified inversions in all sampled Droseraceae species and four species of Utricularia, Pinguicula, Darlingtonia and Triphyophyllum. A few carnivores showed distinct shifts in inverted repeat boundaries and the overall repeat contents. Many ndh genes, along with some other genes, were independently lost in several carnivorous lineages. We detected significant substitution rate variations in most sampled carnivorous lineages. A significant overall substitution rate acceleration characterizes the two largest carnivorous lineages of Droseraceae and Lentibulariaceae. We also observe moderate substitution rates acceleration in many genes of Cephalotus follicularis, Roridula gorgonias, and Drosophyllum lusitanicum. However, only a few genes exhibit significant relaxed selection. CONCLUSION Our results indicate that the carnivory of plants have different effects on plastome evolution across carnivorous lineages. The complex mechanism under carnivorous habitats may have resulted in distinctive plastome evolution with conserved plastome in the Brocchinia hechtioides to strongly reconfigured plastomes structures in Droseraceae. Organic carbon obtained from prey and the efficiency of utilizing prey-derived nutrients might constitute possible explanation.
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Affiliation(s)
- Chao-Nan Fu
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
- Lijiang Forest Biodiversity National Observation and Research Station, Kunming Institute of Botany, Chinese Academy of Sciences, Lijiang, 674100, Yunnan, China
| | - Susann Wicke
- Institute for Biology, Humboldt-University Berlin, Berlin, Germany
- Späth-Arboretum of the Humboldt-University Berlin, Berlin, Germany
| | - An-Dan Zhu
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
| | - De-Zhu Li
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
| | - Lian-Ming Gao
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China.
- Lijiang Forest Biodiversity National Observation and Research Station, Kunming Institute of Botany, Chinese Academy of Sciences, Lijiang, 674100, Yunnan, China.
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Procko C, Chory J, Pirro S. The Genome Sequences of 17 Species of Carnivorous Plants. BIODIVERSITY GENOMES 2023; 2023:10.56179/001c.90164. [PMID: 37990687 PMCID: PMC10662931 DOI: 10.56179/001c.90164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2023]
Abstract
We present the genome sequences of 17 species of carnivorous plants. Illumina sequencing was performed on genetic material from cultivated individuals. The reads were assembled using a de novo method followed by a finishing step. The raw and assembled data are available via Genbank.
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Affiliation(s)
- Carl Procko
- Plant Biology Laboratory, Salk Institute for Biological Studies
| | - Joanne Chory
- Plant Biology Laboratory, Salk Institute for Biological Studies
- Howard Hughes Medical Institute
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Fleck SJ, Jobson RW. Molecular Phylogenomics Reveals the Deep Evolutionary History of Carnivory across Land Plants. PLANTS (BASEL, SWITZERLAND) 2023; 12:3356. [PMID: 37836100 PMCID: PMC10574757 DOI: 10.3390/plants12193356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 09/18/2023] [Accepted: 09/18/2023] [Indexed: 10/15/2023]
Abstract
Plastid molecular phylogenies that broadly sampled angiosperm lineages imply that carnivorous plants evolved at least 11 times independently in 13 families and 6 orders. Within and between these clades, the different prey capture strategies involving flypaper and pitfall structures arose in parallel with the subsequent evolution of snap traps and suction bladders. Attempts to discern the deep ontological history of carnivorous structures using multigene phylogenies have provided a plastid-level picture of sister relationships at the family level. Here, we present a molecular phylogeny of the angiosperms based on nuclear target sequence capture data (Angiosperms-353 probe set), assembled by the Kew Plant Trees of Life initiative, which aims to complete the tree of life for plants. This phylogeny encompasses all carnivorous and protocarnivorous families, although certain genera such as Philcoxia (Plantaginaceae) are excluded. This study offers a novel nuclear gene-based overview of relationships within and between carnivorous families and genera. Consistent with previous broadly sampled studies, we found that most carnivorous families are not affiliated with any single family. Instead, they emerge as sister groups to large clades comprising multiple non-carnivorous families. Additionally, we explore recent genomic studies across various carnivorous clades that examine the evolution of the carnivorous syndrome in relation to whole-genome duplication, subgenome dominance, small-scale gene duplication, and convergent evolution. Furthermore, we discuss insights into genome size evolution through the lens of carnivorous plant genomes.
