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Guo W, Yang Y, Ma B, Wang W, Hu Z, Leng P. Selection and Validation of Reference Genes for Gene Expression Studies in Euonymus japonicus Based on RNA Sequencing. Genes (Basel) 2024; 15:131. [PMID: 38275612 PMCID: PMC10815735 DOI: 10.3390/genes15010131] [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: 12/19/2023] [Revised: 01/13/2024] [Accepted: 01/19/2024] [Indexed: 01/27/2024] Open
Abstract
Euonymus japonicus is one of the most low-temperature-tolerant evergreen broad-leaved tree species in the world and is widely used in urban greening. However, there are very few molecular biology studies on its low-temperature tolerance mechanism. So far, no researcher has selected and reported on its reference genes. In this study, 21 candidate reference genes (12 traditional housekeeping genes and 9 other genes) were initially selected based on gene expression and coefficient of variation (CV) through RNA-Seq (unpublished data), and qRT-PCR was used to detect the expression levels of candidate reference genes in three different groups of samples (leaves under different temperature stresses, leaves of plants at different growth stages, and different organs). After further evaluating the expression stability of these genes using geNorm, NormFinder, Bestkeeper, and RefFind, the results show that the traditional housekeeping gene eIF5A and the new reference gene RTNLB1 have good stability in the three different groups of samples, so they are reference genes with universality. In addition, we used eIF5A and RTNLB1 as reference genes to calibrate the expression pattern of the target gene EjMAH1, which confirmed this view. This article is the first to select and report on the reference gene of E. japonicus, laying the foundation for its low-temperature tolerance mechanism and other molecular biology research.
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Affiliation(s)
- Wei Guo
- College of Landscape Architecture, Beijing University of Agriculture, Beijing 102206, China; (W.G.); (B.M.); (W.W.)
| | - Yihui Yang
- College of Landscape Architecture, Beijing University of Agriculture, Beijing 102206, China; (W.G.); (B.M.); (W.W.)
| | - Bo Ma
- College of Landscape Architecture, Beijing University of Agriculture, Beijing 102206, China; (W.G.); (B.M.); (W.W.)
| | - Wenbo Wang
- College of Landscape Architecture, Beijing University of Agriculture, Beijing 102206, China; (W.G.); (B.M.); (W.W.)
| | - Zenghui Hu
- Engineering Research Center for Ancient Tree Health and Ancient Tree Culture of National Forestry and Grassland Administration, Beijing 102206, China
| | - Pingsheng Leng
- College of Landscape Architecture, Beijing University of Agriculture, Beijing 102206, China; (W.G.); (B.M.); (W.W.)
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Ste-Croix DT, Bélanger RR, Mimee B. Single Nematode Transcriptomic Analysis, Using Long-Read Technology, Reveals Two Novel Virulence Gene Candidates in the Soybean Cyst Nematode, Heterodera glycines. Int J Mol Sci 2023; 24:ijms24119440. [PMID: 37298400 DOI: 10.3390/ijms24119440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 05/18/2023] [Accepted: 05/24/2023] [Indexed: 06/12/2023] Open
Abstract
The soybean cyst nematode (Heterodera glycines, SCN), is the most damaging disease of soybean in North America. While management of this pest using resistant soybean is generally still effective, prolonged exposure to cultivars derived from the same source of resistance (PI 88788) has led to the emergence of virulence. Currently, the underlying mechanisms responsible for resistance breakdown remain unknown. In this study, we combined a single nematode transcriptomic profiling approach with long-read sequencing to reannotate the SCN genome. This resulted in the annotation of 1932 novel transcripts and 281 novel gene features. Using a transcript-level quantification approach, we identified eight novel effector candidates overexpressed in PI 88788 virulent nematodes in the late infection stage. Among these were the novel gene Hg-CPZ-1 and a pioneer effector transcript generated through the alternative splicing of the non-effector gene Hetgly21698. While our results demonstrate that alternative splicing in effectors does occur, we found limited evidence of direct involvement in the breakdown of resistance. However, our analysis highlighted a distinct pattern of effector upregulation in response to PI 88788 resistance indicative of a possible adaptation process by SCN to host resistance.
