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Damerval C, Claudot C, Le Guilloux M, Conde e Silva N, Brunaud V, Soubigou-Taconnat L, Caius J, Delannoy E, Nadot S, Jabbour F, Deveaux Y. Evolutionary analyses and expression patterns of TCP genes in Ranunculales. FRONTIERS IN PLANT SCIENCE 2022; 13:1055196. [PMID: 36531353 PMCID: PMC9752903 DOI: 10.3389/fpls.2022.1055196] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 11/04/2022] [Indexed: 06/17/2023]
Abstract
TCP transcription factors play a role in a large number of developmental processes and are at the crossroads of numerous hormonal biosynthetic and signaling pathways. The complete repertoire of TCP genes has already been characterized in several plant species, but not in any species of early diverging eudicots. We focused on the order Ranunculales because of its phylogenetic position as sister group to all other eudicots and its important morphological diversity. Results show that all the TCP genes expressed in the floral transcriptome of Nigella damascena (Ranunculaceae) are the orthologs of the TCP genes previously identified from the fully sequenced genome of Aquilegia coerulea. Phylogenetic analyses combined with the identification of conserved amino acid motifs suggest that six paralogous genes of class I TCP transcription factors were present in the common ancestor of angiosperms. We highlight independent duplications in core eudicots and Ranunculales within the class I and class II subfamilies, resulting in different numbers of paralogs within the main subclasses of TCP genes. This has most probably major consequences on the functional diversification of these genes in different plant clades. The expression patterns of TCP genes in Nigella damascena were consistent with the general suggestion that CIN and class I TCP genes may have redundant roles or take part in same pathways, while CYC/TB1 genes have more specific actions. Our findings open the way for future studies at the tissue level, and for investigating redundancy and subfunctionalisation in TCP genes and their role in the evolution of morphological novelties.
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Affiliation(s)
- Catherine Damerval
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, Génétique Quantitative et Evolution-Le Moulon, IDEEV, Gif-sur-Yvette, France
| | - Carmine Claudot
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, Génétique Quantitative et Evolution-Le Moulon, IDEEV, Gif-sur-Yvette, France
| | - Martine Le Guilloux
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, Génétique Quantitative et Evolution-Le Moulon, IDEEV, Gif-sur-Yvette, France
| | - Natalia Conde e Silva
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, Génétique Quantitative et Evolution-Le Moulon, IDEEV, Gif-sur-Yvette, France
| | - Véronique Brunaud
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay, France
| | - Ludivine Soubigou-Taconnat
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay, France
| | - José Caius
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay, France
| | - Etienne Delannoy
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay, France
| | - Sophie Nadot
- Université Paris-Saclay, CNRS, AgroParisTech, Ecologie Systématique Evolution, Orsay, France
| | - Florian Jabbour
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d’Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France
| | - Yves Deveaux
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, Génétique Quantitative et Evolution-Le Moulon, IDEEV, Gif-sur-Yvette, France
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In-Depth Analysis of an Obligate Anaerobe Paraclostridium bifermentans Isolated from Uterus of Bubalus bubalis. Animals (Basel) 2022; 12:ani12141765. [PMID: 35883312 PMCID: PMC9311886 DOI: 10.3390/ani12141765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 05/12/2022] [Accepted: 05/18/2022] [Indexed: 11/17/2022] Open
Abstract
Simple Summary Non-specific uterine infections in bovine (uterine line inflammation) are a significant issue for the dairy industry. These infections are responsible for significant financial losses all over the world. Paraclostridium bifermentans is an obligate anaerobe, gram-positive rod-shaped bacteria belonging to the Clostridia class and the Peptostreptococcaceae family produces endospores. This bacterium has the ability to infiltrate bovine uterine endometrial epithelial cells and cause infection in the endometrium epithelial cells. Our study found that an examination of a buffalo uterus with yellowish purulent discharge reported the presence of pathogenic bacteria Paraclostridium bifermentans, where its genomic characterization, substrate utilization, and antibiotic susceptibility potentiality was studied. This discovery indicates the presence of virulence genes as well as pathogenic features. This is the first report of P. bifermentans from the bovine uterus environment. Abstract Chronic non-specific contamination of the reproductive tract in animals is a major issue during early postpartum, natural coitus, or artificial insemination. Uterine infection is one of the major concerns reducing fertility, production loss, and early culling of the animals. Therefore, the aim of this study was to identify any novel bacterium if present in the uterine environment of Bubalus bubalis causing infections. A strictly anaerobic bacterial strain designated as Paraclostridium bifermentans GBRC was isolated and characterized. Bacterium was found to be Gram positive moderate rod with motility. The optimum growth was observed at 40 ± 2 °C. The pathogenic characteristics of the GBRC strain, such as hemolysis, gelatin hydrolysis, and the production of volatile sulfur compounds, were similar to those seen in the epithelial layer invading pathogenic strains. Assembled genome size was 3.6 MB, with 78 contigs, and a G + C content of 28.10%. Furthermore, the whole genome sequence analysis confirmed the presence of genes encoding virulence factors and provided genomic insights on adaptation of the strain in the uterine environment. Based on the phenotypic and genetic differences with phylogenetic relatives, strain GBRC is proposed to represent a first reported species of the genus Paraclostridium with potential pathogenic character, from the buffalo uterine environment. This study analysis of the GBRC strain serves as a key reference point for the investigation of potential pathogenic strains that may cause endometritis and metritis in bovine.
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Xu Y, Ji X, Xu Z, Yuan Y, Chen X, Kong D, Zhang Y, Sun D. Transcriptome Profiling Reveals a Petunia Transcription Factor, PhCOL4, Contributing to Antiviral RNA Silencing. FRONTIERS IN PLANT SCIENCE 2022; 13:876428. [PMID: 35498675 PMCID: PMC9047179 DOI: 10.3389/fpls.2022.876428] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 03/21/2022] [Indexed: 06/12/2023]
Abstract
RNA silencing is a common antiviral mechanism in eukaryotic organisms. However, the transcriptional regulatory mechanism that controls the RNA silencing process remains elusive. Here, we performed high-depth transcriptome analysis on petunia (Petunia hybrida) leaves infected with tobacco rattle virus (TRV) strain PPK20. A total of 7,402 differentially expressed genes (DEGs) were identified. Of them, some RNA silencing-related transcripts, such as RNA-dependent RNA polymerases (RDRs), Dicer-like RNase III enzymes (DCLs), and Argonautes (AGOs), were induced by viral attack. Furthermore, we performed TRV-based virus-induced gene silencing (VIGS) assay on 39 DEGs encoding putative transcription factors (TFs), using green fluorescent protein (GFP) and phytoene desaturase (PhPDS) as reporters. Results showed that the down-regulation of PhbHLH41, PhbHLH93, PhZPT4-3, PhCOL4, PhHSF-B3A, PhNAC90, and PhWRKY75 led to enhanced TRV accumulation and inhibited PhPDS-silenced photobleaching phenotype. In contrast, silencing of PhERF22 repressed virus accumulation and promoted photobleaching development. Thus, these TFs were identified as potential positive and negative regulators of antiviral RNA silencing, respectively. One positive regulator PhCOL4, belonging to the B-box zinc finger family, was selected for further functional characterization. Silencing and transient overexpression of PhCOL4 resulted in decreased and increased expression of several RNA silencing-related genes. DNA affinity purification sequencing analysis revealed that PhCOL4 targeted PhRDR6 and PhAGO4. Dual luciferase and yeast one-hybrid assays determined the binding of PhCOL4 to the PhRDR6 and PhAGO4 promoters. Our findings suggest that TRV-GFP-PhPDS-based VIGS could be helpful to identify transcriptional regulators of antiviral RNA silencing.
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Affiliation(s)
- Yingru Xu
- College of Landscape Architecture and Arts, Northwest A&F University, Yangling, China
| | - Xiaotong Ji
- College of Landscape Architecture and Arts, Northwest A&F University, Yangling, China
| | - Zhuangzhuang Xu
- College of Landscape Architecture and Arts, Northwest A&F University, Yangling, China
| | - Yanping Yuan
- College of Landscape Architecture and Arts, Northwest A&F University, Yangling, China
| | - Xiling Chen
- College of Landscape Architecture and Arts, Northwest A&F University, Yangling, China
| | - Derong Kong
- College of Landscape Architecture and Arts, Northwest A&F University, Yangling, China
| | - Yanlong Zhang
- College of Landscape Architecture and Arts, Northwest A&F University, Yangling, China
- National Engineering Technology Research Center for Oil Peony, Northwest A&F University, Yangling, China
| | - Daoyang Sun
- College of Landscape Architecture and Arts, Northwest A&F University, Yangling, China
- National Engineering Technology Research Center for Oil Peony, Northwest A&F University, Yangling, China
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Gao Z, Guo L, Ramakrishnan M, Xiang Y, Jiao C, Jiang J, Vinod KK, Fei Z, Que F, Ding Y, Yu F, Chen T, Wei Q. Cellular and molecular characterizations of the irregular internode division zone formation of a slow-growing bamboo variant. TREE PHYSIOLOGY 2022; 42:570-584. [PMID: 34633049 DOI: 10.1093/treephys/tpab129] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2021] [Revised: 09/01/2021] [Accepted: 09/24/2021] [Indexed: 05/16/2023]
Abstract
The key molecular mechanisms underlying the sectionalized growth within bamboo or other grass internodes remain largely unknown. Here, we genetically and morphologically compared the culm and rhizome internode division zones (DZs) of a slow-growing bamboo variant (sgv) having dwarf internodes, with those of the corresponding wild type (WT). Histological analysis discovers that the sgv has an irregular internode DZ. However, the shoot apical meristems in height, width, outside shape, cell number and cell width of the sgv and the WT were all similar. The DZ irregularities first appeared post apical meristem development, in 1-mm sgv rhizome internodes. Thus, the sgv is a DZ irregularity bamboo variant, which has been first reported in bamboo according to our investigation. Transcriptome sequencing analysis finds that a number of cell wall biogenesis and cell division-related genes are dramatically downregulated in the sgv DZ. Interestingly, both transcriptomic and brassinosteroid (BR) contents detection, as well as quantitative real-time PCR analyses show that these irregularities have resulted from the BR signaling pathway defects. Brassinosteroid defect might also cause the erect leaves and branches as well as the irregular epidermis of the sgv. These results suggest that BR signaling pathway plays critical roles in bamboo internode DZ and leaf development from a mutant perspective and also explain the upstream mechanisms causing the dwarf internode of the sgv bamboo.