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Affiliation(s)
- Steven J. Fleck
- Department of Biological Sciences, University at Buffalo, Buffalo, NY 14260, USA
| | - Richard W. Jobson
- National Herbarium of New South Wales, Botanic Gardens of Sydney, Locked Bag 6002, Mount Annan, NSW 2567, Australia
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Fleitas AL, Castro A, Blumwald E, Vidal S. Functional specialization of chloroplast vesiculation ( CV) duplicated genes from soybean shows partial overlapping roles during stress-induced or natural senescence. FRONTIERS IN PLANT SCIENCE 2023; 14:1184020. [PMID: 37346131 PMCID: PMC10280078 DOI: 10.3389/fpls.2023.1184020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 05/12/2023] [Indexed: 06/23/2023]
Abstract
Soybean is a globally important legume crop which is highly sensitive to drought. The identification of genes of particular relevance for drought responses provides an important basis to improve tolerance to environmental stress. Chloroplast Vesiculation (CV) genes have been characterized in Arabidopsis and rice as proteins participating in a specific chloroplast-degradation vesicular pathway (CVV) during natural or stress-induced leaf senescence. Soybean genome contains two paralogous genes encoding highly similar CV proteins, CV1 and CV2. In this study, we found that expression of CV1 was differentially upregulated by drought stress in soybean contrasting genotypes exhibiting slow-wilting (tolerant) or fast-wilting (sensitive) phenotypes. CV1 reached higher induction levels in fast-wilting plants, suggesting a negative correlation between CV1 gene expression and drought tolerance. In contrast, autophagy (ATG8) and ATI-PS (ATI1) genes were induced to higher levels in slow-wilting plants, supporting a pro-survival role for these genes in soybean drought tolerance responses. The biological function of soybean CVs in chloroplast degradation was confirmed by analyzing the effect of conditional overexpression of CV2-FLAG fusions on the accumulation of specific chloroplast proteins. Functional specificity of CV1 and CV2 genes was assessed by analyzing their specific promoter activities in transgenic Arabidopsis expressing GUS reporter gene driven by CV1 or CV2 promoters. CV1 promoter responded primarily to abiotic stimuli (hyperosmolarity, salinity and oxidative stress), while the promoter of CV2 was predominantly active during natural senescence. Both promoters were highly responsive to auxin but only CV1 responded to other stress-related hormones, such as ABA, salicylic acid and methyl jasmonate. Moreover, the dark-induced expression of CV2, but not of CV1, was strongly inhibited by cytokinin, indicating similarities in the regulation of CV2 to the reported expression of Arabidopsis and rice CV genes. Finally, we report the expression of both CV1 and CV2 genes in roots of soybean and transgenic Arabidopsis, suggesting a role for the encoded proteins in root plastids. Together, the results indicate differential roles for CV1 and CV2 in development and in responses to environmental stress, and point to CV1 as a potential target for gene editing to improve crop performance under stress without compromising natural development.
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Affiliation(s)
- Andrea Luciana Fleitas
- Laboratorio de Biología Molecular Vegetal, Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Alexandra Castro
- Laboratorio de Biología Molecular Vegetal, Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Eduardo Blumwald
- Department of Plant Sciences, University of California, Davis, Davis, CA, United States
| | - Sabina Vidal
- Laboratorio de Biología Molecular Vegetal, Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
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Lin ES, Huang YH, Chung JC, Su HH, Huang CY. The Inhibitory Effects and Cytotoxic Activities of the Stem Extract of Nepenthes miranda against Single-Stranded DNA-Binding Protein and Oral Carcinoma Cells. PLANTS (BASEL, SWITZERLAND) 2023; 12:plants12112188. [PMID: 37299167 DOI: 10.3390/plants12112188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Revised: 05/25/2023] [Accepted: 05/30/2023] [Indexed: 06/12/2023]
Abstract
The carnivorous pitcher plants of the genus Nepenthes exhibit many ethnobotanical uses, including treatments of stomachache and fever. In this study, we prepared different extracts from the pitcher, stem, and leaf extracts of Nepenthes miranda obtained using 100% methanol and analyzed their inhibitory effects on recombinant single-stranded DNA-binding protein (SSB) from Klebsiella pneumoniae (KpSSB). SSB is essential for DNA replication and cell survival and thus an attractive target for potential antipathogen chemotherapy. Different extracts prepared from Sinningia bullata, a tuberous member of the flowering plant family Gesneriaceae, were also used to investigate anti-KpSSB properties. Among these extracts, the stem extract of N. miranda exhibited the highest anti-KpSSB activity with an IC50 value of 15.0 ± 1.8 μg/mL. The cytotoxic effects of the stem extract of N. miranda on the survival and apoptosis of the cancer cell lines Ca9-22 gingival carcinoma, CAL27 oral adenosquamous carcinoma, PC-9 pulmonary adenocarcinoma, B16F10 melanoma, and 4T1 mammary carcinoma cells were also demonstrated and compared. Based on collective data, the cytotoxic activities of the stem extract at a concentration of 20 μg/mL followed the order Ca9-22 > CAL27 > PC9 > 4T1 > B16F10 cells. The stem extract of N. miranda at a concentration of 40 μg/mL completely inhibited Ca9-22 cell migration and proliferation. In addition, incubation with this extract at a concentration of 20 μg/mL boosted the distribution of the G2 phase from 7.9% to 29.2% in the Ca9-22 cells; in other words, the stem extract might suppress Ca9-22 cell proliferation by inducing G2 cell cycle arrest. Through gas chromatography-mass spectrometry, the 16 most abundant compounds in the stem extract of N. miranda were tentatively identified. The 10 most abundant compounds in the stem extract of N. miranda were used for docking analysis, and their docking scores were compared. The binding capacity of these compounds was in the order sitosterol > hexadecanoic acid > oleic acid > plumbagin > 2-ethyl-3-methylnaphtho[2,3-b]thiophene-4,9-dione > methyl α-d-galactopyranoside > 3-methoxycatechol > catechol > pyrogallol > hydroxyhydroquinone; thus, sitosterol might exhibit the greatest inhibitory capacity against KpSSB among the selected compounds. Overall, these results may indicate the pharmacological potential of N. miranda for further therapeutic applications.
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Affiliation(s)
- En-Shyh Lin
- Department of Beauty Science, National Taichung University of Science and Technology, Taichung City 403, Taiwan
| | - Yen-Hua Huang
- Department of Biomedical Sciences, Chung Shan Medical University, Taichung City 402, Taiwan
| | - Jo-Chi Chung
- Department of Biomedical Sciences, Chung Shan Medical University, Taichung City 402, Taiwan
| | - Hsin-Hui Su
- Department of Pharmacy, Chia Nan University of Pharmacy and Science, Tainan City 717, Taiwan
| | - Cheng-Yang Huang
- Department of Biomedical Sciences, Chung Shan Medical University, Taichung City 402, Taiwan
- Department of Medical Research, Chung Shan Medical University Hospital, Taichung City 402, Taiwan
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Lustofin K, Świątek P, Miranda VFO, Płachno BJ. Phylogenetical Position versus Pollination Syndromes: Floral Trichomes of Central American and Mexican Pinguicula. Int J Mol Sci 2023; 24:ijms24098423. [PMID: 37176130 PMCID: PMC10179228 DOI: 10.3390/ijms24098423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2023] [Revised: 04/27/2023] [Accepted: 04/29/2023] [Indexed: 05/15/2023] Open
Abstract
Central American and Mexican Pinguicula species are characterized by enormous divergence in size and color of flowers and are pollinated by butterflies, flies, bees, and hummingbirds. It is known that floral trichomes are key characters in plant-pollinator interaction. The main aim of our study was to verify our hypothesis that the distribution and diversity of non-glandular and glandular trichomes are related to the pollinator syndromes rather than the phylogenetic relationships. The studied sample consisted of Central American and Mexican species. In our study, we relied on light microscopy and scanning electron microscopy with a phylogenetic perspective based on ITS DNA sequences. The flower morphology of species pollinated by butterflies and hummingbirds was similar in contrast to species pollinated by flies and bees. Species pollinated by butterflies and hummingbirds contained low diversity of non-glandular trichomes, which occurred mostly in the tube and basal part of the spur. Surprisingly, in P. esseriana and P. mesophytica, non-glandular trichomes also occurred at the base of lower lip petals. In the case of species pollinated by flies/bees, we observed a high variety of non-glandular trichomes, which occurred on the surface of corolla petals, in the tube, and at the entrance to the spur. Furthermore, we did not identify any non-glandular trichomes in the spur. The capitate glandular trichomes were of similar morphology in all examined species. There were minor differences in the shape of the trichome head, as well as the length and the number of stalk cells. The distribution and the diversity of non-glandular and glandular trichomes and pollinator syndromes were mapped onto a phylogenetic reconstruction of the genus. Most micromorphological characters appear to be associated more with floral adaptation to pollinators and less with phylogeny.
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Affiliation(s)
- Krzysztof Lustofin
- Department of Plant Cytology and Embryology, Institute of Botany, Faculty of Biology, Jagiellonian University in Cracow, 9 Gronostajowa St., 30-387 Cracow, Poland
- Doctoral School of Exact and Natural Sciences, Jagiellonian University, 30-348 Cracow, Poland
| | - Piotr Świątek
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, 9 Bankowa St., 40-007 Katowice, Poland
| | - Vitor F O Miranda
- Laboratory of Plant Systematics, School of Agricultural and Veterinarian Sciences, São Paulo State University (Unesp), Jaboticabal 14884-900, Brazil
| | - Bartosz J Płachno
- Department of Plant Cytology and Embryology, Institute of Botany, Faculty of Biology, Jagiellonian University in Cracow, 9 Gronostajowa St., 30-387 Cracow, Poland
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12
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Li YX, Chen A, Leu WM. Sessile Trichomes Play Major Roles in Prey Digestion and Absorption, While Stalked Trichomes Function in Prey Predation in Byblis guehoi. Int J Mol Sci 2023; 24:ijms24065305. [PMID: 36982381 PMCID: PMC10048915 DOI: 10.3390/ijms24065305] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 03/07/2023] [Accepted: 03/09/2023] [Indexed: 03/12/2023] Open
Abstract
Carnivorous plants in the genus Byblis obtain nutrients by secreting viscous glue drops and enzymes that trap and digest small organisms. Here, we used B. guehoi to test the long-held theory that different trichomes play different roles in carnivorous plants. In the leaves of B. guehoi, we observed a 1:2.5:14 ratio of long-stalked, short-stalked, and sessile trichomes. We demonstrated that the stalked trichomes play major roles in the production of glue droplets, while the sessile trichomes secrete digestive enzymes, namely proteases and phosphatases. In addition to absorbing digested small molecules via channels/transporters, several carnivorous plants employ a more efficient system: endocytosis of large protein molecules. By feeding B. guehoi fluorescein isothiocyanate-labeled bovine serum albumin (FITC-BSA) to monitor protein transport, we found that sessile trichomes exhibited more endocytosis than long- and short-stalked trichomes. The uptaken FITC-BSA was delivered to the neighboring short epidermal cells in the same row as the sessile trichomes, then to the underlying mesophyll cells; however, no signals were detected in the parallel rows of long epidermis cells. The FITC control could be taken up by sessile trichomes but not transported out. Our study shows that B. guehoi has developed a well-organized system to maximize its food supply, consisting of stalked trichomes for prey predation and sessile trichomes for prey digestion. Moreover, the finding that sessile trichomes transfer large, endocytosed protein molecules to the underlying mesophyll, and putatively to the vascular tissues, but not laterally to the terminally differentiated epidermis, indicates that the nutrient transport system has evolved to maximize efficiency.
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Affiliation(s)
- You-Xian Li
- Ph.D. Program in Microbial Genomics, National Chung Hsing University and Academia Sinica, Taichung 40227, Taiwan
| | - Alvin Chen
- Graduate Institute of Biotechnology, National Chung Hsing University, Taichung 40227, Taiwan
| | - Wei-Ming Leu
- Graduate Institute of Biotechnology, National Chung Hsing University, Taichung 40227, Taiwan
- Correspondence:
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13
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Yu M, Arai N, Ochiai T, Ohyama T. Expression and function of an S1-type nuclease in the digestive fluid of a sundew, Drosera adelae. ANNALS OF BOTANY 2023; 131:335-346. [PMID: 36546767 PMCID: PMC9992940 DOI: 10.1093/aob/mcac150] [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: 08/26/2022] [Accepted: 12/11/2022] [Indexed: 06/17/2023]
Abstract
BACKGROUND AND AIMS Carnivorous plants trap and digest insects and similar-sized animals. Many studies have examined enzymes in the digestive fluids of these plants and have gradually unveiled the origins and gene expression of these enzymes. However, only a few attempts have been made at characterization of nucleases. This study aimed to reveal gene expression and the structural, functional and evolutionary characteristics of an S1-type nuclease (DAN1) in the digestive fluid of an Australian sundew, Drosera adelae, whose trap organ shows unique gene expression and related epigenetic regulation. METHODS Organ-specificity in Dan1 expression was examined using glandular tentacles, laminas, roots and inflorescences, and real-time PCR. The methylation status of the Dan1 promoter in each organ was clarified by bisulphite sequencing. The structural characteristics of DAN1 were studied by a comparison of primary structures of S1-type nucleases of three carnivorous and seven non-carnivorous plants. DAN1 was prepared using a cell-free protein synthesis system. Requirements for metal ions, optimum pH and temperature, and substrate preference were examined using conventional methods. KEY RESULTS Dan1 is exclusively expressed in the glandular tentacles and its promoter is almost completely unmethylated in all organs. This is in contrast to the S-like RNase gene da-I of Dr. adelae, which shows similar organ-specific expression, but is controlled by a promoter that is specifically unmethylated in the glandular tentacles. Comparison of amino acid sequences of S1-type nucleases identifies seven and three positions where amino acid residues are conserved only among the carnivorous plants and only among the non-carnivorous plants, respectively. DAN1 prefers a substrate RNA over DNA in the presence of Zn2+, Mn2+ or Ca2+ at an optimum pH of 4.0. CONCLUSIONS Uptake of phosphates from prey is suggested to be the main function of DAN1, which is very different from the known functions of S1-type nucleases. Evolution has modified the structure and expression of Dan1 to specifically function in the digestive fluid.
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Affiliation(s)
- Meng Yu
- Major in Integrative Bioscience and Biomedical Engineering, Graduate School of Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
| | - Naoki Arai
- Faculty of Engineering, Kanagawa University, 3-27-1 Rokkakubashi, Kanagawa-ku, Yokohama-shi, Kanagawa 221-8686, Japan
| | - Tadahiro Ochiai
- Major in Integrative Bioscience and Biomedical Engineering, Graduate School of Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
| | - Takashi Ohyama
- Major in Integrative Bioscience and Biomedical Engineering, Graduate School of Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
- Department of Biology, Faculty of Education and Integrated Arts and Sciences, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
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14
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Li C, Mo Y, Wang N, Xing L, Qu Y, Chen Y, Yuan Z, Ali A, Qi J, Fernández V, Wang Y, Kopittke PM. The overlooked functions of trichomes: Water absorption and metal detoxication. PLANT, CELL & ENVIRONMENT 2023; 46:669-687. [PMID: 36581782 DOI: 10.1111/pce.14530] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 12/20/2022] [Accepted: 12/28/2022] [Indexed: 06/17/2023]
Abstract
Trichomes are epidermal outgrowths on plant shoots. Their roles in protecting plants against herbivores and in the biosynthesis of specialized metabolites have long been recognized. Recently, studies are increasingly showing that trichomes also play important roles in water absorption and metal detoxication, with these roles having important implications for ecology, the environment, and agriculture. However, these two functions of trichomes have been largely overlooked and much remains unknown. In this review, we show that the trichomes of 37 plant species belonging to 14 plant families are involved in water absorption, while the trichomes of 33 species from 13 families are capable of sequestering metals within their trichomes. The ability of trichomes to absorb water results from their decreased hydrophobicity compared to the remainder of the leaf surface as well as the presence of special structures for collecting and absorbing water. In contrast, the metal detoxication function of trichomes results not only from the good connection of their basal cells to the underlying vascular tissues, but also from the presence of metal-chelating ligands and transporters within the trichomes themselves. Knowledge gaps and critical future research questions regarding these two trichome functions are highlighted. This review improves our understanding on trichomes.
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Affiliation(s)
- Cui Li
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, China
| | - Yingying Mo
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, China
| | - Nina Wang
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, China
| | - Longyi Xing
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, China
| | - Yang Qu
- Baoji Academy of Agriculture Sciences, Baoji, China
| | - Yanlong Chen
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, China
| | - Zuoqiang Yuan
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, China
| | - Arshad Ali
- College of Life Sciences, Hebei University, Hebei, China
| | - Jiyan Qi
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, China
| | - Victoria Fernández
- School of Forest Engineering, Technical University of Madrid, Madrid, Spain
| | - Yuheng Wang
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, China
| | - Peter M Kopittke
- School of Agriculture and Food Sciences, The University of Queensland, St Lucia, Queensland, Australia
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15
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Carnivorous Plants from Nepenthaceae and Droseraceae as a Source of Secondary Metabolites. Molecules 2023; 28:molecules28052155. [PMID: 36903400 PMCID: PMC10004607 DOI: 10.3390/molecules28052155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 02/13/2023] [Accepted: 02/20/2023] [Indexed: 03/03/2023] Open
Abstract
Carnivorous plants are able to attract small animals or protozoa and retain them in their specialized traps. Later, the captured organisms are killed and digested. The nutrients contained in the prey bodies are absorbed by the plants to use for growth and reproduction. These plants produce many secondary metabolites involved in the carnivorous syndrome. The main purpose of this review was to provide an overview of the secondary metabolites in the family Nepenthaceae and Droseraceae, which were studied using modern identification techniques, i.e., high-performance liquid chromatography or ultra-high-performance liquid chromatography with mass spectrometry and nuclear magnetic resonance spectroscopy. After literature screening, there is no doubt that tissues of species from the genera Nepenthes, Drosera, and Dionaea are rich sources of secondary metabolites that can be used in pharmacy and for medical purposes. The main types of the identified compounds include phenolic acids and their derivatives (gallic, protocatechuic, chlorogenic, ferulic, p-coumaric acids, gallic, hydroxybenzoic, vanillic, syringic caffeic acids, and vanillin), flavonoids (myricetin, quercetin, and kaempferol derivatives), including anthocyanins (delphinidin-3-O-glucoside, cyanidin-3-O-glucoside, and cyanidin), naphthoquinones (e.g., plumbagin, droserone, and 5-O-methyl droserone), and volatile organic compounds. Due to the biological activity of most of these substances, the importance of the carnivorous plant as a pharmaceutical crop will increase.
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16
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Cross AT, van der Ent A, Wickmann M, Skates LM, Sumail S, Gebauer G, Robinson A. Capture of mammal excreta by Nepenthes is an effective heterotrophic nutrition strategy. ANNALS OF BOTANY 2022; 130:927-938. [PMID: 36306274 PMCID: PMC9851329 DOI: 10.1093/aob/mcac134] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 10/27/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND AND AIMS While isotopic enrichment of nitrogen (15N) and carbon (13C) is often used to determine whether carnivorous plant species capture and assimilate nutrients from supplemental sources such as invertebrate prey or mammal excreta (heterotrophic nutrition), little is known about how successful the different strategies deployed by carnivorous plants are at obtaining supplemental nutrition. The collection of mammalian faeces by Nepenthes (tropical pitcher plants) is the result of a highly specialized biological mutualism that results in heterotrophic nitrogen gain; however, it remains unknown how effective this strategy is in comparison to Nepenthes species not known to collect mammalian faeces. METHODS We examined how isotopic enrichment varied in the diverse genus Nepenthes, among species producing pitchers for invertebrate capture and species exhibiting mutualisms for the collection of mammal excreta. Enrichment factors were calculated from δ15N and δ13C values from eight Nepenthes species and naturally occurring hybrids along with co-occurring reference (non-carnivorous) plants from three mountain massifs in Borneo: Mount Kinabalu, Mount Tambuyukon and Mount Trus Madi. RESULTS All Nepenthes examined, except N. edwardsiana, were significantly enriched in 15N compared to co-occurring non-carnivorous plants, and 15N enrichment was more than two-fold higher in species with adaptations for the collection of mammal excreta compared with other Nepenthes. CONCLUSIONS The collection of mammal faeces clearly represents a highly effective strategy for heterotrophic nitrogen gain in Nepenthes. Species with adaptations for capturing mammal excreta occur exclusively at high elevation (i.e. are typically summit-occurring) where previous studies suggest invertebrate prey are less abundant and less frequently captured. As such, we propose this strategy may maximize nutritional return by specializing towards ensuring the collection and retention of few but higher-value N sources in environments where invertebrate prey may be scarce.
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Affiliation(s)
- Adam T Cross
- School of Molecular and Life Sciences, Curtin University, Kent Street, Bentley, WA 6102, Australia
- Ecological Health Network, 1330 Beacon St., Suite 355a, Brookline, MA 02446, USA
| | - Antony van der Ent
- Centre for Mined Land Rehabilitation, Sustainable Minerals Institute, The University of Queensland, QLD 4072, Australia
| | - Miriam Wickmann
- Laboratory of Isotope Biogeochemistry, Bayreuth Center of Ecology and Environmental Research (BayCEER), University of Bayreuth, Germany
| | - Laura M Skates
- School of Biological Sciences, University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia
- Kings Park Science, Department of Biodiversity Conservation and Attractions, 2 Kattidj Close, Kings Park, WA 6005, Australia
| | - Sukaibin Sumail
- Herbarium, Sabah Parks, PO Box 10626, Kota Kinabalu, Sabah 88806, Malaysia
| | - Gerhard Gebauer
- Laboratory of Isotope Biogeochemistry, Bayreuth Center of Ecology and Environmental Research (BayCEER), University of Bayreuth, Germany
| | - Alastair Robinson
- National Herbarium of Victoria, Royal Botanic Gardens Victoria, Melbourne, VIC 3004, Australia
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17
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Timilsena PR, Barrett CF, Piñeyro-Nelson A, Wafula EK, Ayyampalayam S, McNeal JR, Yukawa T, Givnish TJ, Graham SW, Pires JC, Davis JI, Ané C, Stevenson DW, Leebens-Mack J, Martínez-Salas E, Álvarez-Buylla ER, dePamphilis CW. Phylotranscriptomic Analyses of Mycoheterotrophic Monocots Show a Continuum of Convergent Evolutionary Changes in Expressed Nuclear Genes From Three Independent Nonphotosynthetic Lineages. Genome Biol Evol 2022; 15:6965378. [PMID: 36582124 PMCID: PMC9887272 DOI: 10.1093/gbe/evac183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 12/13/2022] [Accepted: 12/18/2022] [Indexed: 12/31/2022] Open
Abstract
Mycoheterotrophy is an alternative nutritional strategy whereby plants obtain sugars and other nutrients from soil fungi. Mycoheterotrophy and associated loss of photosynthesis have evolved repeatedly in plants, particularly in monocots. Although reductive evolution of plastomes in mycoheterotrophs is well documented, the dynamics of nuclear genome evolution remains largely unknown. Transcriptome datasets were generated from four mycoheterotrophs in three families (Orchidaceae, Burmanniaceae, Triuridaceae) and related green plants and used for phylogenomic analyses to resolve relationships among the mycoheterotrophs, their relatives, and representatives across the monocots. Phylogenetic trees based on 602 genes were mostly congruent with plastome phylogenies, except for an Asparagales + Liliales clade inferred in the nuclear trees. Reduction and loss of chlorophyll synthesis and photosynthetic gene expression and relaxation of purifying selection on retained genes were progressive, with greater loss in older nonphotosynthetic lineages. One hundred seventy-four of 1375 plant benchmark universally conserved orthologous genes were undetected in any mycoheterotroph transcriptome or the genome of the mycoheterotrophic orchid Gastrodia but were expressed in green relatives, providing evidence for massively convergent gene loss in nonphotosynthetic lineages. We designate this set of deleted or undetected genes Missing in Mycoheterotrophs (MIM). MIM genes encode not only mainly photosynthetic or plastid membrane proteins but also a diverse set of plastid processes, genes of unknown function, mitochondrial, and cellular processes. Transcription of a photosystem II gene (psb29) in all lineages implies a nonphotosynthetic function for this and other genes retained in mycoheterotrophs. Nonphotosynthetic plants enable novel insights into gene function as well as gene expression shifts, gene loss, and convergence in nuclear genomes.
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Affiliation(s)
- Prakash Raj Timilsena
- Department of Biology, The Pennsylvania State University, University Park, Pennsylvania
| | - Craig F Barrett
- Department of Biology, West Virginia University, Morgantown, West Virginia
| | - Alma Piñeyro-Nelson
- Departamento de Producción Agrícola y Animal, Universidad Autónoma Metropolitana-Xochimilco, Mexico City, Mexico,Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Eric K Wafula
- Department of Biology, The Pennsylvania State University, University Park, Pennsylvania
| | | | - Joel R McNeal
- Department of Ecology, Evolution, and Organismal Biology, Kennesaw State University, Georgia
| | - Tomohisa Yukawa
- Tsukuba Botanical Garden, National Museum of Nature and Science, 1-1, Amakubo 4, Tsukuba, 305-0005, Japan
| | - Thomas J Givnish
- Department of Botany, University of Wisconsin-Madison, Madison, Wisconsin
| | - Sean W Graham
- Department of Botany, University of British Columbia, Vancouver, British Columbia, V6T 1Z4Canada
| | - J Chris Pires
- Division of Biological Sciences, University of Missouri–Columbia, Columbia, Missouri
| | - Jerrold I Davis
- School of Integrative Plant Sciences and L.H. Bailey Hortorium, Cornell University, Ithaca, New York, 1485
| | - Cécile Ané
- Department of Botany, University of Wisconsin-Madison, Madison, Wisconsin,Department of Statistics, University of Wisconsin–Madison, Madison, Wisconsin
| | | | - Jim Leebens-Mack
- Department of Plant Biology, University of Georgia, Athens, Georgia, 3060
| | - Esteban Martínez-Salas
- Departmento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, Mexico City, México
| | - Elena R Álvarez-Buylla
- Departamento de Ecología Funcional, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, Mexico,Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, Mexico City, Mexico
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18
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Timilsena PR, Wafula EK, Barrett CF, Ayyampalayam S, McNeal JR, Rentsch JD, McKain MR, Heyduk K, Harkess A, Villegente M, Conran JG, Illing N, Fogliani B, Ané C, Pires JC, Davis JI, Zomlefer WB, Stevenson DW, Graham SW, Givnish TJ, Leebens-Mack J, dePamphilis CW. Phylogenomic resolution of order- and family-level monocot relationships using 602 single-copy nuclear genes and 1375 BUSCO genes. FRONTIERS IN PLANT SCIENCE 2022; 13:876779. [PMID: 36483967 PMCID: PMC9723157 DOI: 10.3389/fpls.2022.876779] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 09/29/2022] [Indexed: 05/26/2023]
Abstract
We assess relationships among 192 species in all 12 monocot orders and 72 of 77 families, using 602 conserved single-copy (CSC) genes and 1375 benchmarking single-copy ortholog (BUSCO) genes extracted from genomic and transcriptomic datasets. Phylogenomic inferences based on these data, using both coalescent-based and supermatrix analyses, are largely congruent with the most comprehensive plastome-based analysis, and nuclear-gene phylogenomic analyses with less comprehensive taxon sampling. The strongest discordance between the plastome and nuclear gene analyses is the monophyly of a clade comprising Asparagales and Liliales in our nuclear gene analyses, versus the placement of Asparagales and Liliales as successive sister clades to the commelinids in the plastome tree. Within orders, around six of 72 families shifted positions relative to the recent plastome analysis, but four of these involve poorly supported inferred relationships in the plastome-based tree. In Poales, the nuclear data place a clade comprising Ecdeiocoleaceae+Joinvilleaceae as sister to the grasses (Poaceae); Typhaceae, (rather than Bromeliaceae) are resolved as sister to all other Poales. In Commelinales, nuclear data place Philydraceae sister to all other families rather than to a clade comprising Haemodoraceae+Pontederiaceae as seen in the plastome tree. In Liliales, nuclear data place Liliaceae sister to Smilacaceae, and Melanthiaceae are placed sister to all other Liliales except Campynemataceae. Finally, in Alismatales, nuclear data strongly place Tofieldiaceae, rather than Araceae, as sister to all the other families, providing an alternative resolution of what has been the most problematic node to resolve using plastid data, outside of those involving achlorophyllous mycoheterotrophs. As seen in numerous prior studies, the placement of orders Acorales and Alismatales as successive sister lineages to all other extant monocots. Only 21.2% of BUSCO genes were demonstrably single-copy, yet phylogenomic inferences based on BUSCO and CSC genes did not differ, and overall functional annotations of the two sets were very similar. Our analyses also reveal significant gene tree-species tree discordance despite high support values, as expected given incomplete lineage sorting (ILS) related to rapid diversification. Our study advances understanding of monocot relationships and the robustness of phylogenetic inferences based on large numbers of nuclear single-copy genes that can be obtained from transcriptomes and genomes.
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Affiliation(s)
- Prakash Raj Timilsena
- Department of Biology and Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, United States
| | - Eric K. Wafula
- Department of Biology and Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, United States
| | - Craig F. Barrett
- Department of Biology, West Virginia University, Morgantown, WV, United States
| | - Saravanaraj Ayyampalayam
- Georgia Advanced Computing Resource Center, University of Georgia, Athens, GA, United States
- Department of Plant Biology, University of Georgia, Athens, GA, United States
| | - Joel R. McNeal
- Department of Ecology, Evolution, and Organismal Biology, Biology Kennesaw State University, Kennesaw, GA, United States
| | - Jeremy D. Rentsch
- Department of Biology, Francis Marion University, Florence, SC, United States
| | - Michael R. McKain
- Department of Biological Sciences, University of Alabama, Tuscaloosa, AL, United States
| | - Karolina Heyduk
- School of Life Sciences, University of Hawai’i at Mānoa, Honolulu, HI, United States
| | - Alex Harkess
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, United States
| | - Matthieu Villegente
- Institut des Sciences Exactes et Appliquees (ISEA), University of New Caledonia, Noumea, New Caledonia
| | - John G. Conran
- Australian Centre for Evolutionary Biology and Biodiversity & Sprigg Geobiology Centre, School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia
| | - Nicola Illing
- Department of Molecular and Cell Biology, University of Cape Town, Cape Town, South Africa
| | - Bruno Fogliani
- Institut des Sciences Exactes et Appliquees (ISEA), University of New Caledonia, Noumea, New Caledonia
| | - Cécile Ané
- Department of Botany, University of Wisconsin-Madison, Madison, WI, United States
- Department of Statistics, University of Wisconsin–Madison, Madison, WI, United States
| | - J. Chris Pires
- Division of Biological Sciences and Bond Life Sciences Center, University of Missouri, Columbia, MO, United States
| | - Jerrold I. Davis
- School of Integrative Plant Sciences and L.H. Bailey Hortorium, Cornell University, Ithaca, NY, United States
| | - Wendy B. Zomlefer
- Department of Plant Biology, University of Georgia, Athens, GA, United States
| | | | | | - Thomas J. Givnish
- Department of Botany, University of Wisconsin-Madison, Madison, WI, United States
| | - James Leebens-Mack
- Department of Plant Biology, University of Georgia, Athens, GA, United States
| | - Claude W. dePamphilis
- Department of Biology and Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, United States
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19
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Freund M, Graus D, Fleischmann A, Gilbert KJ, Lin Q, Renner T, Stigloher C, Albert VA, Hedrich R, Fukushima K. The digestive systems of carnivorous plants. PLANT PHYSIOLOGY 2022; 190:44-59. [PMID: 35604105 PMCID: PMC9434158 DOI: 10.1093/plphys/kiac232] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 04/08/2022] [Indexed: 05/19/2023]
Abstract
To survive in the nutrient-poor habitats, carnivorous plants capture small organisms comprising complex substances not suitable for immediate reuse. The traps of carnivorous plants, which are analogous to the digestive systems of animals, are equipped with mechanisms for the breakdown and absorption of nutrients. Such capabilities have been acquired convergently over the past tens of millions of years in multiple angiosperm lineages by modifying plant-specific organs including leaves. The epidermis of carnivorous trap leaves bears groups of specialized cells called glands, which acquire substances from their prey via digestion and absorption. The digestive glands of carnivorous plants secrete mucilage, pitcher fluids, acids, and proteins, including digestive enzymes. The same (or morphologically distinct) glands then absorb the released compounds via various membrane transport proteins or endocytosis. Thus, these glands function in a manner similar to animal cells that are physiologically important in the digestive system, such as the parietal cells of the stomach and intestinal epithelial cells. Yet, carnivorous plants are equipped with strategies that deal with or incorporate plant-specific features, such as cell walls, epidermal cuticles, and phytohormones. In this review, we provide a systematic perspective on the digestive and absorptive capacity of convergently evolved carnivorous plants, with an emphasis on the forms and functions of glands.
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Affiliation(s)
| | | | - Andreas Fleischmann
- Botanische Staatssammlung München and GeoBio-Center LMU, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Kadeem J Gilbert
- Department of Plant Biology & W.K. Kellogg Biological Station, Michigan State University, Hickory Corners, Michigan 49060, USA
| | - Qianshi Lin
- Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Tanya Renner
- Department of Entomology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Christian Stigloher
- Imaging Core Facility of the Biocenter, University of Würzburg, Würzburg, Germany
| | - Victor A Albert
- Department of Biological Sciences, University at Buffalo, Buffalo, New York 14260, USA
| | - Rainer Hedrich
- Institute for Molecular Plant Physiology and Biophysics, University of Würzburg, Würzburg, Germany
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