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Affiliation(s)
- Dave T Ste-Croix
- Saint-Jean-sur-Richelieu Research and Development Centre, Agriculture and Agri-Food Canada, Saint-Jean-sur-Richelieu, QC J3B 3E6, Canada
- Département de Phytologie, Université Laval, Québec, QC G1V 0A6, Canada
| | - Richard R Bélanger
- Département de Phytologie, Université Laval, Québec, QC G1V 0A6, Canada
- Centre de Recherche et d'Innovation sur les Végétaux (CRIV), Université Laval, Québec, QC G1V 0A6, Canada
| | - Benjamin Mimee
- Saint-Jean-sur-Richelieu Research and Development Centre, Agriculture and Agri-Food Canada, Saint-Jean-sur-Richelieu, QC J3B 3E6, Canada
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Genome Expression Dynamics Reveal the Parasitism Regulatory Landscape of the Root-Knot Nematode Meloidogyne incognita and a Promoter Motif Associated with Effector Genes. Genes (Basel) 2021; 12:genes12050771. [PMID: 34070210 PMCID: PMC8158474 DOI: 10.3390/genes12050771] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 05/04/2021] [Accepted: 05/10/2021] [Indexed: 12/21/2022] Open
Abstract
Root-knot nematodes (genus Meloidogyne) are the major contributor to crop losses caused by nematodes. These nematodes secrete effector proteins into the plant, derived from two sets of pharyngeal gland cells, to manipulate host physiology and immunity. Successful completion of the life cycle, involving successive molts from egg to adult, covers morphologically and functionally distinct stages and will require precise control of gene expression, including effector genes. The details of how root-knot nematodes regulate transcription remain sparse. Here, we report a life stage-specific transcriptome of Meloidogyne incognita. Combined with an available annotated genome, we explore the spatio-temporal regulation of gene expression. We reveal gene expression clusters and predicted functions that accompany the major developmental transitions. Focusing on effectors, we identify a putative cis-regulatory motif associated with expression in the dorsal glands, providing an insight into effector regulation. We combine the presence of this motif with several other criteria to predict a novel set of putative dorsal gland effectors. Finally, we show this motif, and thereby its utility, is broadly conserved across the Meloidogyne genus, and we name it Mel-DOG. Taken together, we provide the first genome-wide analysis of spatio-temporal gene expression in a root-knot nematode and identify a new set of candidate effector genes that will guide future functional analyses.
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Li J, Zhang Z, Xu C, Wang D, Lv M, Xie H. Identification and validation of reference genes for real-time RT-PCR in Aphelenchoides besseyi. Mol Biol Rep 2020; 47:4485-4494. [PMID: 32468259 PMCID: PMC7295731 DOI: 10.1007/s11033-020-05547-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 05/23/2020] [Indexed: 01/08/2023]
Abstract
Fragments of four candidate reference genes of Aphelenchoides besseyi, including actin, glyceraldehyde-3-phosphate dehydrogenase (GAPDH), ubiquitin conjugating-3 enzyme (UBC) and alpha-tubulin (α-tubulin) were cloned from the transcriptome database of A. besseyi. The expression level of these four candidate reference genes and a commonly used reference gene of A. besseyi (18S rRNA) in three experimental conditions, including the four life stages (female, male, juvenile and egg) of two populations and the mixed-stage nematodes of four populations with different origins and hosts were analyzed by RT-qPCR. The expression stability of the five candidate reference genes under the three experimental conditions was analyzed by ΔCt, geNorm, NormFinder and RefFinder respectively. The analysis results of ΔCt, geNorm, NormFinder and RefFinder all indicated that UBC was the gene with the highest average ranking of stability. In conclusion, the expression stability of UBC was optimal under the three experimental conditions, indicating that UBC could be used as a suitable reference gene instead of 18S rRNA in the RT-qPCR analysis for A. besseyi.
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Affiliation(s)
- Junyi Li
- Laboratory of Plant Nematology and Research Center of Nematodes of Plant Quarantine, Department of Plant Pathology/Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Agriculture, South China Agricultural University, 483 Wushan Road, Guangzhou, 510642, Guangdong, People's Republic of China
| | - Zixu Zhang
- Laboratory of Plant Nematology and Research Center of Nematodes of Plant Quarantine, Department of Plant Pathology/Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Agriculture, South China Agricultural University, 483 Wushan Road, Guangzhou, 510642, Guangdong, People's Republic of China
| | - Chunling Xu
- Laboratory of Plant Nematology and Research Center of Nematodes of Plant Quarantine, Department of Plant Pathology/Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Agriculture, South China Agricultural University, 483 Wushan Road, Guangzhou, 510642, Guangdong, People's Republic of China
| | - Dongwei Wang
- Laboratory of Plant Nematology and Research Center of Nematodes of Plant Quarantine, Department of Plant Pathology/Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Agriculture, South China Agricultural University, 483 Wushan Road, Guangzhou, 510642, Guangdong, People's Republic of China
| | - Mei Lv
- Laboratory of Plant Nematology and Research Center of Nematodes of Plant Quarantine, Department of Plant Pathology/Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Agriculture, South China Agricultural University, 483 Wushan Road, Guangzhou, 510642, Guangdong, People's Republic of China
| | - Hui Xie
- Laboratory of Plant Nematology and Research Center of Nematodes of Plant Quarantine, Department of Plant Pathology/Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Agriculture, South China Agricultural University, 483 Wushan Road, Guangzhou, 510642, Guangdong, People's Republic of China.
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Selection and Validation of Reference Genes for Gene Expression Studies in Codonopsis pilosula Based on Transcriptome Sequence Data. Sci Rep 2020; 10:1362. [PMID: 31992780 PMCID: PMC6987187 DOI: 10.1038/s41598-020-58328-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Accepted: 12/31/2019] [Indexed: 01/30/2023] Open
Abstract
Relative gene expression analyses by RT-qPCR (reverse transcription-quantitative PCR) are highly dependent on the reference genes in normalizing the expression data of target genes. Therefore, inappropriate endogenous control genes will lead to inaccurate target gene expression profiles, and the selection and validation of suitable internal reference genes becomes essential. In this study, we retrieved the commonly used reference genes in transcriptome datasets of Codonopsis pilosula by RNA-Seq (unpublished data), and selected 15 candidate reference genes according to the coefficient of variation (CV) and fold change (FC) value of gene expression. The expression levels of candidate reference genes, which is at different growth stages, undergoing cold stress and drought stress, was determined by RT-qPCR. The expression stability of these genes was evaluated using software packages and algorithms including ΔCt, geNorm, NormFinder and Bestkeeper. Then appropriate reference genes were screened and validated by target gene-UDGPase (UDP glucose pyrophosphorylase). The optimal RGs combinations of C. pilosula, including PP2A59γ, CPY20-1, UBCE32, RPL5B and UBC18 for developmental stage, RPL5B, RPL13 and PP2A59γ for cold treatment, RPL13 and PP2A59γ for drought treatment, were found and proposed as reference genes for future work. This paper laid foundations for both the selection of reference genes and exploration in metabolic mechanism of C. pilosula.
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Yang Z, Wang K, Aziz U, Zhao C, Zhang M. Evaluation of duplicated reference genes for quantitative real-time PCR analysis in genome unknown hexaploid oat ( Avena sativa L.). PLANT METHODS 2020; 16:138. [PMID: 33072174 PMCID: PMC7560290 DOI: 10.1186/s13007-020-00679-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 10/05/2020] [Indexed: 05/08/2023]
Abstract
BACKGROUND Oat (Avena sativa L.), a hexaploid crop with unknown genome, has valuable nutritional, medicinal and pharmaceutical uses. However, no suitable RGs (reference genes) for qPCR (quantitative real-time PCR) has been documented for oat yet. Single-copy gene is often selected as RG, which is challengeable or impactable in unexplored polyploids. RESULTS In this study, eleven candidate RGs, including four duplicated genes, were selected from oat transcriptome. The stability and the optimal combination of these candidate RGs were assessed in 18 oat samples by using four statistical algorithms including the ΔCt method, geNorm, NormFinder and BestKeeper. The most stable RGs for "all samples", "shoots and roots of seedlings", "developing seeds" and "developing endosperms" were EIF4A (Eukaryotic initiation factor 4A-3), UBC21 (Ubiquitin-Conjugating Enzyme 21), EP (Expressed protein) and EIF4A respectively. Among these RGs, UBC21 was a four-copy duplicated gene. The reliability was validated by the expression patterns of four various genes normalized to the most and the least stable RGs in different sample sets. CONCLUSIONS Results provide a proof of concept that the duplicated RG is feasible for qPCR in polyploids. To our knowledge, this study is the first systematic research on the optimal RGs for accurate qPCR normalization of gene expression in different organs and tissues of oat.
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Affiliation(s)
- Zheng Yang
- College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Kai Wang
- College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Usman Aziz
- College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Cuizhu Zhao
- College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Meng Zhang
- College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
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Mimee B, Dauphinais N, Bélair G. "Piler Dirt" Survey for the Sampling and Detection of Potato Cyst Nematodes. PLANT DISEASE 2019; 103:2065-2069. [PMID: 31169084 DOI: 10.1094/pdis-12-18-2188-re] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Potato cyst nematodes are a significant threat to potato production worldwide and have important economic impacts due to yield losses but also because of the expenses associated with regulation procedures. In order to reduce the sampling labor, an alternative strategy named the "Piler Dirt" that collects the soil carried with potato tubers during their transfer to storage was proposed. The method showed a better sensitivity than the reference method to detect fields infested with G. rostochiensis. The quantification of the number of cysts per kilogram of soil was proportional between the two methods at low and moderate population densities (R2 = 0.885) but no correlations were found at high density. However, the quantity of soil generated by the method was exceedingly large to be treated by diagnostic labs. It was shown that subsampling six aliquots, each equivalent to 5,000 cm3/ha, from the total quantity of soil generated by the Piler Dirt method, resulted in a probability of 97% to detect infested fields, 95% of the time in our dataset. Overall, Piler Dirt appears as a good compromise to reduce labor time and cost without significantly affecting sensitivity. However, it will be challenging to implement because it needs to be done simultaneously with harvest and will require the participation of farmers during a busy period.
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Affiliation(s)
- Benjamin Mimee
- Agriculture and Agri-Food Canada, Saint-Jean-sur-Richelieu Research and Development Centre, 430 boulevard Gouin, Saint-Jean-sur-Richelieu, QC, J3B 3E6 Canada
| | - Nathalie Dauphinais
- Agriculture and Agri-Food Canada, Saint-Jean-sur-Richelieu Research and Development Centre, 430 boulevard Gouin, Saint-Jean-sur-Richelieu, QC, J3B 3E6 Canada
| | - Guy Bélair
- Agriculture and Agri-Food Canada, Saint-Jean-sur-Richelieu Research and Development Centre, 430 boulevard Gouin, Saint-Jean-sur-Richelieu, QC, J3B 3E6 Canada
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Sabeh M, Lord E, Grenier É, St-Arnaud M, Mimee B. What determines host specificity in hyperspecialized plant parasitic nematodes? BMC Genomics 2019; 20:457. [PMID: 31170914 PMCID: PMC6555003 DOI: 10.1186/s12864-019-5853-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Accepted: 05/28/2019] [Indexed: 12/21/2022] Open
Abstract
Background In hyperspecialized parasites, the ability to grow on a particular host relies on specific virulence factors called effectors. These excreted proteins are involved in the molecular mechanisms of parasitism and distinguish virulent pathogens from non-virulent related species. The potato cyst nematodes (PCN) Globodera rostochiensis and G. pallida are major plant-parasitic nematodes developing on numerous solanaceous species including potato. Their close relatives, G. tabacum and G. mexicana are stimulated by potato root diffusate but unable to establish a feeding site on this plant host. Results RNA sequencing was used to characterize transcriptomic differences among these four Globodera species and to identify genes associated with host specificity. We identified seven transcripts that were unique to PCN species, including a protein involved in ubiquitination. We also found 545 genes that were differentially expressed between PCN and non-PCN species, including 78 genes coding for effector proteins, which represent more than a 6-fold enrichment compared to the whole transcriptome. Gene polymorphism analysis identified 359 homozygous non-synonymous variants showing a strong evidence for selection in PCN species. Conclusions Overall, we demonstrated that the determinant of host specificity resides in the regulation of essential effector gene expression that could be under the control of a single or of very few regulatory genes. Such genes are therefore promising targets for the development of novel and more sustainable resistances against potato cyst nematodes. Electronic supplementary material The online version of this article (10.1186/s12864-019-5853-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Michael Sabeh
- St-Jean-sur-Richelieu Research and Development Center, Agriculture and Agri-Food Canada, St-Jean-sur-Richelieu, Quebec, Canada.,Biodiversity Center, Institut de recherche en biologie végétale, Université de Montréal and Jardin botanique de Montréal, Montreal, Quebec, Canada
| | - Etienne Lord
- St-Jean-sur-Richelieu Research and Development Center, Agriculture and Agri-Food Canada, St-Jean-sur-Richelieu, Quebec, Canada
| | - Éric Grenier
- INRA, UMR1349 IGEPP (Institute of Genetics, Environment and Plant Protection), F-35653, Le Rheu, France
| | - Marc St-Arnaud
- Biodiversity Center, Institut de recherche en biologie végétale, Université de Montréal and Jardin botanique de Montréal, Montreal, Quebec, Canada
| | - Benjamin Mimee
- St-Jean-sur-Richelieu Research and Development Center, Agriculture and Agri-Food Canada, St-Jean-sur-Richelieu, Quebec, Canada.
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