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Affiliation(s)
- Zhipeng Gao
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, 159 Longpan Road Nanjing, Jiangsu 210037, China
| | - Lin Guo
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, 159 Longpan Road Nanjing, Jiangsu 210037, China
| | - Muthusamy Ramakrishnan
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, 159 Longpan Road Nanjing, Jiangsu 210037, China
| | - Yu Xiang
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, 159 Longpan Road Nanjing, Jiangsu 210037, China
| | - Chen Jiao
- Boyce Thompson Institute, Cornell University, 533 Tower Road, Ithaca, NY 14853, USA
- College of Agriculture and Biotechnology, Zhejiang University, 866 Yuhangtang Road, Hangzhou, Zhejiang 310058, China
| | - Jiaweng Jiang
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, 159 Longpan Road Nanjing, Jiangsu 210037, China
| | - Kunnummal K Vinod
- Division of Genetics, ICAR-Indian Agricultural Research Institute, Sahyadri Ave New Delhi, 110012, India
| | - Zhangjun Fei
- Boyce Thompson Institute, Cornell University, 533 Tower Road, Ithaca, NY 14853, USA
| | - Feng Que
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, 159 Longpan Road Nanjing, Jiangsu 210037, China
| | - Yulong Ding
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, 159 Longpan Road Nanjing, Jiangsu 210037, China
| | - Fen Yu
- Jiangxi Provincial Key Laboratory for Bamboo Germplasm Resources and Utilization, Jiangxi Agriculture University, College of Forestry, 1101 Zhimin Road, Nanchang, Jiangxi 330045, China
| | - Tianguo Chen
- Changzhou Agricultural Technology Extension Center, 289-1 Changjiang Middle Road, Changzhou, Jiangsu 213000, China
| | - Qiang Wei
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, 159 Longpan Road Nanjing, Jiangsu 210037, China
- Jiangxi Provincial Key Laboratory for Bamboo Germplasm Resources and Utilization, Jiangxi Agriculture University, College of Forestry, 1101 Zhimin Road, Nanchang, Jiangxi 330045, China
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C-CorA: A Cluster-Based Method for Correlation Analysis of RNA-Seq Data. HORTICULTURAE 2022. [DOI: 10.3390/horticulturae8020124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Correlation analysis is a routine method of biological data analysis. In the process of RNA-Seq analysis, differentially expressed genes could be identified by calculating the correlation coefficients in the comparison of gene expression vs. phenotype or gene expression vs. gene expression. However, due to the complicated genetic backgrounds of perennial fruit, the correlation coefficients between phenotypes and genes are usually not high in fruit quality studies. In this study, a cluster-based correlation analysis method (C-CorA) is presented for fruit RNA-Seq analysis. C-CorA is composed of two main parts: the clustering analysis and the correlation analysis. The algorithm is described and then integrated into the MATLAB code and the C# WPF project. The C-CorA method was applied to RNA-Seq datasets of loquat (Eriobotrya japonica) fruit stored or ripened under different conditions. Low temperature conditioning or heat treatment of loquat fruit can alleviate the extent of lignification that occurs because of postharvest storage under low temperatures (0 °C). The C-CorA method generated correlation coefficients and identified many candidate genes correlated with lignification, including EjCAD3 and EjCAD4 and transcription factors such as MYB (UN00328). C-CorA is an effective new method for the correlation analysis of various types of data with different dimensions and can be applied to RNA-Seq data for candidate gene detection in fruit quality studies.
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Mathijs E, Haegeman A, De Clercq K, Van Borm S, Vandenbussche F. A robust, cost-effective and widely applicable whole-genome sequencing protocol for capripoxviruses. J Virol Methods 2022; 301:114464. [PMID: 35032481 PMCID: PMC8872832 DOI: 10.1016/j.jviromet.2022.114464] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 01/10/2022] [Accepted: 01/11/2022] [Indexed: 12/22/2022]
Abstract
Robust method for the genomic characterization of all Capripoxviruses. Pre-sequencing enrichment method based on targeted long-range PCR amplification. Method applicable to low titre samples such as blood samples and vaccine batches. Viral DNA enrichment compatible with various sample types and sequencing platforms. Complete coding genome sequencing evaluated on three different sequencing platforms.
The diseases caused by capripoxviruses (CaPVs) are of major economic concern in sheep, goat and cattle as they are inexorably spreading into non-endemic regions. As CaPV strains are serologically indistinguishable and genetically highly homologous, typing closely related strains can only be achieved by whole genome sequencing. Unfortunately the number of publicly available genomes remains low as most sequencing methods rely on virus isolation. Therefore, we developed a robust, cost-effective and widely applicable method that allows to generate (nearly) complete CaPV genomes directly from clinical samples or commercial vaccine batches. A set of pan-CaPVs long-range PCRs spanning the entire genome was designed to generate PCR amplicons that can be sequenced on commonly used high-throughput sequencing platforms: MiSeq (Illumina), RSII (PacBio) and MinION (Oxford Nanopore Technologies). The robustness of the LR-PCR strategy was evaluated for all 3 members of CaPV directly from a variety of samples, including clinical samples (N = 7), vaccine batches (N = 6), and virus isolates (N = 2). The sequencing method described here allows to reconstruct (nearly) complete CaPV genomes in less than a week and will aid researchers studying closely-related CaPV strains worldwide.
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Affiliation(s)
- Elisabeth Mathijs
- Infectious Diseases in Animals, Sciensano, Rue Juliette Wytsmanstraat 14, 1050, Brussels, Belgium.
| | - Andy Haegeman
- Infectious Diseases in Animals, Sciensano, Rue Juliette Wytsmanstraat 14, 1050, Brussels, Belgium
| | - Kris De Clercq
- Infectious Diseases in Animals, Sciensano, Rue Juliette Wytsmanstraat 14, 1050, Brussels, Belgium
| | - Steven Van Borm
- Infectious Diseases in Animals, Sciensano, Rue Juliette Wytsmanstraat 14, 1050, Brussels, Belgium
| | - Frank Vandenbussche
- Infectious Diseases in Animals, Sciensano, Rue Juliette Wytsmanstraat 14, 1050, Brussels, Belgium
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Transcriptome analysis of Rafflesia cantleyi flower stages reveals insights into the regulation of senescence. Sci Rep 2021; 11:23661. [PMID: 34880337 PMCID: PMC8654902 DOI: 10.1038/s41598-021-03028-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 11/26/2021] [Indexed: 11/08/2022] Open
Abstract
Rafflesia is a unique plant species existing as a single flower and produces the largest flower in the world. While Rafflesia buds take up to 21 months to develop, its flowers bloom and wither within about a week. In this study, transcriptome analysis was carried out to shed light on the molecular mechanism of senescence in Rafflesia. A total of 53.3 million high quality reads were obtained from two Rafflesia cantleyi flower developmental stages and assembled to generate 64,152 unigenes. Analysis of this dataset showed that 5,166 unigenes were differentially expressed, in which 1,073 unigenes were identified as genes involved in flower senescence. Results revealed that as the flowers progress to senescence, more genes related to flower senescence were significantly over-represented compared to those related to plant growth and development. Senescence of the R. cantleyi flower activates senescence-associated genes in the transcription activity (members of the transcription factor families MYB, bHLH, NAC, and WRKY), nutrient remobilization (autophagy-related protein and transporter genes), and redox regulation (CATALASE). Most of the senescence-related genes were found to be differentially regulated, perhaps for the fine-tuning of various responses in the senescing R. cantleyi flower. Additionally, pathway analysis showed the activation of genes such as ETHYLENE RECEPTOR, ETHYLENE-INSENSITIVE 2, ETHYLENE-INSENSITIVE 3, and ETHYLENE-RESPONSIVE TRANSCRIPTION FACTOR, indicating the possible involvement of the ethylene hormone response pathway in the regulation of R. cantleyi senescence. Our results provide a model of the molecular mechanism underlying R. cantleyi flower senescence, and contribute essential information towards further understanding the biology of the Rafflesiaceae family.
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Zhao P, Zheng X, Yu Y, Hou Z, Diao C, Wang H, Kang H, Ning C, Li J, Feng W, Wang W, Liu GE, Li B, Smith J, Chamba Y, Liu JF. Mining Unknown Porcine Protein Isoforms by Tissue-based Map of Proteome Enhances Pig Genome Annotation. GENOMICS, PROTEOMICS & BIOINFORMATICS 2021; 19:772-786. [PMID: 33631433 PMCID: PMC9170766 DOI: 10.1016/j.gpb.2021.02.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Revised: 09/05/2019] [Accepted: 11/29/2019] [Indexed: 11/29/2022]
Abstract
A lack of the complete pig proteome has left a gap in our knowledge of the pig genome and has restricted the feasibility of using pigs as a biomedical model. In this study, we developed a tissue-based proteome map using 34 major normal pig tissues. A total of 5841 unknown protein isoforms were identified and systematically characterized, including 2225 novel protein isoforms, 669 protein isoforms from 460 genes symbolized beginning with LOC, and 2947 protein isoforms without clear NCBI annotation in the current pig reference genome. These newly identified protein isoforms were functionally annotated through profiling the pig transcriptome with high-throughput RNA sequencing of the same pig tissues, further improving the genome annotation of the corresponding protein-coding genes. Combining the well-annotated genes that have parallel expression pattern and subcellular witness, we predicted the tissue-related subcellularlocations and potential functions for these unknown proteins. Finally, we mined 3081 orthologous genes for 52.7% of unknown protein isoforms across multiple species, referring to 68 KEGG pathways as well as 23 disease signaling pathways. These findings provide valuable insights and a rich resource for enhancing studies of pig genomics and biology, as well as biomedical model application to human medicine.
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Affiliation(s)
- Pengju Zhao
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Xianrui Zheng
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Ying Yu
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Zhuocheng Hou
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Chenguang Diao
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Haifei Wang
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Huimin Kang
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Chao Ning
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Junhui Li
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Wen Feng
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Wen Wang
- Center for Ecological and Environmental Sciences, Northwestern Polytechnical University, Xi'an 710072, China
| | - George E Liu
- Animal Genomics and Improvement Laboratory, Beltsville Agricultural Research Center, U.S. Department of Agriculture, Beltsville, MD 20705, USA
| | - Bugao Li
- Department of Animal Sciences and Veterinary Medicine, Shanxi Agricultural University, Taigu 030801, China
| | - Jacqueline Smith
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK
| | - Yangzom Chamba
- Tibet Agriculture and Animal Husbandry College, Linzhi 860000, China
| | - Jian-Feng Liu
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China.
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9
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Deveaux Y, Conde e Silva N, Manicacci D, Le Guilloux M, Brunaud V, Belcram H, Joets J, Soubigou-Taconnat L, Delannoy E, Corti H, Balzergue S, Caius J, Nadot S, Damerval C. Transcriptome Analysis Reveals Putative Target Genes of APETALA3-3 During Early Floral Development in Nigella damascena L. FRONTIERS IN PLANT SCIENCE 2021; 12:660803. [PMID: 34149759 PMCID: PMC8212990 DOI: 10.3389/fpls.2021.660803] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 05/04/2021] [Indexed: 05/29/2023]
Abstract
Even though petals are homoplastic structures, their identity consistently involves genes of the APETALA3 (AP3) lineage. However, the extent to which the networks downstream of AP3 are conserved in species with petals of different evolutionary origins is unknown. In Ranunculaceae, the specificity of the AP3-III lineage offers a great opportunity to identify the petal gene regulatory network in a comparative framework. Using a transcriptomic approach, we investigated putative target genes of the AP3-III ortholog NdAP3-3 in Nigella damascena at early developmental stages when petal identity is determined, and we compared our data with that from selected eudicot species. We generated a de novo reference transcriptome to carry out a differential gene expression analysis between the wild-type and mutant NdAP3-3 genotypes differing by the presence vs. absence of petals at early stages of floral development. Among the 1,620 genes that were significantly differentially expressed between the two genotypes, functional annotation suggested a large involvement of nuclear activities, including regulation of transcription, and enrichment in processes linked to cell proliferation. Comparing with Arabidopsis data, we found that highly conserved genes between the two species are enriched in homologs of direct targets of the AtAP3 protein. Integrating AP3-3 binding site data from another Ranunculaceae species, Aquilegia coerulea, allowed us to identify a set of 18 putative target genes that were conserved between the three species. Our results suggest that, despite the independent evolutionary origin of petals in core eudicots and Ranunculaceae, a small conserved set of genes determines petal identity and early development in these taxa.
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Affiliation(s)
- Yves Deveaux
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, Génétique Quantitative et Evolution-Le Moulon, Gif-sur-Yvette, France
| | - Natalia Conde e Silva
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, Génétique Quantitative et Evolution-Le Moulon, Gif-sur-Yvette, France
| | - Domenica Manicacci
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, Génétique Quantitative et Evolution-Le Moulon, Gif-sur-Yvette, France
| | - Martine Le Guilloux
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, Génétique Quantitative et Evolution-Le Moulon, Gif-sur-Yvette, France
| | - Véronique Brunaud
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay, France
| | - Harry Belcram
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, Génétique Quantitative et Evolution-Le Moulon, Gif-sur-Yvette, France
| | - Johann Joets
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, Génétique Quantitative et Evolution-Le Moulon, Gif-sur-Yvette, France
| | - Ludivine Soubigou-Taconnat
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay, France
- Université de Paris, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay, France
| | - Etienne Delannoy
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay, France
- Université de Paris, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay, France
| | - Hélène Corti
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, Génétique Quantitative et Evolution-Le Moulon, Gif-sur-Yvette, France
| | - Sandrine Balzergue
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay, France
- Univ Angers, Institut Agro, INRAE, IRHS, SFR QUASAV, Angers, France
| | - Jose Caius
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay, France
- Université de Paris, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay, France
| | - Sophie Nadot
- Université Paris-Saclay, CNRS, AgroParisTech, Ecologie Systématique Evolution, Orsay, France
| | - Catherine Damerval
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, Génétique Quantitative et Evolution-Le Moulon, Gif-sur-Yvette, France
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10
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Jiang X, Chi X, Zhou R, Li Y, Li W, Liu Q, Wang K, Liu Q. Transcriptome profiling to identify tepal cell enlargement and pigmentation genes and the function of LtEXLB1 in Lilium tsingtauense. FUNCTIONAL PLANT BIOLOGY : FPB 2021; 48:241-256. [PMID: 33059816 DOI: 10.1071/fp20253] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 09/07/2020] [Indexed: 06/11/2023]
Abstract
To understand the molecular mechanism underlying tepal development and pigmentation in Lilium tsingtauense Gilg, we performed whole-transcriptome profiles from closed buds at the greenish tepal stage (CBS), the full-bloom with un-horizontal tepal stage (UFS), and the completely opened bud with reflected tepal stage (RFS) of L. tsingtauense. More than 95699 transcripts were generated using a de novo assembly approach. Gene ontology and pathway analysis of the assembled transcripts revealed carbon metabolism is involved in tepal development and pigmentation. In total, 8171 differentially expression genes (DEGs) in three tepal stages were identified. Among these DEGs, ~994 genes putatively encoded transcription factors (TFs), whereas 693 putatively encoded protein kinases. Regarding hormone pathways, 51 DEGs involved in auxin biosynthesis and signalling and 10 DEGs involved in ethylene biosynthesis and signalling. We also isolated seven LtEXPANSINs, including four EXPAs, one EXPB, one EXLA and one EXLB. LtEXLB1 (GenBank: MN856627) was expressed at higher levels in UFS and RFS, compared with CBS. Silencing LtEXLB1 in leaf discs and tepals by virus-induced gene silencing significantly decreased cell expansion under rehydration conditions. Further analysis revealed that more cell numbers were existed in the abaxial and adaxial subepidermis in the silenced LtEXLB1 samples. As the first transcriptome of L. tsingtauense, the unigenes are a valuable resource for future studies on tepal development, and LtEXLB1 functions in cell expansion.
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Affiliation(s)
- Xinqiang Jiang
- College of Landscape Architecture and Forestry, Qingdao Agricultural University, 700 Changcheng Road, ChengYang District, Qingdao 266109, PR China
| | - Xiufeng Chi
- College of Landscape Architecture and Forestry, Qingdao Agricultural University, 700 Changcheng Road, ChengYang District, Qingdao 266109, PR China
| | - Rui Zhou
- College of Landscape Architecture and Forestry, Qingdao Agricultural University, 700 Changcheng Road, ChengYang District, Qingdao 266109, PR China
| | - Yanshuo Li
- College of Landscape Architecture and Forestry, Qingdao Agricultural University, 700 Changcheng Road, ChengYang District, Qingdao 266109, PR China
| | - Wei Li
- College of Landscape Architecture and Forestry, Qingdao Agricultural University, 700 Changcheng Road, ChengYang District, Qingdao 266109, PR China
| | - Qingchao Liu
- College of Landscape Architecture and Forestry, Qingdao Agricultural University, 700 Changcheng Road, ChengYang District, Qingdao 266109, PR China
| | - Kuiling Wang
- College of Landscape Architecture and Forestry, Qingdao Agricultural University, 700 Changcheng Road, ChengYang District, Qingdao 266109, PR China
| | - Qinghua Liu
- College of Landscape Architecture and Forestry, Qingdao Agricultural University, 700 Changcheng Road, ChengYang District, Qingdao 266109, PR China; and Corresponding author.
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11
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Posso-Terranova A, Andrés J. Skin transcriptional profiles in Oophaga poison frogs. Genet Mol Biol 2020; 43:e20190401. [PMID: 33211057 PMCID: PMC7678260 DOI: 10.1590/1678-4685-gmb-2019-0401] [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: 12/17/2019] [Accepted: 06/06/2020] [Indexed: 12/03/2022] Open
Abstract
Aposematic organisms advertise their defensive toxins to predators using a variety of warning
signals, including bright coloration. While most Neotropical poison frogs (Dendrobatidae) rely on
crypsis to avoid predators, Oophaga poison frogs from South America advertise their
chemical defenses, a complex mix of diet-derived alkaloids, by using conspicuous hues. The present
study aimed to characterize the skin transcriptomic profiles of South American
Oophaga poison frogs. Our analyses showed very similar transcriptomic profiles for
these closely related species in terms of functional annotation and relative abundance of gene
ontology terms expressed. Analyses of expression profiles of Oophaga and available
skin transcriptomes of cryptic anurans allowed us to propose initial hypotheses for the active
sequestration of alkaloid-based chemical defenses and to highlight some genes that may be
potentially involved in resistance mechanisms to avoid self-intoxication and skin coloration. In
doing so, we provide an important molecular resource for the study of warning signals that will
facilitate the assembly and annotation of future poison frog genomes.
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Affiliation(s)
- Andrés Posso-Terranova
- University of Saskatchewan, Department of Biology, Saskatoon, SK, Canada.,Universidad Nacional de Colombia sede Palmira, Palmira, Colombia
| | - José Andrés
- University of Saskatchewan, Department of Biology, Saskatoon, SK, Canada.,Cornell University, Department of Ecology and Evolution, Ithaca, NY, USA
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12
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González G, Aguilera F, D'Afonseca V. Transcriptome profiling of raspberry ( Rubus idaeus Var. Amira) in response to infection by tomato ringspot virus (ToRSV). Heliyon 2020; 6:e04518. [PMID: 32817888 PMCID: PMC7424221 DOI: 10.1016/j.heliyon.2020.e04518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 10/28/2019] [Accepted: 07/17/2020] [Indexed: 11/01/2022] Open
Abstract
Raspberry (Rubus sp.) is a berries fruit with an ongoing agricultural and commercial interest due to its high contents of flavonoids and nutrients beneficial for human health. The growing demand for raspberries is facing great challenges associated mainly with the dispersal of diseases, which produces a decrease in productivity and fruit quality. A broad range of genomic resources is available for other Rosaceae species; however, genomic resources for species of the Rubus genus are still limited. Here, we characterize the transcriptome of the Rubus idaeus (Var. Amira) in order to 1) provide clues in the transcriptional changes of R. idaeus against tomato ringspot virus (ToRSV); and 2) generate genomic resources for this economically important species. We generate more than 200 million sequencing reads from two mRNA samples of raspberry, infected and not infected by ToRSV, using Illumina technology. After de novo assembly, we obtained 68,853 predicted protein-coding sequences of which 71.3% and 61.3% were annotated using Gene Ontology and Pfam databases, respectively. Moreover, we find 2,340 genes with differential expression between raspberries infected and not infected by ToRSV. Analysis of these genes shows functional enrichments of the oxidation-reduction process, cell wall biogenesis, terpene synthase activity, and lyase activity. These genes could be involved in the raspberry immune response through the interaction of different metabolic pathways; however, this statement needs further investigations. Up-regulation of genes encoding terpene synthases, multicopper oxidases, laccases, and beta-glucosidases might suggest that these enzymes appear to be the predominant transcriptome immune response of R. idaeus against ToRSV. Furthermore, we identify thousands of molecular markers (i.e., SSRs and SNPs), increasing considerably the genomic resources currently available for raspberries. This study is the first report on investigating the transcriptional changes of R. idaeus against ToRSV.
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Affiliation(s)
- Gloria González
- Center of Biotechnology for Natural Resources (CenBIO), Faculty of Agricultural Sciences and Forestry, Universidad Católica del Maule, Talca, Chile
| | - Felipe Aguilera
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile
| | - Vívian D'Afonseca
- Vice Rectory of Research and Post-Graduation (VRIP), Universidad Católica del Maule, Talca, Chile
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13
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Xu Y, Zhao X, Aiwaili P, Mu X, Zhao M, Zhao J, Cheng L, Ma C, Gao J, Hong B. A zinc finger protein BBX19 interacts with ABF3 to affect drought tolerance negatively in chrysanthemum. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 103:1783-1795. [PMID: 32488968 PMCID: PMC7496117 DOI: 10.1111/tpj.14863] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2019] [Revised: 05/17/2020] [Accepted: 05/21/2020] [Indexed: 05/09/2023]
Abstract
Drought is an environmental factor that can severely influence plant development and distribution, and greatly affect the yield and economic value of crops. We characterized CmBBX19, a BBX family subgroup IV member gene, from the transcriptome database of Chrysanthemum morifolium in response to drought stress. Drought stress and ABA treatments downregulated the expression of CmBBX19. We generated CmBBX19-overexpressing (CmBBX19-OX) lines and CmBBX19-suppressing lines (CmBBX19-RNAi), and found that suppressed expression of CmBBX19 led to enhanced drought tolerance compared with the wild-type (WT) controls, while CmBBX19-OX lines exhibited reduced drought tolerance. Downstream gene analysis showed that CmBBX19 modulates drought tolerance mainly through inducing changes in the expression of ABA-dependent pathway genes, including protective protein, redox balance and cell wall biogenesis genes, such as responsive to ABA 18, peroxidase 12, and cellulose synthase-like protein G2. Moreover, CmBBX19 was shown to interact with CmABF3, a master ABA signaling component, to suppress expression of these downstream genes. We conclude that BBX19-ABF3 module functions in the regulation of drought tolerance of chrysanthemum through an ABA-dependent pathway.
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Affiliation(s)
- Yanjie Xu
- State Key Laborary of AgrobiotechnologyBeijing Key Laboratory of Development and Quality Control of Ornamental CropsDepartment of Ornamental HorticultureCollege of HorticultureChina Agricultural UniversityBeijing100193China
| | - Xin Zhao
- State Key Laborary of AgrobiotechnologyBeijing Key Laboratory of Development and Quality Control of Ornamental CropsDepartment of Ornamental HorticultureCollege of HorticultureChina Agricultural UniversityBeijing100193China
| | - Palinuer Aiwaili
- State Key Laborary of AgrobiotechnologyBeijing Key Laboratory of Development and Quality Control of Ornamental CropsDepartment of Ornamental HorticultureCollege of HorticultureChina Agricultural UniversityBeijing100193China
| | - Xianying Mu
- State Key Laborary of AgrobiotechnologyBeijing Key Laboratory of Development and Quality Control of Ornamental CropsDepartment of Ornamental HorticultureCollege of HorticultureChina Agricultural UniversityBeijing100193China
| | - Meng Zhao
- State Key Laborary of AgrobiotechnologyBeijing Key Laboratory of Development and Quality Control of Ornamental CropsDepartment of Ornamental HorticultureCollege of HorticultureChina Agricultural UniversityBeijing100193China
| | - Jian Zhao
- State Key Laborary of AgrobiotechnologyBeijing Key Laboratory of Development and Quality Control of Ornamental CropsDepartment of Ornamental HorticultureCollege of HorticultureChina Agricultural UniversityBeijing100193China
| | - Lina Cheng
- State Key Laborary of AgrobiotechnologyBeijing Key Laboratory of Development and Quality Control of Ornamental CropsDepartment of Ornamental HorticultureCollege of HorticultureChina Agricultural UniversityBeijing100193China
| | - Chao Ma
- State Key Laborary of AgrobiotechnologyBeijing Key Laboratory of Development and Quality Control of Ornamental CropsDepartment of Ornamental HorticultureCollege of HorticultureChina Agricultural UniversityBeijing100193China
| | - Junping Gao
- State Key Laborary of AgrobiotechnologyBeijing Key Laboratory of Development and Quality Control of Ornamental CropsDepartment of Ornamental HorticultureCollege of HorticultureChina Agricultural UniversityBeijing100193China
| | - Bo Hong
- State Key Laborary of AgrobiotechnologyBeijing Key Laboratory of Development and Quality Control of Ornamental CropsDepartment of Ornamental HorticultureCollege of HorticultureChina Agricultural UniversityBeijing100193China
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14
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Jiao C, Sørensen I, Sun X, Sun H, Behar H, Alseekh S, Philippe G, Palacio Lopez K, Sun L, Reed R, Jeon S, Kiyonami R, Zhang S, Fernie AR, Brumer H, Domozych DS, Fei Z, Rose JKC. The Penium margaritaceum Genome: Hallmarks of the Origins of Land Plants. Cell 2020; 181:1097-1111.e12. [PMID: 32442406 DOI: 10.1016/j.cell.2020.04.019] [Citation(s) in RCA: 126] [Impact Index Per Article: 31.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 02/14/2020] [Accepted: 04/13/2020] [Indexed: 10/24/2022]
Abstract
The evolutionary features and molecular innovations that enabled plants to first colonize land are not well understood. Here, insights are provided through our report of the genome sequence of the unicellular alga Penium margaritaceum, a member of the Zygnematophyceae, the sister lineage to land plants. The genome has a high proportion of repeat sequences that are associated with massive segmental gene duplications, likely facilitating neofunctionalization. Compared with representatives of earlier diverging algal lineages, P. margaritaceum has expanded repertoires of gene families, signaling networks, and adaptive responses that highlight the evolutionary trajectory toward terrestrialization. These encompass a broad range of physiological processes and protective cellular features, such as flavonoid compounds and large families of modifying enzymes involved in cell wall biosynthesis, assembly, and remodeling. Transcriptome profiling further elucidated adaptations, responses, and selective pressures associated with the semi-terrestrial ecosystems of P. margaritaceum, where a simple body plan would be an advantage.
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Affiliation(s)
- Chen Jiao
- Boyce Thompson Institute, Ithaca, NY, USA
| | - Iben Sørensen
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, USA
| | | | - Honghe Sun
- Boyce Thompson Institute, Ithaca, NY, USA
| | - Hila Behar
- Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, BC V6T 1Z4, Canada; Department of Biochemistry and Molecular Biology, University of British Columbia, 2350 Health Sciences Mall, Life Sciences Centre, Vancouver, BC V6T 1Z3, Canada
| | - Saleh Alseekh
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany; Center of Plant Systems Biology and Biotechnology, 4000 Plovdiv, Bulgaria
| | - Glenn Philippe
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, USA
| | | | - Li Sun
- Skidmore College, Saratoga Springs, NY, USA
| | | | - Susan Jeon
- Skidmore College, Saratoga Springs, NY, USA
| | - Reiko Kiyonami
- Thermo Fisher Scientific, 355 River Oaks Parkway, San Jose, CA, USA
| | - Sheng Zhang
- Institute of Biotechnology, Cornell University, Ithaca, NY, USA
| | - Alisdair R Fernie
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany; Center of Plant Systems Biology and Biotechnology, 4000 Plovdiv, Bulgaria
| | - Harry Brumer
- Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, BC V6T 1Z4, Canada; Department of Biochemistry and Molecular Biology, University of British Columbia, 2350 Health Sciences Mall, Life Sciences Centre, Vancouver, BC V6T 1Z3, Canada; Department of Botany, University of British Columbia, 3200-6270 University Blvd., Vancouver, BC V6H 1Z4, Canada; Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC V6T 1Z4, Canada
| | | | - Zhangjun Fei
- Boyce Thompson Institute, Ithaca, NY, USA; U.S. Department of Agriculture-Agricultural Research Service, Robert W. Holley Center for Agriculture and Health, Ithaca, NY, USA.
| | - Jocelyn K C Rose
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, USA.
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15
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Zheng Y, Wu S, Bai Y, Sun H, Jiao C, Guo S, Zhao K, Blanca J, Zhang Z, Huang S, Xu Y, Weng Y, Mazourek M, K Reddy U, Ando K, McCreight JD, Schaffer AA, Burger J, Tadmor Y, Katzir N, Tang X, Liu Y, Giovannoni JJ, Ling KS, Wechter WP, Levi A, Garcia-Mas J, Grumet R, Fei Z. Cucurbit Genomics Database (CuGenDB): a central portal for comparative and functional genomics of cucurbit crops. Nucleic Acids Res 2020; 47:D1128-D1136. [PMID: 30321383 PMCID: PMC6324010 DOI: 10.1093/nar/gky944] [Citation(s) in RCA: 103] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 10/04/2018] [Indexed: 11/17/2022] Open
Abstract
The Cucurbitaceae family (cucurbit) includes several economically important crops, such as melon, cucumber, watermelon, pumpkin, squash and gourds. During the past several years, genomic and genetic data have been rapidly accumulated for cucurbits. To store, mine, analyze, integrate and disseminate these large-scale datasets and to provide a central portal for the cucurbit research and breeding community, we have developed the Cucurbit Genomics Database (CuGenDB; http://cucurbitgenomics.org) using the Tripal toolkit. The database currently contains all available genome and expressed sequence tag (EST) sequences, genetic maps, and transcriptome profiles for cucurbit species, as well as sequence annotations, biochemical pathways and comparative genomic analysis results such as synteny blocks and homologous gene pairs between different cucurbit species. A set of analysis and visualization tools and user-friendly query interfaces have been implemented in the database to facilitate the usage of these large-scale data by the community. In particular, two new tools have been developed in the database, a ‘SyntenyViewer’ to view genome synteny between different cucurbit species and an ‘RNA-Seq’ module to analyze and visualize gene expression profiles. Both tools have been packed as Tripal extension modules that can be adopted in other genomics databases developed using the Tripal system.
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Affiliation(s)
- Yi Zheng
- Boyce Thompson Institute, Cornell University, Ithaca, NY 14853, USA
| | - Shan Wu
- Boyce Thompson Institute, Cornell University, Ithaca, NY 14853, USA
| | - Yang Bai
- Boyce Thompson Institute, Cornell University, Ithaca, NY 14853, USA
| | - Honghe Sun
- Boyce Thompson Institute, Cornell University, Ithaca, NY 14853, USA.,National Engineering Research Center for Vegetables, Beijing Academy of Agriculture and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing 100097, China
| | - Chen Jiao
- Boyce Thompson Institute, Cornell University, Ithaca, NY 14853, USA
| | - Shaogui Guo
- Boyce Thompson Institute, Cornell University, Ithaca, NY 14853, USA.,National Engineering Research Center for Vegetables, Beijing Academy of Agriculture and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing 100097, China
| | - Kun Zhao
- Boyce Thompson Institute, Cornell University, Ithaca, NY 14853, USA
| | - Jose Blanca
- Institute for the Conservation and Breeding of Agricultural Biodiversity (COMAV-UPV), Universitat Politècnica de València, Valencia 46022, Spain
| | - Zhonghua Zhang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Sanwen Huang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China.,Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518124, China
| | - Yong Xu
- National Engineering Research Center for Vegetables, Beijing Academy of Agriculture and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing 100097, China
| | - Yiqun Weng
- U.S. Department of Agriculture-Agricultural Research Service, Vegetable Crops Research Unit, Madison, WI 53706, USA.,Department of Horticulture, University of Wisconsin, Madison, WI 53706, USA
| | - Michael Mazourek
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
| | - Umesh K Reddy
- Department of Biology, West Virginia State University, Institute, WV 25112, USA
| | - Kaori Ando
- U.S. Department of Agriculture-Agricultural Research Service, Crop Improvement and Protection Research Unit, Salinas, CA 93905, USA
| | - James D McCreight
- U.S. Department of Agriculture-Agricultural Research Service, Crop Improvement and Protection Research Unit, Salinas, CA 93905, USA
| | - Arthur A Schaffer
- Plant Science Institute, Agricultural Research Organization, The Volcani Center, P.O.B. 6, Bet-Dagan 50250, Israel
| | - Joseph Burger
- Plant Science Institute, Agricultural Research Organization, Newe Yaar Research Center, Ramat Yishai 30095, Israel
| | - Yaakov Tadmor
- Plant Science Institute, Agricultural Research Organization, Newe Yaar Research Center, Ramat Yishai 30095, Israel
| | - Nurit Katzir
- Plant Science Institute, Agricultural Research Organization, Newe Yaar Research Center, Ramat Yishai 30095, Israel
| | - Xuemei Tang
- Boyce Thompson Institute, Cornell University, Ithaca, NY 14853, USA
| | - Yang Liu
- Boyce Thompson Institute, Cornell University, Ithaca, NY 14853, USA.,Horticulture Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
| | - James J Giovannoni
- Boyce Thompson Institute, Cornell University, Ithaca, NY 14853, USA.,U.S. Department of Agriculture-Agricultural Research Service, Robert W. Holley Center for Agriculture and Health, Ithaca, NY 14853, USA
| | - Kai-Shu Ling
- U.S. Department of Agriculture-Agricultural Research Service, U.S. Vegetable Laboratory, 2700 Savannah Highway, Charleston, SC 29414, USA
| | - W Patrick Wechter
- U.S. Department of Agriculture-Agricultural Research Service, U.S. Vegetable Laboratory, 2700 Savannah Highway, Charleston, SC 29414, USA
| | - Amnon Levi
- U.S. Department of Agriculture-Agricultural Research Service, U.S. Vegetable Laboratory, 2700 Savannah Highway, Charleston, SC 29414, USA
| | - Jordi Garcia-Mas
- Centre for Research in Agricultural Genomics CSIC-IRTA-UAB-UB, Barcelona 08193, Spain.,Institut de Recerca i Tecnologia Agroalimentàries, Barcelona 08193, Spain
| | - Rebecca Grumet
- Department of Horticulture, Michigan State University, East Lansing, MI 48824, USA
| | - Zhangjun Fei
- Boyce Thompson Institute, Cornell University, Ithaca, NY 14853, USA.,U.S. Department of Agriculture-Agricultural Research Service, Robert W. Holley Center for Agriculture and Health, Ithaca, NY 14853, USA
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16
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López-Carvallo JA, Mazón-Suástegui JM, Hernández-Oñate MÁ, Tovar-Ramírez D, Abasolo-Pacheco F, Morelos-Castro RM, Arcos-Ortega GF. Transcriptome analysis of Catarina scallop (Argopecten ventricosus) juveniles treated with highly-diluted immunomodulatory compounds reveals activation of non-self-recognition system. PLoS One 2020; 15:e0233064. [PMID: 32407349 PMCID: PMC7224555 DOI: 10.1371/journal.pone.0233064] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 04/27/2020] [Indexed: 12/14/2022] Open
Abstract
Marine bivalve hatchery productivity is continuously challenged by apparition and propagation of new diseases, mainly those related to vibriosis. Disinfectants and antibiotics are frequently overused to prevent pathogen presence, generating a potential negative impact on the environment. Recently, the use of highly diluted compounds with immunostimulant properties in marine organisms has been trailed successfully to activate the self-protection mechanisms of marine bivalves. Despite their potential as immunostimulants, little is known about their way of action. To understand their effect, a comparative transcriptomic analysis was performed with Argopecten ventricosus juveniles. The experimental design consisted of four treatments formulated from pathogenic Vibrio lysates at two dilutions: [(T1) Vibrio parahaemolyticus and Vibrio alginolyticus 1D; (T2) V. parahaemolyticus and V. alginolyticus 7C]; minerals [(T3) PhA+SiT 7C], scorpion venom [(T4) ViT 31C]; and one control (C1) hydro-alcoholic solution (ethanol 1%). The RNA sequencing (RNAseq) analysis showed a higher modulation of differentially expressed genes (DEG) in mantle tissue compared to gill tissue. The scallops that showed a higher number of DEG related to immune response in mantle tissue corresponded to T1 (V. parahaemolyticus and V. alginolyticus lysate) and T3 (Silicea terra® - Phosphoric acid®). The transcriptome analysis allowed understanding some interactions between A. ventricosus juveniles and highly-diluted treatments.
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Affiliation(s)
- Jesús Antonio López-Carvallo
- Laboratorio Experimental de Cultivo de Moluscos, Centro de Investigaciones Biológicas del Noroeste, La Paz, México
| | - José Manuel Mazón-Suástegui
- Laboratorio Experimental de Cultivo de Moluscos, Centro de Investigaciones Biológicas del Noroeste, La Paz, México
| | - Miguel Ángel Hernández-Oñate
- CONACyT, Centro de Investigación en Alimentación y Desarrollo A.C, Hermosillo, Sonora, México
- * E-mail: (GFAO); (MAHO)
| | - Dariel Tovar-Ramírez
- Laboratorio de Fisiología Comparada y Genómica Funcional, Centro de Investigaciones Biológicas del Noroeste, La Paz, México
| | - Fernando Abasolo-Pacheco
- Facultad de Ciencias Agrarias, Universidad Técnica Estatal de Quevedo, Quevedo, Los Ríos, Ecuador
| | - Rosa María Morelos-Castro
- Laboratorio de Imunogenómica Marina, Centro de Investigaciones Biológicas del Noroeste, La Paz, México
| | - Guadalupe Fabiola Arcos-Ortega
- Laboratorio de Imunogenómica Marina, Centro de Investigaciones Biológicas del Noroeste, La Paz, México
- * E-mail: (GFAO); (MAHO)
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17
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Fan Y, Liu J, Zou J, Zhang X, Jiang L, Liu K, Lü P, Gao J, Zhang C. The RhHB1/ RhLOX4 module affects the dehydration tolerance of rose flowers ( Rosa hybrida) by fine-tuning jasmonic acid levels. HORTICULTURE RESEARCH 2020; 7:74. [PMID: 32377364 PMCID: PMC7195446 DOI: 10.1038/s41438-020-0299-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Revised: 03/11/2020] [Accepted: 03/16/2020] [Indexed: 05/14/2023]
Abstract
Phytohormones are key factors in plant responsiveness to abiotic and biotic stresses, and maintaining hormone homeostasis is critically important during stress responses. Cut rose (Rosa hybrida) flowers experience dehydration stress during postharvest handling, and jasmonic acid (JA) levels change as a result of this stress. However, how JA is involved in dehydration tolerance remains unclear. We investigated the functions of the JA- and dehydration-induced RhHB1 gene, which encodes a homeodomain-leucine zipper I γ-clade transcription factor, in rose flowers. Silencing RhHB1 decreased petal dehydration tolerance and resulted in a persistent increase in JA-Ile content and reduced dehydration tolerance. An elevated JA-Ile level had a detrimental effect on rose petal dehydration tolerance. RhHB1 was shown to lower the transient induction of JA-Ile accumulation in response to dehydration. In addition to transcriptomic data, we obtained evidence that RhHB1 suppresses the expression of the lipoxygenase 4 (RhLOX4) gene by directly binding to its promoter both in vivo and in vitro. We propose that increased JA-Ile levels weaken the capacity for osmotic adjustment in petal cells, resulting in reduced dehydration tolerance. In conclusion, a JA feedback loop mediated by an RhHB1/RhLOX4 regulatory module provides dehydration tolerance by fine-tuning bioactive JA levels in dehydrated flowers.
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Affiliation(s)
- Youwei Fan
- Department of Ornamental Horticulture, College of Horticulture, China Agricultural University, Beijing, 100193 China
| | - Jitao Liu
- Department of Ornamental Horticulture, College of Horticulture, China Agricultural University, Beijing, 100193 China
- Crop Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Provincial Key Laboratory of Crop Genetic Improvement, Guangzhou, Guangdong 510642 China
| | - Jing Zou
- Department of Ornamental Horticulture, College of Horticulture, China Agricultural University, Beijing, 100193 China
| | - Xiangyu Zhang
- Department of Ornamental Horticulture, College of Horticulture, China Agricultural University, Beijing, 100193 China
| | - Liwei Jiang
- Department of Ornamental Horticulture, College of Horticulture, China Agricultural University, Beijing, 100193 China
| | - Kun Liu
- Department of Ornamental Horticulture, College of Horticulture, China Agricultural University, Beijing, 100193 China
| | - Peitao Lü
- Department of Ornamental Horticulture, College of Horticulture, China Agricultural University, Beijing, 100193 China
| | - Junping Gao
- Department of Ornamental Horticulture, College of Horticulture, China Agricultural University, Beijing, 100193 China
| | - Changqing Zhang
- Department of Ornamental Horticulture, College of Horticulture, China Agricultural University, Beijing, 100193 China
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18
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Liu Y, Tang L, Wang C, Li J. NAA and 6-BA promote accumulation of oleanolic acid by JA regulation in Achyranthes bidentata Bl. PLoS One 2020; 15:e0229490. [PMID: 32107496 PMCID: PMC7046271 DOI: 10.1371/journal.pone.0229490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 02/07/2020] [Indexed: 11/25/2022] Open
Abstract
Application of plant growth regulators has become one of the most important means of improving yield and quality of medicinal plants. To understand the molecular basis of phytohormone-regulated oleanolic acid metabolism, RNA-seq was used to analyze global gene expression in Achyranthes bidentata treated with 2.0 mg/L 1-naphthaleneacetic acid (NAA) and 1.0 mg/L 6-benzyladenine (6-BA). Compared with untreated controls, the expression levels of 20,896 genes were significantly altered with phytohormone treatment. We found that 13071 (62.5%) unigenes were up-regulated, and a lot of differentially expressed genes involved in hormone or terpenoid biosynthesis, or transcription factors were significantly up-regulated. These results suggest that oleanolic acid biosynthesis induced by NAA and 6-BA occurs due to the expression of key genes involved in jasmonic acid signal transduction. This study is the first to analyze the production and hormonal regulation of medicinal A. bidentata metabolites at the molecular level. The results herein contribute to a better understanding of the regulation of oleanane-type triterpenoid saponins accumulation and define strategies to improve the yield of these useful metabolites.
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Affiliation(s)
- Yanqing Liu
- College of Life Sciences, Henan Normal University, Xinxiang, China
| | - Li Tang
- College of Life Sciences, Henan Normal University, Xinxiang, China
| | - Can Wang
- College of Life Sciences, Henan Normal University, Xinxiang, China
| | - Jinting Li
- College of Life Sciences, Henan Normal University, Xinxiang, China
- Engineering Laboratory of Biotechnology for Green Medicinal Plant of Henan Province, Xinxiang, China
- * E-mail:
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19
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De Mori G, Falchi R, Testolin R, Bassi D, Savazzini F, Dondini L, Tartarini S, Palmisano F, Minafra A, Spadotto A, Scalabrin S, Geuna F. Resistance to Sharka in Apricot: Comparison of Phase-Reconstructed Resistant and Susceptible Haplotypes of 'Lito' Chromosome 1 and Analysis of Candidate Genes. FRONTIERS IN PLANT SCIENCE 2019; 10:1576. [PMID: 31867032 PMCID: PMC6905379 DOI: 10.3389/fpls.2019.01576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Accepted: 11/12/2019] [Indexed: 06/10/2023]
Abstract
Sharka, a common disease among most stone fruit crops, is caused by the Plum Pox Virus (PPV). Resistant genotypes have been found in apricot (Prunus armeniaca L.), one of which-the cultivar 'Lito' heterozygous for the resistance-has been used to map a major quantitative trait locus (QTL) on linkage group 1, following a pseudo-test-cross mating design with 231 individuals. In addition, 19 SNP markers were selected from among the hundreds previously developed, which allowed the region to be limited to 236 kb on chromosome 1. A 'Lito' bacterial artificial chromosome (BAC) library was produced, screened with markers of the region, and positive BAC clones were sequenced. Resistant (R) and susceptible (S) haplotypes were assembled independently. To refine the assembly, the whole genome of 'Lito' was sequenced to high coverage (98×) using PacBio technology, enabling the development of a detailed assembly of the region that was able to predict and annotate the genes in the QTL region. The selected cultivar 'Lito' allowed not only to discriminate structural variants between the two haplotypic regions but also to distinguish specific allele expression, contributing towards mining the PPVres locus. In light of these findings, genes previously indicated (i.e., MATHd genes) to have a possible role in PPV resistance were further analyzed, and new candidates were discussed. Although the results are not conclusive, the accurate and independent assembly of R and S haplotypes of 'Lito' is a valuable resource to predict and test alternative transcription and regulation mechanisms underpinning PPV resistance.
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Affiliation(s)
- Gloria De Mori
- Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, Udine, Italy
| | - Rachele Falchi
- Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, Udine, Italy
| | - Raffaele Testolin
- Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, Udine, Italy
| | - Daniele Bassi
- Department of Agricultural and Environmental Sciences (DISAA), University of Milan, Milan, Italy
| | - Federica Savazzini
- Department of Agricultural Sciences, University of Bologna, Bologna, Italy
| | - Luca Dondini
- Department of Agricultural Sciences, University of Bologna, Bologna, Italy
| | - Stefano Tartarini
- Department of Agricultural Sciences, University of Bologna, Bologna, Italy
| | - Francesco Palmisano
- Centro di Ricerca, Sperimentazione e Formazione in Agricoltura “Basile Caramia”, Locorotondo, Italy
| | - Angelantonio Minafra
- National Research Council, Institute for Sustainable Plant Protection, Bari, Italy
| | | | - Simone Scalabrin
- IGA Technology Services, Science and Technology Park, ZIU, Udine, Italy
| | - Filippo Geuna
- Department of Agricultural and Environmental Sciences (DISAA), University of Milan, Milan, Italy
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20
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Gao Y, Liu Y, Liang Y, Lu J, Jiang C, Fei Z, Jiang CZ, Ma C, Gao J. Rosa hybrida RhERF1 and RhERF4 mediate ethylene- and auxin-regulated petal abscission by influencing pectin degradation. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 99:1159-1171. [PMID: 31111587 DOI: 10.1111/tpj.14412] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Revised: 04/06/2019] [Accepted: 05/13/2019] [Indexed: 05/25/2023]
Abstract
The timing of plant organ abscission is modulated by the balance of two hormones, ethylene and auxin, while the mechanism of organ shedding depends on the loss of middle lamella pectin in the abscission zone (AZ). However, the mechanisms involved in sensing the balance of auxin and ethylene and that affect pectin degradation during abscission are not well understood. In this study, we identified two members of the APETALA2/ethylene-responsive factor (AP2/ERF) transcription factor family in rose (Rosa hybrida), RhERF1 and RhERF4 which play a role in petal abscission. The expression of RhERF1 and RhERF4 was influenced by ethylene and auxin, respectively. Reduced expression of RhERF1 or RhERF4 was observed to accelerate petal abscission. Global expression analysis and real-time PCR assays revealed that RhERF1 and RhERF4 modulate the expression of genes encoding pectin-metabolizing enzymes. A reduction in the abundance of pectin epitopes was detected in the AZs of RhERF1 and RhERF4-silenced plants by immunofluorescence microscopy analysis. In addition, RhERF1 and RhERF4 were shown to bind to the promoter of the pectin-metabolizing gene β-GALACTOSIDASE 1 (RhBGLA1), and reduced expression of RhBGLA1 delayed petal abscission. We conclude that during petal abscission, RhERF1 and RhERF4 integrate and coordinate ethylene and auxin signals to modulate pectin metabolism, in part by regulating the expression of RhBGLA1.
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Affiliation(s)
- Yuerong Gao
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Yang Liu
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Yue Liang
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Jingyun Lu
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Chuyan Jiang
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Zhangjun Fei
- Robert W. Holley Center for Agriculture and Health, United States Department of Agriculture, Agricultural Research Service, Ithaca, 14853, NY, USA
- Boyce Thompson Institute, Ithaca, 14853, NY, USA
| | - Cai-Zhong Jiang
- Crops Pathology and Genetic Research Unit, United States Department of Agriculture, Agricultural Research Service, Davis, 95616, CA, USA
- Department of Plant Sciences, University of California at Davis, Davis, 95616, CA, USA
| | - Chao Ma
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Junping Gao
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, College of Horticulture, China Agricultural University, Beijing, 100193, China
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21
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Fugacium Spliced Leader Genes Identified from Stranded RNA-Seq Datasets. Microorganisms 2019; 7:microorganisms7060171. [PMID: 31212635 PMCID: PMC6616646 DOI: 10.3390/microorganisms7060171] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Revised: 05/27/2019] [Accepted: 06/05/2019] [Indexed: 01/10/2023] Open
Abstract
Trans-splicing mechanisms have been documented in many lineages that are widely distributed phylogenetically, including dinoflagellates. The spliced leader (SL) sequence itself is conserved in dinoflagellates, although its gene sequences and arrangements have diversified within or across different species. In this study, we present 18 Fugacium kawagutii SL genes identified from stranded RNA-seq reads. These genes typically have a single SL but can contain several partial SLs with lengths ranging from 103 to 292 bp. Unexpectedly, we find the SL gene transcripts contain sequences upstream of the canonical SL, suggesting that generation of mature transcripts will require additional modifications following trans-splicing. We have also identified 13 SL-like genes whose expression levels and length are comparable to Dino-SL genes. Lastly, introns in these genes were identified and a new site for Sm-protein binding was proposed. Overall, this study provides a strategy for fast identification of SL genes and identifies new sequences of F. kawagutii SL genes to supplement our understanding of trans-splicing.
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22
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Dittmer J, Alafndi A, Gabrieli P. Fat body-specific vitellogenin expression regulates host-seeking behaviour in the mosquito Aedes albopictus. PLoS Biol 2019; 17:e3000238. [PMID: 31071075 PMCID: PMC6508604 DOI: 10.1371/journal.pbio.3000238] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Accepted: 04/04/2019] [Indexed: 11/22/2022] Open
Abstract
The high vector competence of mosquitoes is intrinsically linked to their reproductive strategy because females need a vertebrate blood meal to develop large batches of eggs. However, the molecular mechanisms and pathways regulating mosquito host-seeking behaviour are largely unknown. Here, we test whether host-seeking behaviour may be linked to the female's energy reserves, with low energy levels triggering the search for a nutrient-rich blood meal. Our results demonstrate that sugar feeding delays host-seeking behaviour in the invasive tiger mosquito Aedes albopictus, but the levels of energy reserves do not correlate with changes in host-seeking behaviour. Using tissue-specific gene expression analyses, we show for the first time, to our knowledge, that sugar feeding alone induces a transient up-regulation of several vitellogenesis-related genes in the female fat body, resembling the transcriptional response after a blood meal. Specifically, high expression levels of a vitellogenin gene (Vg-2) correlated with the lowest host-seeking activity of sugar-fed females. Knocking down the Vg-2 gene via RNA interference (RNAi) restored host-seeking behaviour in these females, firmly establishing that Vg-2 gene expression has a pivotal role in regulating host-seeking behaviour in young Ae. albopictus females. The identification of a molecular mechanism regulating host-seeking behaviour in mosquitoes could pave the way for novel vector control strategies aiming to reduce the biting activity of mosquitoes. From an evolutionary perspective, this is the first demonstration of vitellogenin genes controlling feeding-related behaviours in nonsocial insects, while vitellogenins are known to regulate caste-specific foraging and brood-care behaviours in eusocial insects. Hence, this work confirms the key role of vitellogenin in controlling feeding-related behaviours in distantly related insect orders, suggesting that this function could be more ubiquitous than previously thought.
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Affiliation(s)
- Jessica Dittmer
- Department of Biology and Biotechnology, Università degli Studi di Pavia, Pavia, Italy
| | - Ayad Alafndi
- Department of Biology and Biotechnology, Università degli Studi di Pavia, Pavia, Italy
| | - Paolo Gabrieli
- Department of Biology and Biotechnology, Università degli Studi di Pavia, Pavia, Italy
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23
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Liu W, Zhang J, Jiao C, Yin X, Fei Z, Wu Q, Chen K. Transcriptome analysis provides insights into the regulation of metabolic processes during postharvest cold storage of loquat ( Eriobotrya japonica) fruit. HORTICULTURE RESEARCH 2019; 6:49. [PMID: 30962941 PMCID: PMC6441654 DOI: 10.1038/s41438-019-0131-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Revised: 01/02/2019] [Accepted: 01/03/2019] [Indexed: 05/18/2023]
Abstract
Loquat (Eriobotrya japonica) fruit accumulates lignin during postharvest storage under chilling conditions (0 °C), while low-temperature conditioning (LTC; 5 °C for 6 days followed by transfer to 0 °C) or heat treatment (HT; 40 °C for 4 h followed by transfer to 0 °C) can alleviate lignification. Here we compared transcriptome profiles of loquat fruit samples under LTC or HT to those stored at 0 °C at five time points from day 1 to day 8 after treatment. High-throughput transcriptome sequences were de novo assembled into 53,319 unique transcripts with an N50 length of 1306 bp. A total of 2235 differentially expressed genes were identified in LTC, and 1020 were identified in HT compared to 0 °C. Key genes in the lignin biosynthetic pathway, including EjPAL2, EjCAD1, EjCAD3, 4CL, COMT, and HCT, were responsive to LTC or HT treatment, but they showed different expression patterns during the treatments, indicating that different structural genes could regulate lignification at different treatment stages. Coexpression network analysis showed that these candidate biosynthetic genes were associated with a number of transcription factors, including those belonging to the AP2, MYB, and NAC families. Gene ontology (GO) enrichment analysis of differentially expressed genes indicated that biological processes such as stress responses, cell wall and lignin metabolism, hormone metabolism, and metal ion transport were significantly affected under LTC or HT treatment when compared to 0 °C. Our analyses provide insights into transcriptome responses to postharvest treatments in loquat fruit.
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Affiliation(s)
- Wenli Liu
- School of Mathematical Science, Zhejiang University, Yuquan Campus, 310027 Hangzhou, P.R. China
- Boyce Thompson Institute, Cornell University, Ithaca, NY 14853 USA
- Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang University, Zijingang Campus, 310058 Hangzhou, P.R. China
| | - Jing Zhang
- Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang University, Zijingang Campus, 310058 Hangzhou, P.R. China
| | - Chen Jiao
- Boyce Thompson Institute, Cornell University, Ithaca, NY 14853 USA
| | - Xueren Yin
- Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang University, Zijingang Campus, 310058 Hangzhou, P.R. China
| | - Zhangjun Fei
- Boyce Thompson Institute, Cornell University, Ithaca, NY 14853 USA
- USDA-ARS Robert W. Holley Center for Agriculture and Health, Ithaca, NY 14853 USA
| | - Qingbiao Wu
- School of Mathematical Science, Zhejiang University, Yuquan Campus, 310027 Hangzhou, P.R. China
| | - Kunsong Chen
- Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang University, Zijingang Campus, 310058 Hangzhou, P.R. China
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24
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Shabelnikov SV, Bobkov DE, Sharlaimova NS, Petukhova OA. Injury affects coelomic fluid proteome of the common starfish, Asterias rubens. ACTA ACUST UNITED AC 2019; 222:jeb.198556. [PMID: 30877231 DOI: 10.1242/jeb.198556] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 02/11/2019] [Indexed: 01/04/2023]
Abstract
Echinoderms, possessing outstanding regenerative capabilities, provide a unique model system for the study of response to injury. However, little is known about the proteomic composition of coelomic fluid, an important biofluid circulating throughout the animal's body and reflecting the overall biological status of the organism. In this study, we used LC-MALDI tandem mass spectrometry to characterize the proteome of the cell-free coelomic fluid of the starfish Asterias rubens and to follow the changes occurring in response to puncture wound and blood loss. In total, 91 proteins were identified, of which 61 were extracellular soluble and 16 were bound to the plasma membrane. The most represented functional terms were 'pattern recognition receptor activity' and 'peptidase inhibitor activity'. A series of candidate proteins involved in early response to injury was revealed. Ependymin, β-microseminoprotein, serum amyloid A and avidin-like proteins, which are known to be involved in intestinal regeneration in the sea cucumber, were also identified as injury-responsive proteins. Our results expand the list of proteins potentially involved in defense and regeneration in echinoderms and demonstrate dramatic effects of injury on the coelomic fluid proteome.
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Affiliation(s)
- Sergey V Shabelnikov
- Laboratory of Regulation of Gene Expression, Institute of Cytology, Russian Academy of Sciences, 194064 St Petersburg, Russia
| | - Danila E Bobkov
- Department of Cell Cultures, Institute of Cytology, Russian Academy of Sciences, 194064 St Petersburg, Russia
| | - Natalia S Sharlaimova
- Department of Cell Cultures, Institute of Cytology, Russian Academy of Sciences, 194064 St Petersburg, Russia
| | - Olga A Petukhova
- Department of Cell Cultures, Institute of Cytology, Russian Academy of Sciences, 194064 St Petersburg, Russia
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25
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Wu J, Jin Y, Liu C, Vonapartis E, Liang J, Wu W, Gazzarrini S, He J, Yi M. GhNAC83 inhibits corm dormancy release by regulating ABA signaling and cytokinin biosynthesis in Gladiolus hybridus. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:1221-1237. [PMID: 30517656 PMCID: PMC6382327 DOI: 10.1093/jxb/ery428] [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: 06/06/2018] [Accepted: 11/27/2018] [Indexed: 05/18/2023]
Abstract
Corm dormancy is an important trait for breeding in many bulb flowers, including the most cultivated Gladiolus hybridus. Gladiolus corms are modified underground stems that function as storage organs and remain dormant to survive adverse environmental conditions. Unlike seed dormancy, not much is known about corm dormancy. Here, we characterize the mechanism of corm dormancy release (CDR) in Gladiolus. We identified an important ABA (abscisic acid) signaling regulator, GhPP2C1 (protein phosphatase 2C1), by transcriptome analysis of CDR. GhPP2C1 expression increased during CDR, and silencing of GhPP2C1 expression in dormant cormels delayed CDR. Furthermore, we show that GhPP2C1 expression is directly regulated by GhNAC83, which was identified by yeast one-hybrid library screening. In planta assays show that GhNAC83 is a negative regulator of GhPP2C1, and silencing of GhNAC83 promoted CDR. As expected, silencing of GhNAC83 decreased the ABA level, but also dramatically increased cytokinin (CK; zeatin) content in cormels. Binding assays demonstrate that GhNAC83 associates with the GhIPT (ISOPENTENYLTRANSFERASE) promoter and negatively regulates zeatin biosynthesis. Taken together, our results reveal that GhNAC83 promotes ABA signaling and synthesis, and inhibits CK biosynthesis pathways, thereby inhibiting CDR. These findings demonstrate that GhNAC83 regulates the ABA and CK pathways, and therefore controls corm dormancy.
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Affiliation(s)
- Jian Wu
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture and Landscape Architecture, China Agricultural University, Beijing, China
- Department of Biological Sciences, University of Toronto Scarborough, ON, Canada
| | - Yujie Jin
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture and Landscape Architecture, China Agricultural University, Beijing, China
| | - Chen Liu
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture and Landscape Architecture, China Agricultural University, Beijing, China
| | - Eliana Vonapartis
- Department of Cell and Systems Biology, University of Toronto, ON, Canada
- Department of Biological Sciences, University of Toronto Scarborough, ON, Canada
| | - Jiahui Liang
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture and Landscape Architecture, China Agricultural University, Beijing, China
| | - Wenjing Wu
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture and Landscape Architecture, China Agricultural University, Beijing, China
| | - Sonia Gazzarrini
- Department of Cell and Systems Biology, University of Toronto, ON, Canada
- Department of Biological Sciences, University of Toronto Scarborough, ON, Canada
| | - Junna He
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture and Landscape Architecture, China Agricultural University, Beijing, China
- Correspondence: or
| | - Mingfang Yi
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture and Landscape Architecture, China Agricultural University, Beijing, China
- Correspondence: or
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26
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Zheng Y, Wu S, Bai Y, Sun H, Jiao C, Guo S, Zhao K, Blanca J, Zhang Z, Huang S, Xu Y, Weng Y, Mazourek M, K Reddy U, Ando K, McCreight JD, Schaffer AA, Burger J, Tadmor Y, Katzir N, Tang X, Liu Y, Giovannoni JJ, Ling KS, Wechter WP, Levi A, Garcia-Mas J, Grumet R, Fei Z. Cucurbit Genomics Database (CuGenDB): a central portal for comparative and functional genomics of cucurbit crops. Nucleic Acids Res 2019; 47:D1128-D1136. [PMID: 30321383 DOI: 10.1093/nar/gky944s] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 10/04/2018] [Indexed: 05/20/2023] Open
Abstract
The Cucurbitaceae family (cucurbit) includes several economically important crops, such as melon, cucumber, watermelon, pumpkin, squash and gourds. During the past several years, genomic and genetic data have been rapidly accumulated for cucurbits. To store, mine, analyze, integrate and disseminate these large-scale datasets and to provide a central portal for the cucurbit research and breeding community, we have developed the Cucurbit Genomics Database (CuGenDB; http://cucurbitgenomics.org) using the Tripal toolkit. The database currently contains all available genome and expressed sequence tag (EST) sequences, genetic maps, and transcriptome profiles for cucurbit species, as well as sequence annotations, biochemical pathways and comparative genomic analysis results such as synteny blocks and homologous gene pairs between different cucurbit species. A set of analysis and visualization tools and user-friendly query interfaces have been implemented in the database to facilitate the usage of these large-scale data by the community. In particular, two new tools have been developed in the database, a 'SyntenyViewer' to view genome synteny between different cucurbit species and an 'RNA-Seq' module to analyze and visualize gene expression profiles. Both tools have been packed as Tripal extension modules that can be adopted in other genomics databases developed using the Tripal system.
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Affiliation(s)
- Yi Zheng
- Boyce Thompson Institute, Cornell University, Ithaca, NY 14853, USA
| | - Shan Wu
- Boyce Thompson Institute, Cornell University, Ithaca, NY 14853, USA
| | - Yang Bai
- Boyce Thompson Institute, Cornell University, Ithaca, NY 14853, USA
| | - Honghe Sun
- Boyce Thompson Institute, Cornell University, Ithaca, NY 14853, USA
- National Engineering Research Center for Vegetables, Beijing Academy of Agriculture and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing 100097, China
| | - Chen Jiao
- Boyce Thompson Institute, Cornell University, Ithaca, NY 14853, USA
| | - Shaogui Guo
- Boyce Thompson Institute, Cornell University, Ithaca, NY 14853, USA
- National Engineering Research Center for Vegetables, Beijing Academy of Agriculture and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing 100097, China
| | - Kun Zhao
- Boyce Thompson Institute, