1
|
Zhang T, Li Y, Li C, Zang J, Gao E, Kroon JT, Qu X, Hussey PJ, Wang P. Exo84c interacts with VAP27 to regulate exocytotic compartment degradation and stigma senescence. Nat Commun 2023; 14:4888. [PMID: 37580356 PMCID: PMC10425460 DOI: 10.1038/s41467-023-40729-5] [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: 11/14/2022] [Accepted: 08/08/2023] [Indexed: 08/16/2023] Open
Abstract
In plants, exocyst subunit isoforms exhibit significant functional diversity in that they are involved in either protein secretion or autophagy, both of which are essential for plant development and survival. Although the molecular basis of autophagy is widely reported, its contribution to plant reproduction is not very clear. Here, we have identified Exo84c, a higher plant-specific Exo84 isoform, as having a unique function in modulating exocytotic compartment degradation during stigmatic tissue senescence. This process is achieved through its interaction with the ER localised VAP27 proteins, which regulate the turnover of Exo84c through the autophagy pathway. VAP27 recruits Exo84c onto the ER membrane as well as numerous ER-derived autophagosomes that are labelled with ATG8. These Exo84c/exocyst and VAP27 positive structures are accumulated in the vacuole for degradation, and this process is partially perturbed in the exo84c knock-out mutants. Interestingly, the exo84c mutant showed a prolonged effective pollination period with higher seed sets, possibly because of the delayed stigmatic senescence when Exo84c regulated autophagy is blocked. In conclusion, our studies reveal a link between the exocyst complex and the ER network in regulating the degradation of exocytosis vesicles, a process that is essential for normal papilla cell senescence and flower receptivity.
Collapse
Affiliation(s)
- Tong Zhang
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, Hubei Province, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
| | - Yifan Li
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, Hubei Province, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
| | - Chengyang Li
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, Hubei Province, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
| | - Jingze Zang
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, Hubei Province, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
- Department of Biosciences, Durham University, South Road, Durham, DH1 3LE, UK
| | - Erlin Gao
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, Hubei Province, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
| | - Johan T Kroon
- Department of Biosciences, Durham University, South Road, Durham, DH1 3LE, UK
| | - Xiaolu Qu
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, Hubei Province, China
| | - Patrick J Hussey
- Department of Biosciences, Durham University, South Road, Durham, DH1 3LE, UK
| | - Pengwei Wang
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, Hubei Province, China.
- Hubei Hongshan Laboratory, Wuhan, 430070, China.
| |
Collapse
|
2
|
Casey M, Marchioni I, Lear B, Cort AP, Baldwin A, Rogers HJ, Stead AD. Senescence in dahlia flowers is regulated by a complex interplay between flower age and floret position. FRONTIERS IN PLANT SCIENCE 2023; 13:1085933. [PMID: 36714770 PMCID: PMC9880482 DOI: 10.3389/fpls.2022.1085933] [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: 10/31/2022] [Accepted: 12/14/2022] [Indexed: 06/18/2023]
Abstract
Mechanisms regulating flower senescence are not fully understood in any species and are particularly complex in composite flowers. Dahlia (Dahlia pinnata Cav.) florets develop sequentially, hence each composite flower head includes florets of different developmental stages as the whole flower head ages. Moreover, the wide range of available cultivars enables assessment of intraspecific variation. Transcriptomes were compared amongst inner (younger) and outer (older) florets of two flower head ages to assess the effect of floret vs. flower head ageing. More gene expression, including ethylene and cytokinin pathway expression changed between inner and outer florets of older flower heads than between inner florets of younger and older flower heads. Additionally, based on Arabidopsis network analysis, different patterns of co-expressed ethylene response genes were elicited. This suggests that changes occur in young inner florets as the whole flower head ages that are different to ageing florets within a flower head. In some species floral senescence is orchestrated by the plant growth regulator ethylene. However, there is both inter and intra-species variation in its importance. There is a lack of conclusive data regarding ethylene sensitivity in dahlia. Speed of senescence progression, effects of ethylene signalling perturbation, and patterns of ethylene biosynthesis gene expression differed across three dahlia cultivars ('Sylvia', 'Karma Prospero' and 'Onesta') suggesting differences in the role of ethylene in their floral senescence, while effects of exogenous cytokinin were less cultivar-specific.
Collapse
Affiliation(s)
- Matthew Casey
- School of Biological Sciences, Royal Holloway University of London, Egham, Surrey, United Kingdom
| | - Ilaria Marchioni
- School of Biosciences, Cardiff University, Cardiff, United Kingdom
- Dipartimento di Scienze Agrarie, Alimentari e Agro-alimentari, Università di Pisa, Pisa, Italy
| | - Bianca Lear
- School of Biological Sciences, Royal Holloway University of London, Egham, Surrey, United Kingdom
| | - Alex P. Cort
- School of Biosciences, Cardiff University, Cardiff, United Kingdom
| | - Ashley Baldwin
- School of Biosciences, Cardiff University, Cardiff, United Kingdom
| | - Hilary J. Rogers
- School of Biosciences, Cardiff University, Cardiff, United Kingdom
| | - Anthony D. Stead
- School of Biological Sciences, Royal Holloway University of London, Egham, Surrey, United Kingdom
| |
Collapse
|
3
|
Astigueta FH, Baigorria AH, García MN, Delfosse VC, González SA, Pérez de la Torre MC, Moschen S, Lia VV, Heinz RA, Fernández P, Trupkin SA. Characterization and expression analysis of WRKY genes during leaf and corolla senescence of Petunia hybrida plants. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2022; 28:1765-1784. [PMID: 36387973 PMCID: PMC9636358 DOI: 10.1007/s12298-022-01243-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 10/14/2022] [Accepted: 10/17/2022] [Indexed: 06/16/2023]
Abstract
Several families of transcription factors (TFs) control the progression of senescence. Many key TFs belonging to the WRKY family have been described to play crucial roles in the regulation of leaf senescence, mainly in Arabidopsis thaliana. However, little is known about senescence-associated WRKY members in floricultural species. Delay of senescence in leaves and petals of Petunia hybrida, a worldwide ornamental crop are highly appreciated traits. In this work, starting from 28 differentially expressed WRKY genes of A. thaliana during the progression of leaf senescence, we identified the orthologous in P. hybrida and explored the expression profiles of 20 PhWRKY genes during the progression of natural (age-related) leaf and corolla senescence as well as in the corollas of flowers undergoing pollination-induced senescence. Simultaneous visualization showed consistent and similar expression profiles of PhWRKYs during natural leaf and corolla senescence, although weak expression changes were observed during pollination-induced senescence. Comparable expression trends between PhWRKYs and the corresponding genes of A. thaliana were observed during leaf senescence, although more divergence was found in petals of pollinated petunia flowers. Integration of expression data with phylogenetics, conserved motif and cis-regulatory element analyses were used to establish a list of candidates that could regulate more than one senescence process. Our results suggest that several members of the WRKY family of TFs are tightly linked to the regulation of senescence in P. hybrida. Supplementary Information The online version contains supplementary material available at 10.1007/s12298-022-01243-y.
Collapse
Affiliation(s)
- Francisco H. Astigueta
- Consejo Nacional de Investigaciones Científicas y Técnicas, Ciudad Autónoma de
Buenos Aires, 1425 Buenos Aires, Argentina
- Escuela de Ciencia Y Tecnología, Universidad Nacional de San Martín, 1650 San Martín, Buenos Aires Argentina
| | - Amilcar H. Baigorria
- Escuela de Ciencia Y Tecnología, Universidad Nacional de San Martín, 1650 San Martín, Buenos Aires Argentina
| | - Martín N. García
- Consejo Nacional de Investigaciones Científicas y Técnicas, Ciudad Autónoma de
Buenos Aires, 1425 Buenos Aires, Argentina
- Instituto de Agrobiotecnología y Biología Molecular (INTA-CONICET), Centro de Investigaciones en Ciencias Agronómicas Y Veterinarias, Instituto Nacional de Tecnología Agropecuaria, 1686 Hurlingham, Buenos Aires Argentina
| | - Verónica C. Delfosse
- Consejo Nacional de Investigaciones Científicas y Técnicas, Ciudad Autónoma de
Buenos Aires, 1425 Buenos Aires, Argentina
- Escuela de Ciencia Y Tecnología, Universidad Nacional de San Martín, 1650 San Martín, Buenos Aires Argentina
| | - Sergio A. González
- Consejo Nacional de Investigaciones Científicas y Técnicas, Ciudad Autónoma de
Buenos Aires, 1425 Buenos Aires, Argentina
| | - Mariana C. Pérez de la Torre
- Instituto de Floricultura, Centro de Investigación de Recursos Naturales, Instituto Nacional de Tecnología Agropecuaria, 1686 Hurlingham, Buenos Aires Argentina
| | - Sebastián Moschen
- Consejo Nacional de Investigaciones Científicas y Técnicas, Ciudad Autónoma de
Buenos Aires, 1425 Buenos Aires, Argentina
- Instituto Nacional de Tecnología Agropecuaria, Estación Experimental Agropecuaria Famaillá, 4142 Tucumán, Argentina
| | - Verónica V. Lia
- Consejo Nacional de Investigaciones Científicas y Técnicas, Ciudad Autónoma de
Buenos Aires, 1425 Buenos Aires, Argentina
- Instituto de Agrobiotecnología y Biología Molecular (INTA-CONICET), Centro de Investigaciones en Ciencias Agronómicas Y Veterinarias, Instituto Nacional de Tecnología Agropecuaria, 1686 Hurlingham, Buenos Aires Argentina
- Facultad de Ciencias Exactas Y Naturales, Universidad de Buenos Aires, 1428 Buenos Aires, Argentina
| | - Ruth A. Heinz
- Consejo Nacional de Investigaciones Científicas y Técnicas, Ciudad Autónoma de
Buenos Aires, 1425 Buenos Aires, Argentina
- Instituto de Agrobiotecnología y Biología Molecular (INTA-CONICET), Centro de Investigaciones en Ciencias Agronómicas Y Veterinarias, Instituto Nacional de Tecnología Agropecuaria, 1686 Hurlingham, Buenos Aires Argentina
| | - Paula Fernández
- Consejo Nacional de Investigaciones Científicas y Técnicas, Ciudad Autónoma de
Buenos Aires, 1425 Buenos Aires, Argentina
- Escuela de Ciencia Y Tecnología, Universidad Nacional de San Martín, 1650 San Martín, Buenos Aires Argentina
- Instituto de Agrobiotecnología y Biología Molecular (INTA-CONICET), Centro de Investigaciones en Ciencias Agronómicas Y Veterinarias, Instituto Nacional de Tecnología Agropecuaria, 1686 Hurlingham, Buenos Aires Argentina
| | - Santiago A. Trupkin
- Consejo Nacional de Investigaciones Científicas y Técnicas, Ciudad Autónoma de
Buenos Aires, 1425 Buenos Aires, Argentina
- Instituto de Floricultura, Centro de Investigación de Recursos Naturales, Instituto Nacional de Tecnología Agropecuaria, 1686 Hurlingham, Buenos Aires Argentina
| |
Collapse
|
4
|
Zhu X, Su M, Wang B, Wei X. Transcriptome analysis reveals the main metabolic pathway of c-GMP induced by salt stress in tomato ( Solanum lycopersicum) seedlings. FUNCTIONAL PLANT BIOLOGY : FPB 2022; 49:784-798. [PMID: 35930479 DOI: 10.1071/fp21337] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 04/24/2022] [Indexed: 06/15/2023]
Abstract
Tomato (Solanum lycopersicum L.) is a model crop as well as an important food worldwide. In arid areas, increasing soil salinity has limited higher yields in tomato production. As a second messenger molecule, cyclic guanosine monophosphate (c-GMP) plays an indispensable role in plant response to salt stress by regulating cell processes to promote plant growth and development. However, this mechanism has not been fully explored in tomato seedlings. In this experiment, tomato seeds were cultured in four treatments: (1) distilled water (CK); (2) 20μM c-GMP (T1); (3) 50mM NaCl (T2); and (4) 20μM c-GMP+50mM NaCl (T3). The results show that 20μM c-GMP effectively alleviated the inhibitory effect of 50mM NaCl on growth and development, and induced the expression of 1580 differentially expressed genes (DEGs). Seedlings in the CK vs T1 shared 95 upregulated and 442 downregulated DEGs, whereas T2 vs T3 shared 271 upregulated and 772 downregulated DEGs. Based on KEGG (Kyoto Encyclopaedia of Genes and Genomes) analysis, the majority of DEGs were involved in metabolism; exogenous c-GMP induced significant enrichment of pathways associated with carbohydrates, phenylpropanoids and fatty acid metabolism. Most PMEs , acCoA , PAL , PODs , FADs , and AD were upregulated, and GAPDHs , PL , PG , BXL4 , and β-G were downregulated, which reduced susceptibility of tomato seedlings to salt and promoted their salt tolerance. The application of c-GMP increased soluble sugar, flavonoid and lignin contents, reduced accumulation of malondialdehyde (MDA), and enhanced the activity of peroxidase (POD). Thus, our results provide insights into the molecular mechanisms associated with salt tolerance of tomato seedlings.
Collapse
Affiliation(s)
- Xiaolin Zhu
- College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China; and Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou 730070, China; and College of Life Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | - Meifei Su
- Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou 730070, China; and College of Life Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | - Baoqiang Wang
- Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou 730070, China; and College of Life Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | - Xiaohong Wei
- College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China; and Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou 730070, China; and College of Life Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
| |
Collapse
|
5
|
Lin Y, Jones ML. CRISPR/Cas9-Mediated Editing of Autophagy Gene 6 in Petunia Decreases Flower Longevity, Seed Yield, and Phosphorus Remobilization by Accelerating Ethylene Production and Senescence-Related Gene Expression. FRONTIERS IN PLANT SCIENCE 2022; 13:840218. [PMID: 35557714 PMCID: PMC9088004 DOI: 10.3389/fpls.2022.840218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 04/07/2022] [Indexed: 06/15/2023]
Abstract
Developmental petal senescence is a type of programmed cell death (PCD), during which the production of ethylene is induced, the expression of PCD-related genes is upregulated, and nutrients are recycled. Autophagy is an intracellular mechanism involved in PCD modulation and nutrient cycling. As a central component of the autophagy pathway, Autophagy Gene 6 (ATG6) was previously shown as a negative regulator of petal senescence. To better understand the role of autophagy in ethylene biosynthesis and nutrient remobilization during petal senescence, we generated and characterized the knockout (KO) mutants of PhATG6 using CRISPR/Cas9 in Petunia × hybrida 'Mitchell Diploid.' PhATG6-KO lines exhibited decreased flower longevity when compared to the flowers of the wild-type or a non-mutated regenerative line (controls), confirming the negative regulatory role of ATG6 in petal senescence. Smaller capsules and fewer seeds per capsule were produced in the KO plants, indicating the crucial function of autophagy in seed production. Ethylene production and ethylene biosynthesis genes were upregulated earlier in the KO lines than the controls, indicating that autophagy affects flower longevity through ethylene. The transcript levels of petal PCD-related genes, including PhATG6, PhATG8d, PhPI3K (Phosphatidylinositol 3-Kinase), and a metacaspase gene PhMC1, were upregulated earlier in the corollas of PhATG6-KO lines, which supported the accelerated PCD in the KO plants. The remobilization of phosphorus was reduced in the KO lines, showing that nutrient recycling was compromised. Our study demonstrated the important role of autophagy in flower lifespan and seed production and supported the interactions between autophagy and various regulatory factors during developmental petal senescence.
Collapse
|
6
|
Zhong S, Sang L, Zhao Z, Deng Y, Liu H, Yu Y, Liu J. Phosphoproteome analysis reveals the involvement of protein dephosphorylation in ethylene-induced corolla senescence in petunia. BMC PLANT BIOLOGY 2021; 21:512. [PMID: 34732145 PMCID: PMC8565076 DOI: 10.1186/s12870-021-03286-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Accepted: 10/18/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND Senescence represents the last stage of flower development. Phosphorylation is the key posttranslational modification that regulates protein functions, and kinases may be more required than phosphatases during plant growth and development. However, little is known about global phosphorylation changes during flower senescence. RESULTS In this work, we quantitatively investigated the petunia phosphoproteome following ethylene or air treatment. In total, 2170 phosphosites in 1184 protein groups were identified, among which 2059 sites in 1124 proteins were quantified. To our surprise, treatment with ethylene resulted in 697 downregulated and only 117 upregulated phosphosites using a 1.5-fold threshold (FDR < 0.05), which showed that ethylene negatively regulates global phosphorylation levels and that phosphorylation of many proteins was not necessary during flower senescence. Phosphoproteome analysis showed that ethylene regulates ethylene and ABA signalling transduction pathways via phosphorylation levels. One of the major targets of ethylene-induced dephosphorylation is the plant mRNA splicing machinery, and ethylene treatment increases the number of alternative splicing events of precursor RNAs in petunia corollas. CONCLUSIONS Protein dephosphorylation could play an important role in ethylene-induced senescence, and ethylene treatment increased the number of AS precursor RNAs in petunia corollas.
Collapse
Affiliation(s)
- Shiwei Zhong
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, 510642 China
- School of Landscape Architecture School of Tourism and Health, Zhejiang A & F University, Zhejiang, 311300 Hangzhou China
| | - Lina Sang
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, 510642 China
| | - Zhixia Zhao
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, 510642 China
| | - Ying Deng
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, 510642 China
| | - Haitao Liu
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, 510642 China
| | - Yixun Yu
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, 510642 China
- Lingnan Guangdong Laboratory of Modern Agriculture, Guangzhou, 510642 China
| | - Juanxu Liu
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, 510642 China
- School of Landscape Architecture School of Tourism and Health, Zhejiang A & F University, Zhejiang, 311300 Hangzhou China
| |
Collapse
|
7
|
Tran Q, Osabe K, Entani T, Nagai T. A novel petal up-regulated PhXTH7 promoter analysis in Petunia hybrida by using bioluminescence reporter gene. PLANT BIOTECHNOLOGY (TOKYO, JAPAN) 2021; 38:197-204. [PMID: 34393598 PMCID: PMC8329265 DOI: 10.5511/plantbiotechnology.21.0130a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 01/30/2021] [Indexed: 06/13/2023]
Abstract
Flower opening is an important phenomenon in plant that indicates the readiness of the flower for pollination leading to petal expansion and pigmentation. This phenomenon has great impact on crop yield, which makes researches of its mechanism attractive for both plant physiology study and agriculture. Gene promoters directing the expression in petal during the petal cell wall modification and expansion when flower opens could be a convenient tool to analyze or monitor gene expression targeting this event. However, there are no reports of isolated gene promoters that can direct gene expression in petal or petal limb during the rapid cell wall dynamics when the flower opens. Xyloglucan endotransglucosylase/hydrolase 7 (XTH7), a cell wall modifying enzyme, was reported having up-regulated gene expression in the petal of Arabidopsis thaliana and Petunia hybrida. In this study, we fused a 1,904 bp length P. hybrida XTH7 promoter with a gene encoding a bright bioluminescent protein (Green enhanced Nano-lantern) to report gene expression and observed petal up-regulated bioluminescence activity by means of a consumer-grade camera. More importantly, this novel promoter demonstrated up-regulated activity in the petal limb of P. hybrida matured flower during flower opening. P. hybrida XTH7 promoter would be a useful tool for flowering study, especially for petal expansion research during flower opening.
Collapse
Affiliation(s)
- Quang Tran
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Kenji Osabe
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
- SANKEN (The Institute of Scientific and Industrial Research), Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan
| | - Tetsuyuki Entani
- SANKEN (The Institute of Scientific and Industrial Research), Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan
| | - Takeharu Nagai
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
- SANKEN (The Institute of Scientific and Industrial Research), Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan
| |
Collapse
|
8
|
Chung M, Bruno VM, Rasko DA, Cuomo CA, Muñoz JF, Livny J, Shetty AC, Mahurkar A, Dunning Hotopp JC. Best practices on the differential expression analysis of multi-species RNA-seq. Genome Biol 2021; 22:121. [PMID: 33926528 PMCID: PMC8082843 DOI: 10.1186/s13059-021-02337-8] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 04/01/2021] [Indexed: 02/07/2023] Open
Abstract
Advances in transcriptome sequencing allow for simultaneous interrogation of differentially expressed genes from multiple species originating from a single RNA sample, termed dual or multi-species transcriptomics. Compared to single-species differential expression analysis, the design of multi-species differential expression experiments must account for the relative abundances of each organism of interest within the sample, often requiring enrichment methods and yielding differences in total read counts across samples. The analysis of multi-species transcriptomics datasets requires modifications to the alignment, quantification, and downstream analysis steps compared to the single-species analysis pipelines. We describe best practices for multi-species transcriptomics and differential gene expression.
Collapse
Affiliation(s)
- Matthew Chung
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201 USA
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD 21201 USA
| | - Vincent M. Bruno
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201 USA
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD 21201 USA
| | - David A. Rasko
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201 USA
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD 21201 USA
| | - Christina A. Cuomo
- Infectious Disease and Microbiome Program, Broad Institute, Cambridge, MA 02142 USA
| | - José F. Muñoz
- Infectious Disease and Microbiome Program, Broad Institute, Cambridge, MA 02142 USA
| | - Jonathan Livny
- Infectious Disease and Microbiome Program, Broad Institute, Cambridge, MA 02142 USA
| | - Amol C. Shetty
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201 USA
| | - Anup Mahurkar
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201 USA
| | - Julie C. Dunning Hotopp
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201 USA
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD 21201 USA
- Greenebaum Cancer Center, University of Maryland, Baltimore, MD 21201 USA
| |
Collapse
|
9
|
Lobaton J, Andrew R, Duitama J, Kirkland L, Macfadyen S, Rader R. Using RNA-seq to characterize pollen-stigma interactions for pollination studies. Sci Rep 2021; 11:6635. [PMID: 33758263 PMCID: PMC7988043 DOI: 10.1038/s41598-021-85887-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Accepted: 03/08/2021] [Indexed: 11/18/2022] Open
Abstract
Insects are essential for the reproduction of pollinator-dependent crops and contribute to the pollination of 87% of wild plants and 75% of the world’s food crops. Understanding pollen flow dynamics between plants and pollinators is thus essential to manage and conserve wild plants and ensure yields are maximized in food crops. However, the determination of pollen transfer in the field is complex and laborious. We developed a field experiment in a pollinator-dependent crop and used high throughput RNA sequencing (RNA-seq) to quantify pollen flow by measuring changes in gene expression between pollination treatments across different apple (Malus domestica Borkh.) cultivars. We tested three potential molecular indicators of successful pollination and validated these results with field data by observing single and multiple visits by honey bees (Apis mellifera) to apple flowers and measured fruit set in a commercial apple orchard. The first indicator of successful outcrossing was revealed via differential gene expression in the cross-pollination treatments after 6 h. The second indicator of successful outcrossing was revealed by the expression of specific genes related to pollen tube formation and defense response at three different time intervals in the stigma and the style following cross-pollination (i.e. after 6, 24, and 48 h). Finally, genotyping variants specific to donor pollen could be detected in cross-pollination treatments, providing a third indicator of successful outcrossing. Field data indicated that one or five flower visits by honey bees were insufficient and at least 10 honey bee flower visits were required to achieve a 25% probability of fruit set under orchard conditions. By combining the genotyping data, the differential expression analysis, and the traditional fruit set field experiments, it was possible to evaluate the pollination effectiveness of honey bee visits under orchards conditions. This is the first time that pollen-stigma-style mRNA expression analysis has been conducted after a pollinator visit (honey bee) to a plant (in vivo apple flowers). This study provides evidence that mRNA sequencing can be used to address complex questions related to stigma–pollen interactions over time in pollination ecology.
Collapse
Affiliation(s)
- Juan Lobaton
- School of Environmental and Rural Science, University of New England, Armidale, Australia. .,CSIRO, Clunies Ross St., Acton, ACT, Australia.
| | - Rose Andrew
- School of Environmental and Rural Science, University of New England, Armidale, Australia
| | - Jorge Duitama
- Systems and Computing, Engineering Department, Universidad de Los Andes, Bogota, Colombia
| | - Lindsey Kirkland
- School of Environmental and Rural Science, University of New England, Armidale, Australia
| | | | - Romina Rader
- School of Environmental and Rural Science, University of New England, Armidale, Australia
| |
Collapse
|
10
|
Liu F, Simasotchi C, Vibert F, Zhu W, Gil S, Degrelle SA, Fournier T. Age and Sex-Related Changes in Human First-Trimester Placenta Transcriptome and Insights into Adaptative Responses to Increased Oxygen. Int J Mol Sci 2021; 22:ijms22062901. [PMID: 33809345 PMCID: PMC8001632 DOI: 10.3390/ijms22062901] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 03/09/2021] [Accepted: 03/10/2021] [Indexed: 12/17/2022] Open
Abstract
Physiological oxygen tension rises dramatically in the placenta between 8 and 14 weeks of gestation. Abnormalities in this period can lead to gestational diseases, whose underlying mechanisms remain unclear. We explored the changes at mRNA level by comparing the transcriptomes of human placentas at 8–10 gestational weeks and 12–14 gestational weeks. A total of 20 samples were collected and divided equally into four groups based on sex and age. Cytotrophoblasts were isolated and sequenced using RNAseq. Key genes were identified using two different methods: DESeq2 and weighted gene co-expression network analysis (WGCNA). We also constructed a local database of known targets of hypoxia-inducible factor (HIF) subunits, alpha and beta, to investigate expression patterns likely linked with changes in oxygen. Patterns of gene enrichment in and among the four groups were analyzed based on annotations of gene ontology (GO) and KEGG pathways. We characterized the similarities and differences between the enrichment patterns revealed by the two methods and the two conditions (age and sex), as well as those associated with HIF targets. Our results provide a broad perspective of the processes that are active in cytotrophoblasts during the rise in physiological oxygen, which should benefit efforts to discover possible drug-targeted genes or pathways in the human placenta.
Collapse
Affiliation(s)
- Fulin Liu
- Pathophysiology & Pharmacotoxicology of the Human Placenta, Pre & Postnatal Microbiota, Université de Paris, INSERM, 3PHM, F-75006 Paris, France; (F.L.); (C.S.); (F.V.); (S.G.); (S.A.D.)
| | - Christelle Simasotchi
- Pathophysiology & Pharmacotoxicology of the Human Placenta, Pre & Postnatal Microbiota, Université de Paris, INSERM, 3PHM, F-75006 Paris, France; (F.L.); (C.S.); (F.V.); (S.G.); (S.A.D.)
- Fondation PremUp, F-75006 Paris, France
| | - Françoise Vibert
- Pathophysiology & Pharmacotoxicology of the Human Placenta, Pre & Postnatal Microbiota, Université de Paris, INSERM, 3PHM, F-75006 Paris, France; (F.L.); (C.S.); (F.V.); (S.G.); (S.A.D.)
| | - Wencan Zhu
- UMR Applied Mathematics & Informatics, AgroParisTech-Université Paris-Saclay, F-75005 Paris, France;
| | - Sophie Gil
- Pathophysiology & Pharmacotoxicology of the Human Placenta, Pre & Postnatal Microbiota, Université de Paris, INSERM, 3PHM, F-75006 Paris, France; (F.L.); (C.S.); (F.V.); (S.G.); (S.A.D.)
- Fondation PremUp, F-75006 Paris, France
| | - Séverine A. Degrelle
- Pathophysiology & Pharmacotoxicology of the Human Placenta, Pre & Postnatal Microbiota, Université de Paris, INSERM, 3PHM, F-75006 Paris, France; (F.L.); (C.S.); (F.V.); (S.G.); (S.A.D.)
- Inovarion, F-75005 Paris, France
| | - Thierry Fournier
- Pathophysiology & Pharmacotoxicology of the Human Placenta, Pre & Postnatal Microbiota, Université de Paris, INSERM, 3PHM, F-75006 Paris, France; (F.L.); (C.S.); (F.V.); (S.G.); (S.A.D.)
- Correspondence:
| |
Collapse
|
11
|
Lin Y, Jones ML. Silencing ATG6 and PI3K accelerates petal senescence and reduces flower number and shoot biomass in petunia. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2021; 302:110713. [PMID: 33288020 DOI: 10.1016/j.plantsci.2020.110713] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 09/30/2020] [Accepted: 10/03/2020] [Indexed: 06/12/2023]
Abstract
Petal senescence is a form of developmental programmed cell death (PCD) that is regulated by internal and environmental signals. Autophagy, a metabolic pathway that regulates intercellular nutrient recycling, is thought to play an important role in the regulation of petal senescence-associated PCD. To characterize the function of two central autophagy genes in petal senescence, we down-regulated Autophagy Gene 6 (PhATG6) and Phosphoinositide 3-Kinase (PhPI3K) using Virus-Induced Gene Silencing (VIGS) in Petunia × hybrida. The silencing of PhATG6 and PhPI3K accelerated petal senescence, thereby reducing flower longevity. Both PhATG6- and PhPI3K-silenced petunias had reduced flower numbers, flower biomass, and vegetative shoot biomass. These phenotypes were intensified when plants were grown under low nutrient conditions. Additionally, two important regulators of senescence, an ethylene biosynthesis gene (PhACS) and a type I metacaspase gene (PhMC1), were suppressed in senescing petals of PhATG6- and PhPI3K-silenced plants. In conclusion, our study identified PhATG6 and PhPI3K as negative regulators of flower senescence and demonstrated the influence of nutrient limitation on the function of autophagy during petal senescence. Our study also found that autophagy genes potentially influence the transcriptional regulation of metacaspases and ethylene biosynthetic genes during petal senescence. The results of this project will be fundamental for future studies of petal senescence and will provide genetic information for future crop improvement.
Collapse
Affiliation(s)
- Yiyun Lin
- Department of Horticulture and Crop Science, The Ohio State University, Ohio Agricultural Research and Development Center (OARDC), 1680 Madison Avenue, Wooster, OH, 44691, USA
| | - Michelle L Jones
- Department of Horticulture and Crop Science, The Ohio State University, Ohio Agricultural Research and Development Center (OARDC), 1680 Madison Avenue, Wooster, OH, 44691, USA.
| |
Collapse
|
12
|
Kataria R, Duhan N, Kaundal R. Computational Systems Biology of Alfalfa - Bacterial Blight Host-Pathogen Interactions: Uncovering the Complex Molecular Networks for Developing Durable Disease Resistant Crop. FRONTIERS IN PLANT SCIENCE 2021; 12:807354. [PMID: 35251063 PMCID: PMC8891223 DOI: 10.3389/fpls.2021.807354] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 12/29/2021] [Indexed: 05/04/2023]
Abstract
Medicago sativa (also known as alfalfa), a forage legume, is widely cultivated due to its high yield and high-value hay crop production. Infectious diseases are a major threat to the crops, owing to huge economic losses to the agriculture industry, worldwide. The protein-protein interactions (PPIs) between the pathogens and their hosts play a critical role in understanding the molecular basis of pathogenesis. Pseudomonas syringae pv. syringae ALF3 suppresses the plant's innate immune response by secreting type III effector proteins into the host cell, causing bacterial stem blight in alfalfa. The alfalfa-P. syringae system has little information available for PPIs. Thus, to understand the infection mechanism, we elucidated the genome-scale host-pathogen interactions (HPIs) between alfalfa and P. syringae using two computational approaches: interolog-based and domain-based method. A total of ∼14 M putative PPIs were predicted between 50,629 alfalfa proteins and 2,932 P. syringae proteins by combining these approaches. Additionally, ∼0.7 M consensus PPIs were also predicted. The functional analysis revealed that P. syringae proteins are highly involved in nucleotide binding activity (GO:0000166), intracellular organelle (GO:0043229), and translation (GO:0006412) while alfalfa proteins are involved in cellular response to chemical stimulus (GO:0070887), oxidoreductase activity (GO:0016614), and Golgi apparatus (GO:0005794). According to subcellular localization predictions, most of the pathogen proteins targeted host proteins within the cytoplasm and nucleus. In addition, we discovered a slew of new virulence effectors in the predicted HPIs. The current research describes an integrated approach for deciphering genome-scale host-pathogen PPIs between alfalfa and P. syringae, allowing the researchers to better understand the pathogen's infection mechanism and develop pathogen-resistant lines.
Collapse
Affiliation(s)
- Raghav Kataria
- Department of Plants, Soils, and Climate, College of Agriculture and Applied Sciences, Utah State University, Logan, UT, United States
| | - Naveen Duhan
- Department of Plants, Soils, and Climate, College of Agriculture and Applied Sciences, Utah State University, Logan, UT, United States
| | - Rakesh Kaundal
- Department of Plants, Soils, and Climate, College of Agriculture and Applied Sciences, Utah State University, Logan, UT, United States
- Bioinformatics Facility, Center for Integrated Biosystems, Utah State University, Logan, UT, United States
- Department of Computer Science, College of Science, Utah State University, Logan, UT, United States
- *Correspondence: Rakesh Kaundal, ;
| |
Collapse
|
13
|
Guo Y, Warner RM. Dissecting genetic diversity and genomic background of Petunia cultivars with contrasting growth habits. HORTICULTURE RESEARCH 2020; 7:155. [PMID: 33082962 PMCID: PMC7528118 DOI: 10.1038/s41438-020-00373-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 07/13/2020] [Accepted: 08/05/2020] [Indexed: 05/15/2023]
Abstract
The cultivated petunia (Petunia ×hybrida) is derived from the progenitor species P. axillaris and P. integrifolia. The hybridization dates back only to the 1830s, though intensive breeding efforts have yielded cultivars exhibiting incredible diversity for many traits, including growth habit, flower color, and flower size. Until now, little is known about the genetic diversity and genomic background of modern cultivars. Here we selected a panel of 13 cultivars with contrasting growth habits and three wild species (the progenitors and P. exserta) to estimate the genomic contribution from the ancestral species and to study whether the variation of the genetic origin could be associated with different breeding programs or morphological variability. Transcriptome sequencing identified 1,164,566 SNPs representing 98.4% (32,451) of the transcripts that cover 99.2% (of 52,697,361 bp) of the P. axillaris transcriptome. Cultivars with an upright growth habit had more homozygous alleles and more P. axillaris-derived alleles than trailing cultivars, while mounded cultivars had intermediate heterozygosity. Unlike previous studies, we found the proportions of alleles derived from each progenitor species varied across cultivars but overall were not biased toward one progenitor species, suggesting diverse selection during cultivar development. For trailing cultivars, alleles potentially introgressed from other wild species ("out" alleles) were enriched. The "out" alleles were clustered in particular regions of chromosomes, suggesting that these regions may be hotspots of introgression. Transcripts in these regions were enriched with gene ontology terms associated with growth habit. This study provides novel insight into the contributions of progenitor species to the genomic background of modern petunia cultivars and identifies genome regions that may harbor genes conferring the trailing growth habit for further exploration.
Collapse
Affiliation(s)
- Yufang Guo
- Department of Horticulture, Michigan State University, East Lansing, MI 48824 USA
| | - Ryan M. Warner
- Department of Horticulture, Michigan State University, East Lansing, MI 48824 USA
| |
Collapse
|
14
|
Illumina-based Analysis of Endophytic Bacterial Diversity of four Allium species. Sci Rep 2019; 9:15271. [PMID: 31649302 PMCID: PMC6813343 DOI: 10.1038/s41598-019-51707-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Accepted: 10/07/2019] [Indexed: 11/08/2022] Open
Abstract
Allium species are popular vegetables in China and possess antifungal and antibacterial activities. This study aimed to compare the endophytic bacterial community in the four crucial Allium species in China, Chinese leek (CL), garlic (GA), onion (ON,) and Welsh onion (WO), using sequences of the V3–V4 region of the bacterial 16S rRNA gene. A total of 1,036,637 high-quality sequences and 719 operational taxonomic units (OTUs) were obtained across all libraries. A total of 20 phyla, 50 classes, 80 orders, 134 families, and 234 genera were identified. Among them, 18 OTUs and 19 genera were shared among the four Allium species. Proteobacteria (42.68%) and Bacteroidetes (20.18%) were the dominant phyla in CL, while one unclassified (>70%) was the dominant phyla in the other three Allium species. The alpha-diversity analysis showed the bacterial richness and diversity in CL were significantly higher than those in the other three Allium species. Principal coordinate analysis (PCA) showed endophytic bacterial communities in GA, WO, and ON were more similar than those in CL. Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) analysis revealed endophytic bacteria mostly enriched in Membrane Transport, Amino Acid Metabolism and Carbohydrate Metabolism pathway. 17 of the 23 Kyoto Encyclopedia of Genes and Genomes (KEGG) categories and 159 of the 206 lower-level KEGG pathways in CL were significantly higher than those in the other three Allium species. Pearson’s correlation indicated that KEGG pathways with significant differences among the Allium species were closely related to the bacterial genera with significant differences between the Allium species. The findings of our study provided insight into the complex endophytic microbial communities in Allium species.
Collapse
|
15
|
Trupkin SA, Astigueta FH, Baigorria AH, García MN, Delfosse VC, González SA, Pérez de la Torre MC, Moschen S, Lía VV, Fernández P, Heinz RA. Identification and expression analysis of NAC transcription factors potentially involved in leaf and petal senescence in Petunia hybrida. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2019; 287:110195. [PMID: 31481223 DOI: 10.1016/j.plantsci.2019.110195] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Revised: 07/17/2019] [Accepted: 07/19/2019] [Indexed: 05/23/2023]
Abstract
Progression of leaf senescence depends on several families of transcription factors. In Arabidopsis, the NAC family plays crucial roles in the modulation of leaf senescence; however, the mechanisms involved in this NAC-mediated regulation have not been extensively explored in agronomic species. Petunia hybrida is an ornamental plant that is commonly found worldwide. Decreasing the rate of leaf and petal senescence in P. hybrida is essential for maintaining plant quality. In this study, we examined the NAC-mediated networks involved in regulating senescence in this species. From 41 NAC genes, the expression of which changed in Arabidopsis during leaf senescence, we identified 29 putative orthologs in P. hybrida. Analysis using quantitative real-time-PCR indicated that 24 genes in P. hybrida changed their transcript levels during natural leaf senescence. Leaf-expressed genes were subsequently assessed in petals undergoing natural and pollination-induced senescence. Expression data and phylogenetic analysis were used to generate a list of 10-15 candidate genes; 7 of these were considered key regulatory candidates in senescence because of their consistent upregulation in the three senescence processes examined. Altogether, we identified common and distinct patterns of gene expression at different stages of leaf and petal development and during progression of senescence. The results obtained in this study will contribute to the understanding of NAC-mediated regulatory networks in petunia.
Collapse
Affiliation(s)
- Santiago A Trupkin
- Instituto de Floricultura, Centro de Investigación de Recursos Naturales, Instituto Nacional de Tecnología Agropecuaria, Hurlingham, Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas, Ciudad Autónoma de Buenos Aires, Argentina
| | - Francisco H Astigueta
- Consejo Nacional de Investigaciones Científicas y Técnicas, Ciudad Autónoma de Buenos Aires, Argentina; Escuela de Ciencia y Tecnología, Universidad Nacional de San Martín, San Martín, Buenos Aires, Argentina
| | - Amilcar H Baigorria
- Escuela de Ciencia y Tecnología, Universidad Nacional de San Martín, San Martín, Buenos Aires, Argentina
| | - Martín N García
- Instituto de Agrobiotecnología y Biología Molecular (IABiMo - INTA-CONICET), Centro de Investigaciones en Ciencias Agronómicas y Veterinarias, Instituto Nacional de Tecnología Agropecuaria, Hurlingham, Buenos Aires, Argentina
| | - Verónica C Delfosse
- Consejo Nacional de Investigaciones Científicas y Técnicas, Ciudad Autónoma de Buenos Aires, Argentina; Escuela de Ciencia y Tecnología, Universidad Nacional de San Martín, San Martín, Buenos Aires, Argentina
| | - Sergio A González
- Consejo Nacional de Investigaciones Científicas y Técnicas, Ciudad Autónoma de Buenos Aires, Argentina
| | - Mariana Cecilia Pérez de la Torre
- Instituto de Floricultura, Centro de Investigación de Recursos Naturales, Instituto Nacional de Tecnología Agropecuaria, Hurlingham, Buenos Aires, Argentina
| | - Sebastián Moschen
- Consejo Nacional de Investigaciones Científicas y Técnicas, Ciudad Autónoma de Buenos Aires, Argentina
| | - Verónica V Lía
- Instituto de Agrobiotecnología y Biología Molecular (IABiMo - INTA-CONICET), Centro de Investigaciones en Ciencias Agronómicas y Veterinarias, Instituto Nacional de Tecnología Agropecuaria, Hurlingham, Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas, Ciudad Autónoma de Buenos Aires, Argentina; Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina
| | - Paula Fernández
- Instituto de Agrobiotecnología y Biología Molecular (IABiMo - INTA-CONICET), Centro de Investigaciones en Ciencias Agronómicas y Veterinarias, Instituto Nacional de Tecnología Agropecuaria, Hurlingham, Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas, Ciudad Autónoma de Buenos Aires, Argentina; Escuela de Ciencia y Tecnología, Universidad Nacional de San Martín, San Martín, Buenos Aires, Argentina.
| | - Ruth A Heinz
- Instituto de Agrobiotecnología y Biología Molecular (IABiMo - INTA-CONICET), Centro de Investigaciones en Ciencias Agronómicas y Veterinarias, Instituto Nacional de Tecnología Agropecuaria, Hurlingham, Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas, Ciudad Autónoma de Buenos Aires, Argentina; Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina.
| |
Collapse
|
16
|
Joly V, Tebbji F, Nantel A, Matton DP. Pollination Type Recognition from a Distance by the Ovary Is Revealed Through a Global Transcriptomic Analysis. PLANTS (BASEL, SWITZERLAND) 2019; 8:E185. [PMID: 31238522 PMCID: PMC6630372 DOI: 10.3390/plants8060185] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Revised: 06/09/2019] [Accepted: 06/12/2019] [Indexed: 02/06/2023]
Abstract
Sexual reproduction in flowering plants involves intimate contact and continuous interactions between the growing pollen tube and the female reproductive structures. These interactions can trigger responses in distal regions of the flower well ahead of fertilization. While pollination-induced petal senescence has been studied extensively, less is known about how pollination is perceived at a distance in the ovary, and how specific this response is to various pollen genotypes. To address this question, we performed a global transcriptomic analysis in the ovary of a wild potato species, Solanum chacoense, at various time points following compatible, incompatible, and heterospecific pollinations. In all cases, pollen tube penetration in the stigma was initially perceived as a wounding aggression. Then, as the pollen tubes grew in the style, a growing number of genes became specific to each pollen genotype. Functional classification analyses revealed sharp differences in the response to compatible and heterospecific pollinations. For instance, the former induced reactive oxygen species (ROS)-related genes while the latter affected genes associated to ethylene signaling. In contrast, incompatible pollination remained more akin to a wound response. Our analysis reveals that every pollination type produces a specific molecular signature generating diversified and specific responses at a distance in the ovary in preparation for fertilization.
Collapse
Affiliation(s)
- Valentin Joly
- Institut de Recherche en Biologie Végétale, Université de Montréal, Montréal, QC H1X 2B2, Canada.
| | - Faïza Tebbji
- CRCHU de Québec, Université Laval, Québec, QC G1V 4G2, Canada.
| | - André Nantel
- National Research Council Canada, Montréal, QC H4P 2R2, Canada.
| | - Daniel P Matton
- Institut de Recherche en Biologie Végétale, Université de Montréal, Montréal, QC H1X 2B2, Canada.
| |
Collapse
|
17
|
Liu F, Marshall RS, Li F. Understanding and exploiting the roles of autophagy in plants through multi-omics approaches. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2018; 274:146-152. [PMID: 30080598 PMCID: PMC6082170 DOI: 10.1016/j.plantsci.2018.05.009] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Revised: 05/15/2018] [Accepted: 05/15/2018] [Indexed: 05/20/2023]
Abstract
Autophagy is a highly conserved pathway in eukaryotes that promotes nutrient recycling and cellular homeostasis through the degradation of excess or damaged cytoplasmic constituents. In plants, autophagy is increasingly recognized as a key contributor to development, reproduction, metabolism, leaf senescence, endosperm and grain development, pathogen defense, and tolerance to abiotic and biotic stresses. Characterizing the functional transcriptomic, proteomic, and metabolomic networks relating to autophagy in plants subjected to various extra- and intra-cellular stimuli may help to identify components associated with the pathway. As such, the integration of multi-omics approaches (i.e., transcriptomics, proteomics and metabolomics), along with cellular, genetic and functional analyses, could provide a global perspective regarding the effects of autophagy on plant metabolism, development and stress responses. In this mini-review, recent research progress in plant autophagy is discussed, highlighting the importance of high-throughput omics approaches for defining the underpinning molecular mechanisms of autophagy and understanding its associated regulatory network.
Collapse
Affiliation(s)
- Fen Liu
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China; Department of Biology, Washington University in St. Louis, St. Louis, MO 63130, USA; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Richard S Marshall
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Faqiang Li
- College of Life Sciences, South China Agricultural University, Guangzhou 510642, China.
| |
Collapse
|
18
|
Amano I, Kitajima S, Suzuki H, Koeduka T, Shitan N. Transcriptome analysis of Petunia axillaris flowers reveals genes involved in morphological differentiation and metabolite transport. PLoS One 2018; 13:e0198936. [PMID: 29902274 PMCID: PMC6002047 DOI: 10.1371/journal.pone.0198936] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Accepted: 05/29/2018] [Indexed: 01/21/2023] Open
Abstract
The biosynthesis of plant secondary metabolites is associated with morphological and metabolic differentiation. As a consequence, gene expression profiles can change drastically, and primary and secondary metabolites, including intermediate and end-products, move dynamically within and between cells. However, little is known about the molecular mechanisms underlying differentiation and transport mechanisms. In this study, we performed a transcriptome analysis of Petunia axillaris subsp. parodii, which produces various volatiles in its corolla limbs and emits metabolites to attract pollinators. RNA-sequencing from leaves, buds, and limbs identified 53,243 unigenes. Analysis of differentially expressed genes, combined with gene ontology and Kyoto Encyclopedia of Genes and Genomes pathway analyses, showed that many biological processes were highly enriched in limbs. These included catabolic processes and signaling pathways of hormones, such as gibberellins, and metabolic pathways, including phenylpropanoids and fatty acids. Moreover, we identified five transporter genes that showed high expression in limbs, and we performed spatiotemporal expression analyses and homology searches to infer their putative functions. Our systematic analysis provides comprehensive transcriptomic information regarding morphological differentiation and metabolite transport in the Petunia flower and lays the foundation for establishing the specific mechanisms that control secondary metabolite biosynthesis in plants.
Collapse
Affiliation(s)
- Ikuko Amano
- Laboratory of Medicinal Cell Biology, Kobe Pharmaceutical University, Motoyamakita-machi, Higashinada-ku, Kobe, Japan
| | - Sakihito Kitajima
- Department of Applied Biology, Kyoto Institute of Technology, Matsugasaki Sakyo-ku, Kyoto, Japan
- The Center for Advanced Insect Research Promotion, Kyoto Institute of Technology, Matsugasaki Sakyo-ku, Kyoto, Japan
| | - Hideyuki Suzuki
- Department of Research and Development, Kazusa DNA Research Institute, Chiba, Japan
| | - Takao Koeduka
- Graduate School of Sciences and Technology for Innovation (Agriculture), Department of Biological Chemistry, Yamaguchi University, Yamaguchi, Japan
| | - Nobukazu Shitan
- Laboratory of Medicinal Cell Biology, Kobe Pharmaceutical University, Motoyamakita-machi, Higashinada-ku, Kobe, Japan
- * E-mail:
| |
Collapse
|
19
|
Gao Z, Daneva A, Salanenka Y, Van Durme M, Huysmans M, Lin Z, De Winter F, Vanneste S, Karimi M, Van de Velde J, Vandepoele K, Van de Walle D, Dewettinck K, Lambrecht BN, Nowack MK. KIRA1 and ORESARA1 terminate flower receptivity by promoting cell death in the stigma of Arabidopsis. NATURE PLANTS 2018; 4:365-375. [PMID: 29808023 PMCID: PMC7116356 DOI: 10.1038/s41477-018-0160-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Accepted: 04/26/2018] [Indexed: 05/09/2023]
Abstract
Flowers have a species-specific functional life span that determines the time window in which pollination, fertilization and seed set can occur. The stigma tissue plays a key role in flower receptivity by intercepting pollen and initiating pollen tube growth toward the ovary. In this article, we show that a developmentally controlled cell death programme terminates the functional life span of stigma cells in Arabidopsis. We identified the leaf senescence regulator ORESARA1 (also known as ANAC092) and the previously uncharacterized KIRA1 (also known as ANAC074) as partially redundant transcription factors that modulate stigma longevity by controlling the expression of programmed cell death-associated genes. KIRA1 expression is sufficient to induce cell death and terminate floral receptivity, whereas lack of both KIRA1 and ORESARA1 substantially increases stigma life span. Surprisingly, the extension of stigma longevity is accompanied by only a moderate extension of flower receptivity, suggesting that additional processes participate in the control of the flower's receptive life span.
Collapse
Affiliation(s)
- Zhen Gao
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center of Plant Systems Biology, Ghent, Belgium
- Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Anna Daneva
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center of Plant Systems Biology, Ghent, Belgium
| | - Yuliya Salanenka
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center of Plant Systems Biology, Ghent, Belgium
- Institute of Science and Technology (IST), Klosterneuburg, Austria
| | - Matthias Van Durme
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center of Plant Systems Biology, Ghent, Belgium
| | - Marlies Huysmans
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center of Plant Systems Biology, Ghent, Belgium
| | - Zongcheng Lin
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center of Plant Systems Biology, Ghent, Belgium
| | - Freya De Winter
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center of Plant Systems Biology, Ghent, Belgium
| | - Steffen Vanneste
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center of Plant Systems Biology, Ghent, Belgium
- Lab of Plant Growth Analysis, Ghent University Global Campus, Yeonsu-gu, Incheon, Republic of Korea
| | - Mansour Karimi
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center of Plant Systems Biology, Ghent, Belgium
| | - Jan Van de Velde
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center of Plant Systems Biology, Ghent, Belgium
| | - Klaas Vandepoele
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center of Plant Systems Biology, Ghent, Belgium
| | - Davy Van de Walle
- Laboratory of Food Technology and Engineering, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Koen Dewettinck
- Laboratory of Food Technology and Engineering, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Bart N Lambrecht
- VIB Center for Inflammation Research, Ghent, Belgium
- Department of Internal Medicine, Ghent University, Ghent, Belgium
- Department of Pulmonary Medicine, Ersamus MC, Rotterdam, the Netherlands
| | - Moritz K Nowack
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.
- VIB Center of Plant Systems Biology, Ghent, Belgium.
| |
Collapse
|
20
|
Wang H, Chang X, Lin J, Chang Y, Chen JC, Reid MS, Jiang CZ. Transcriptome profiling reveals regulatory mechanisms underlying corolla senescence in petunia. HORTICULTURE RESEARCH 2018; 5:16. [PMID: 29619227 PMCID: PMC5878830 DOI: 10.1038/s41438-018-0018-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Revised: 01/09/2018] [Accepted: 01/12/2018] [Indexed: 05/08/2023]
Abstract
The genetic regulatory mechanisms that govern natural corolla senescence in petunia are not well understood. To identify key genes and pathways that regulate the process, we performed a transcriptome analysis in petunia corolla at four developmental stages, including corolla fully opening without anther dehiscence (D0), corolla expansion, 2 days after anthesis (D2), corolla with initial signs of senescence (D4), and wilting corolla (D7). We identified large numbers of differentially expressed genes (DEGs), ranging from 4626 between the transition from D0 and D2, 1116 between D2 and D4, a transition to the onset of flower senescence, and 327 between D4 and D7, a developmental stage representing flower senescence. KEGG analysis showed that the auxin- and ethylene-related hormone biosynthesis and signaling transduction pathways were significantly activated during the flower development and highly upregulated at onset of flower senescence. Ethylene emission was detected at the D2 to D4 transition, followed by a large eruption at the D4 to D7 transition. Furthermore, large numbers of transcription factors (TFs) were activated over the course of senescence. Functional analysis by virus-induced gene silencing (VIGS) experiments demonstrated that inhibition of the expression of TFs, such as ethylene-related ERF, auxin-related ARF, bHLH, HB, and MADS-box, significantly extended or shortened flower longevity. Our data suggest that hormonal interaction between auxin and ethylene may play critical regulatory roles in the onset of natural corolla senescence in petunia.
Collapse
Affiliation(s)
- Hong Wang
- Institute of Pomology/Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Jiangsu Academy of Agricultural Sciences, 210014 Nanjing, China
- Department of Plant Sciences, University of California, Davis, Davis, CA 95616 USA
| | - XiaoXiao Chang
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Science, 510640 Guangzhou, China
| | - Jing Lin
- Institute of Pomology/Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Jiangsu Academy of Agricultural Sciences, 210014 Nanjing, China
| | - Youhong Chang
- Institute of Pomology/Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Jiangsu Academy of Agricultural Sciences, 210014 Nanjing, China
| | - Jen-Chih Chen
- Department of Plant Sciences, University of California, Davis, Davis, CA 95616 USA
- Institute of Biotechnology, National Taiwan University, 10617 Taipei, Taiwan
| | - Michael S. Reid
- Department of Plant Sciences, University of California, Davis, Davis, CA 95616 USA
| | - Cai-Zhong Jiang
- Department of Plant Sciences, University of California, Davis, Davis, CA 95616 USA
- United States Department of Agriculture, Crops Pathology and Genetics Research Unit, Agricultural Research Service, Davis, CA 95616 USA
| |
Collapse
|
21
|
Shibuya K. Molecular aspects of flower senescence and strategies to improve flower longevity. BREEDING SCIENCE 2018; 68:99-108. [PMID: 29681752 PMCID: PMC5903976 DOI: 10.1270/jsbbs.17081] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 11/14/2017] [Indexed: 05/06/2023]
Abstract
Flower longevity is one of the most important traits for ornamental plants. Ethylene plays a crucial role in flower senescence in some plant species. In several species that show ethylene-dependent flower senescence, genetic modification targeting genes for ethylene biosynthesis or signaling has improved flower longevity. Although little is known about regulatory mechanisms of petal senescence in flowers that show ethylene-independent senescence, a recent study of Japanese morning glory revealed that a NAC transcription factor, EPHEMERAL1 (EPH1), is a key regulator in ethylene-independent petal senescence. EPH1 is induced in an age-dependent manner irrespective of ethylene signal, and suppression of EPH1 expression dramatically delays petal senescence. In ethylene-dependent petal senescence, comprehensive transcriptome analyses revealed the involvement of transcription factors, a basic helix-loop-helix protein and a homeodomain-leucine zipper protein, in the transcriptional regulation of the ethylene biosynthesis enzymes. This review summarizes molecular aspects of flower senescence and discusses strategies to improve flower longevity by molecular breeding.
Collapse
Affiliation(s)
- Kenichi Shibuya
- Institute of Vegetable and Floriculture Science, NARO,
2-1 Fujimoto, Tsukuba, Ibaraki 305-0852,
Japan
| |
Collapse
|
22
|
Villarino GH, Hu Q, Scanlon MJ, Mueller L, Bombarely A, Mattson NS. Dissecting Tissue-Specific Transcriptomic Responses from Leaf and Roots under Salt Stress in Petunia hybrida Mitchell. Genes (Basel) 2017; 8:genes8080195. [PMID: 28771200 PMCID: PMC5575659 DOI: 10.3390/genes8080195] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2017] [Revised: 07/01/2017] [Accepted: 07/27/2017] [Indexed: 12/21/2022] Open
Abstract
One of the primary objectives of plant biotechnology is to increase resistance to abiotic stresses, such as salinity. Salinity is a major abiotic stress and increasing crop resistant to salt continues to the present day as a major challenge. Salt stress disturbs cellular environment leading to protein misfolding, affecting normal plant growth and causing agricultural losses worldwide. The advent of state-of-the-art technologies such as high throughput mRNA sequencing (RNA-seq) has revolutionized whole-transcriptome analysis by allowing, with high precision, to measure changes in gene expression. In this work, we used tissue-specific RNA-seq to gain insight into the Petunia hybrida transcriptional responses under NaCl stress using a controlled hydroponic system. Roots and leaves samples were taken from a continuum of 48 h of acute 150 mM NaCl. This analysis revealed a set of tissue and time point specific differentially expressed genes, such as genes related to transport, signal transduction, ion homeostasis as well as novel and undescribed genes, such as Peaxi162Scf00003g04130 and Peaxi162Scf00589g00323 expressed only in roots under salt stress. In this work, we identified early and late expressed genes in response to salt stress while providing a core of differentially express genes across all time points and tissues, including the trehalose-6-phosphate synthase 1 (TPS1), a glycosyltransferase reported in salt tolerance in other species. To test the function of the novel petunia TPS1 allele, we cloned and showed that TPS1 is a functional plant gene capable of complementing the trehalose biosynthesis pathway in a yeast tps1 mutant. The list of candidate genes to enhance salt tolerance provided in this work constitutes a major effort to better understand the detrimental effects of salinity in petunia with direct implications for other economically important Solanaceous species.
Collapse
Affiliation(s)
- Gonzalo H Villarino
- School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA.
| | - Qiwen Hu
- Institute for Translational Medicine and Therapeutics (ITMAT), University of Pennsylvania, Philadelphia, PA 19104, USA.
| | - Michael J Scanlon
- School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA.
| | - Lukas Mueller
- Boyce Thompson Institute, Cornell University, Ithaca, NY 14853, USA.
| | - Aureliano Bombarely
- Department of Horticulture, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA.
| | - Neil S Mattson
- School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA.
| |
Collapse
|
23
|
Wang X, Zhao M, Wu W, Korir NK, Qian Y, Wang Z. Comparative transcriptome analysis of berry-sizing effects of gibberellin (GA3) on seedless Vitis vinifera L. Genes Genomics 2017. [DOI: 10.1007/s13258-016-0500-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
|
24
|
Yang M, Zhu L, Li L, Li J, Xu L, Feng J, Liu Y. Digital Gene Expression Analysis Provides Insight into the Transcript Profile of the Genes Involved in Aporphine Alkaloid Biosynthesis in Lotus ( Nelumbo nucifera). FRONTIERS IN PLANT SCIENCE 2017; 8:80. [PMID: 28197160 PMCID: PMC5281601 DOI: 10.3389/fpls.2017.00080] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Accepted: 01/13/2017] [Indexed: 05/21/2023]
Abstract
The predominant alkaloids in lotus leaves are aporphine alkaloids. These are the most important active components and have many pharmacological properties, but little is known about their biosynthesis. We used digital gene expression (DGE) technology to identify differentially-expressed genes (DEGs) between two lotus cultivars with different alkaloid contents at four leaf development stages. We also predicted potential genes involved in aporphine alkaloid biosynthesis by weighted gene co-expression network analysis (WGCNA). Approximately 335 billion nucleotides were generated; and 94% of which were aligned against the reference genome. Of 22 thousand expressed genes, 19,000 were differentially expressed between the two cultivars at the four stages. Gene Ontology (GO) enrichment analysis revealed that catalytic activity and oxidoreductase activity were enriched significantly in most pairwise comparisons. In Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, dozens of DEGs were assigned to the categories of biosynthesis of secondary metabolites, isoquinoline alkaloid biosynthesis, and flavonoid biosynthesis. The genes encoding norcoclaurine synthase (NCS), norcoclaurine 6-O-methyltransferase (6OMT), coclaurine N-methyltransferase (CNMT), N-methylcoclaurine 3'-hydroxylase (NMCH), and 3'-hydroxy-N-methylcoclaurine 4'-O-methyltransferase (4'OMT) in the common pathways of benzylisoquinoline alkaloid biosynthesis and the ones encoding corytuberine synthase (CTS) in aporphine alkaloid biosynthetic pathway, which have been characterized in other plants, were identified in lotus. These genes had positive effects on alkaloid content, albeit with phenotypic lag. The WGCNA of DEGs revealed that one network module was associated with the dynamic change of alkaloid content. Eleven genes encoding proteins with methyltransferase, oxidoreductase and CYP450 activities were identified. These were surmised to be genes involved in aporphine alkaloid biosynthesis. This transcriptomic database provides new directions for future studies on clarifying the aporphine alkaloid pathway.
Collapse
Affiliation(s)
- Mei Yang
- Key Laboratory of Aquatic Plant and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of SciencesWuhan, China
| | - Lingping Zhu
- Key Laboratory of Aquatic Plant and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of SciencesWuhan, China
- Department of Agricultural Sciences, Viikki Plant Science Center, University of HelsinkiHelsinki, Finland
| | - Ling Li
- Key Laboratory of Aquatic Plant and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of SciencesWuhan, China
- College of Life Science, University of Chinese Academy of SciencesBeijing, China
| | - Juanjuan Li
- Key Laboratory of Aquatic Plant and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of SciencesWuhan, China
- College of Life Science, University of Chinese Academy of SciencesBeijing, China
| | - Liming Xu
- Key Laboratory of Aquatic Plant and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of SciencesWuhan, China
| | - Ji Feng
- Tobacco Research Institute of Hubei ProvinceWuhan, China
| | - Yanling Liu
- Key Laboratory of Aquatic Plant and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of SciencesWuhan, China
- *Correspondence: Yanling Liu
| |
Collapse
|
25
|
Zhong J, Powell S, Preston JC. Organ boundary NAC-domain transcription factors are implicated in the evolution of petal fusion. PLANT BIOLOGY (STUTTGART, GERMANY) 2016; 18:893-902. [PMID: 27500862 DOI: 10.1111/plb.12493] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Accepted: 08/05/2016] [Indexed: 05/25/2023]
Abstract
UNLABELLED Research rationale: Evolution of fused petals (sympetaly) is considered to be an important innovation that has repeatedly led to increased pollination efficiency, resulting in accelerated rates of plant diversification. Although little is known about the underlying regulation of sympetaly, genetic pathways ancestrally involved in organ boundary establishment (e.g. CUP SHAPED COTYLEDON [CUC] 1-3 genes) are strong candidates. In sympetalous petunia, mutations in the CUC1/2-like orthologue NO APICAL MERISTEM (NAM) inhibit shoot apical meristem formation. Despite this, occasional 'escape shoots' develop flowers with extra petals and fused inter-floral whorl organs. Central methods: To To determine if petunia CUC-like genes regulate additional floral patterning, we used virus-induced silencing (VIGS) following establishment of healthy shoot apices to re-examine the role of NAM in petunia petal development, and uniquely characterise the CUC3 orthologue NH16. KEY RESULTS Confirming previous results, we found that reduced floral NAM/NH16 expression caused increased petal-stamen and stamen-carpel fusion, and often produced extra petals. However, further to previous results, all VIGS plants infected with NAM or NH16 constructs exhibited reduced fusion in the petal whorl compared to control plants. MAIN CONCLUSIONS Together with previous data, our results demonstrate conservation of petunia CUC-like genes in establishing inter-floral whorl organ boundaries, as well as functional evolution to affect the fusion of petunia petals.
Collapse
Affiliation(s)
- J Zhong
- Department of Plant Biology, The University of Vermont, Burlington, VT, USA
| | - S Powell
- Department of Plant Biology, The University of Vermont, Burlington, VT, USA
| | - J C Preston
- Department of Plant Biology, The University of Vermont, Burlington, VT, USA.
| |
Collapse
|
26
|
Shibuya K, Yamada T, Ichimura K. Morphological changes in senescing petal cells and the regulatory mechanism of petal senescence. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:5909-5918. [PMID: 27625416 DOI: 10.1093/jxb/erw337] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Petal senescence, or programmed cell death (PCD) in petals, is a developmentally regulated and genetically programmed process. During petal senescence, petal cells show morphological changes associated with PCD: tonoplast rupture and rapid destruction of the cytoplasm. This type of PCD is classified as vacuolar cell death or autolytic PCD based on morphological criteria. In PCD of petal cells, characteristic morphological features including an autophagy-like process, chromatin condensation, and nuclear fragmentation are also observed. While the phytohormone ethylene is known to play a crucial role in petal senescence in some plant species, little is known about the early regulation of ethylene-independent petal senescence. Recently, a NAC (NAM/ATAF1,2/CUC2) transcription factor was reported to control the progression of PCD during petal senescence in Japanese morning glory, which shows ethylene-independent petal senescence. In ethylene-dependent petal senescence, functional analyses of transcription factor genes have revealed the involvement of a basic helix-loop-helix protein and a homeodomain-leucine zipper protein in the transcriptional regulation of the ethylene biosynthesis pathway. Here we review the recent advances in our knowledge of petal senescence, mostly focusing on the morphology of senescing petal cells and the regulatory mechanisms of PCD by senescence-associated transcription factors during petal senescence.
Collapse
Affiliation(s)
- Kenichi Shibuya
- Institute of Vegetable and Floriculture Science, NARO, Tsukuba 305-0852, Japan
| | - Tetsuya Yamada
- Tokyo University of Agriculture and Technology, Tokyo 183-8509, Japan
| | - Kazuo Ichimura
- Institute of Vegetable and Floriculture Science, NARO, Tsukuba 305-0852, Japan
| |
Collapse
|
27
|
Daneva A, Gao Z, Van Durme M, Nowack MK. Functions and Regulation of Programmed Cell Death in Plant Development. Annu Rev Cell Dev Biol 2016; 32:441-468. [PMID: 27298090 DOI: 10.1146/annurev-cellbio-111315-124915] [Citation(s) in RCA: 137] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Programmed cell death (PCD) is a collective term for diverse processes causing an actively induced, tightly controlled cellular suicide. PCD has a multitude of functions in the development and health of multicellular organisms. In comparison to intensively studied forms of animal PCD such as apoptosis, our knowledge of the regulation of PCD in plants remains limited. Despite the importance of PCD in plant development and as a response to biotic and abiotic stresses, the complex molecular networks controlling different forms of plant PCD are only just beginning to emerge. With this review, we provide an update on the considerable progress that has been made over the last decade in our understanding of PCD as an inherent part of plant development. We highlight both functions of developmental PCD and central aspects of its molecular regulation.
Collapse
Affiliation(s)
- Anna Daneva
- Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium; .,Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium
| | - Zhen Gao
- Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium; .,Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium
| | - Matthias Van Durme
- Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium; .,Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium
| | - Moritz K Nowack
- Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium; .,Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium
| |
Collapse
|
28
|
Moschen S, Higgins J, Di Rienzo JA, Heinz RA, Paniego N, Fernandez P. Network and biosignature analysis for the integration of transcriptomic and metabolomic data to characterize leaf senescence process in sunflower. BMC Bioinformatics 2016; 17 Suppl 5:174. [PMID: 27295368 PMCID: PMC4905614 DOI: 10.1186/s12859-016-1045-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Background In recent years, high throughput technologies have led to an increase of datasets from omics disciplines allowing the understanding of the complex regulatory networks associated with biological processes. Leaf senescence is a complex mechanism controlled by multiple genetic and environmental variables, which has a strong impact on crop yield. Transcription factors (TFs) are key proteins in the regulation of gene expression, regulating different signaling pathways; their function is crucial for triggering and/or regulating different aspects of the leaf senescence process. The study of TF interactions and their integration with metabolic profiles under different developmental conditions, especially for a non-model organism such as sunflower, will open new insights into the details of gene regulation of leaf senescence. Results Weighted Gene Correlation Network Analysis (WGCNA) and BioSignature Discoverer (BioSD, Gnosis Data Analysis, Heraklion, Greece) were used to integrate transcriptomic and metabolomic data. WGCNA allowed the detection of 10 metabolites and 13 TFs whereas BioSD allowed the detection of 1 metabolite and 6 TFs as potential biomarkers. The comparative analysis demonstrated that three transcription factors were detected through both methodologies, highlighting them as potentially robust biomarkers associated with leaf senescence in sunflower. Conclusions The complementary use of network and BioSignature Discoverer analysis of transcriptomic and metabolomic data provided a useful tool for identifying candidate genes and metabolites which may have a role during the triggering and development of the leaf senescence process. The WGCNA tool allowed us to design and test a hypothetical network in order to infer relationships across selected transcription factor and metabolite candidate biomarkers involved in leaf senescence, whereas BioSignature Discoverer selected transcripts and metabolites which discriminate between different ages of sunflower plants. The methodology presented here would help to elucidate and predict novel networks and potential biomarkers of leaf senescence in sunflower. Electronic supplementary material The online version of this article (doi:10.1186/s12859-016-1045-2) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Sebastián Moschen
- Instituto de Biotecnología, Centro de Investigaciones en Ciencias Agronómicas y Veterinarias, Instituto Nacional de Tecnología Agropecuaria, Hurlingham, Buenos Aires, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas, Ciudad Autónoma de Buenos Aires, Argentina
| | - Janet Higgins
- The Genome Analysis Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Julio A Di Rienzo
- Facultad de Ciencias Agropecuarias, Universidad Nacional de Córdoba, Córdoba, Argentina
| | - Ruth A Heinz
- Instituto de Biotecnología, Centro de Investigaciones en Ciencias Agronómicas y Veterinarias, Instituto Nacional de Tecnología Agropecuaria, Hurlingham, Buenos Aires, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas, Ciudad Autónoma de Buenos Aires, Argentina
| | - Norma Paniego
- Instituto de Biotecnología, Centro de Investigaciones en Ciencias Agronómicas y Veterinarias, Instituto Nacional de Tecnología Agropecuaria, Hurlingham, Buenos Aires, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas, Ciudad Autónoma de Buenos Aires, Argentina
| | - Paula Fernandez
- Instituto de Biotecnología, Centro de Investigaciones en Ciencias Agronómicas y Veterinarias, Instituto Nacional de Tecnología Agropecuaria, Hurlingham, Buenos Aires, Argentina. .,Consejo Nacional de Investigaciones Científicas y Técnicas, Ciudad Autónoma de Buenos Aires, Argentina. .,Escuela de Ciencia y Tecnología, Universidad Nacional de San Martín, San Martín, Buenos Aires, Argentina.
| |
Collapse
|
29
|
Vandenbussche M, Chambrier P, Rodrigues Bento S, Morel P. Petunia, Your Next Supermodel? FRONTIERS IN PLANT SCIENCE 2016; 7:72. [PMID: 26870078 PMCID: PMC4735711 DOI: 10.3389/fpls.2016.00072] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Accepted: 01/15/2016] [Indexed: 05/24/2023]
Abstract
Plant biology in general, and plant evo-devo in particular would strongly benefit from a broader range of available model systems. In recent years, technological advances have facilitated the analysis and comparison of individual gene functions in multiple species, representing now a fairly wide taxonomic range of the plant kingdom. Because genes are embedded in gene networks, studying evolution of gene function ultimately should be put in the context of studying the evolution of entire gene networks, since changes in the function of a single gene will normally go together with further changes in its network environment. For this reason, plant comparative biology/evo-devo will require the availability of a defined set of 'super' models occupying key taxonomic positions, in which performing gene functional analysis and testing genetic interactions ideally is as straightforward as, e.g., in Arabidopsis. Here we review why petunia has the potential to become one of these future supermodels, as a representative of the Asterid clade. We will first detail its intrinsic qualities as a model system. Next, we highlight how the revolution in sequencing technologies will now finally allows exploitation of the petunia system to its full potential, despite that petunia has already a long history as a model in plant molecular biology and genetics. We conclude with a series of arguments in favor of a more diversified multi-model approach in plant biology, and we point out where the petunia model system may further play a role, based on its biological features and molecular toolkit.
Collapse
|
30
|
Li YH, Zhang W, Li Y. Transcriptomic Analysis of Flower Blooming in Jasminum sambac through De Novo RNA Sequencing. Molecules 2015; 20:10734-47. [PMID: 26065837 PMCID: PMC6272439 DOI: 10.3390/molecules200610734] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Revised: 06/01/2015] [Accepted: 06/08/2015] [Indexed: 12/21/2022] Open
Abstract
Flower blooming is a critical and complicated plant developmental process in flowering plants. However, insufficient information is available about the complex network that regulates flower blooming in Jasminum sambac. In this study, we used the RNA-Seq platform to analyze the molecular regulation of flower blooming in J. sambac by comparing the transcript profiles at two flower developmental stages: budding and blooming. A total of 4577 differentially-expressed genes (DEGs) were identified between the two floral stages. The Gene Ontology and the Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses revealed that the DEGs in the “oxidation-reduction process”, “extracellular region”, “steroid biosynthesis”, “glycosphingolipid biosynthesis”, “plant hormone signal transduction” and “pentose and glucuronate interconversions” might be associated with flower development. A total of 103 and 92 unigenes exhibited sequence similarities to the known flower development and floral scent genes from other plants. Among these unigenes, five flower development and 19 floral scent unigenes exhibited at least four-fold differences in expression between the two stages. Our results provide abundant genetic resources for studying the flower blooming mechanisms and molecular breeding of J. sambac.
Collapse
Affiliation(s)
- Yong-Hua Li
- College of Forestry, Henan Agricultural University, Zhengzhou 450002, China.
| | - Wei Zhang
- College of Life Sciences, Xinyang Normal University, Xinyang 464000, China.
| | - Yong Li
- College of Forestry, Henan Agricultural University, Zhengzhou 450002, China.
| |
Collapse
|
31
|
Zhao P, Zhang L, Zhao L. Dissection of the style's response to pollination using transcriptome profiling in self-compatible (Solanum pimpinellifolium) and self-incompatible (Solanum chilense) tomato species. BMC PLANT BIOLOGY 2015; 15:119. [PMID: 25976872 PMCID: PMC4431037 DOI: 10.1186/s12870-015-0492-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2015] [Accepted: 04/10/2015] [Indexed: 05/05/2023]
Abstract
BACKGROUND Tomato (Solanum lycopersicum) self-compatibility (SC) is defined as self-pollen tubes that can penetrate their own stigma, elongate in the style and fertilize their own ovules. Self-incompatibility (SI) is defined as self-pollen tubes that are prevented from developing in the style. To determine the influence of gene expression on style self-pollination, a transcriptome-wide comparative analysis of SC and SI tomato unpollinated/pollinated styles was performed using RNA-sequencing (RNA-seq) data. RESULTS Transcriptome profiles of 24-h unpollination (UP) and self-pollination (P) styles from SC and SI tomato species were generated using high-throughput next generation sequencing. From the comparison of SC self-pollinated and unpollinated styles, 1341 differentially expressed genes (DEGs) were identified, of which 753 were downregulated and 588 were upregulated. From the comparison of SI self-pollinated and unpollinated styles, 804 DEGs were identified, of which 215 were downregulated and 589 were upregulated. Nine gene ontology (GO) terms were enriched significantly in SC and 78 GO terms were enriched significantly in SI. A total of 105 enriched Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were identified in SC and 80 enriched KEGG pathways were identified in SI, among which "Cysteine and methionine metabolism pathway" and "Plant hormone signal transduction pathway" were significantly enriched in SI. CONCLUSIONS This study is the first global transcriptome-wide comparative analysis of SC and SI tomato unpollinated/pollinated styles. Advanced bioinformatic analysis of DEGs uncovered the pathways of "Cysteine and methionine metabolism" and "Plant hormone signal transduction", which are likely to play important roles in the control of pollen tubes growth in SI species.
Collapse
Affiliation(s)
- Panfeng Zhao
- Joint Tomato Research Institute, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China.
- Plant Biotechnology Research Center, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China.
| | - Lida Zhang
- Plant Biotechnology Research Center, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China.
| | - Lingxia Zhao
- Joint Tomato Research Institute, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China.
- Plant Biotechnology Research Center, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China.
| |
Collapse
|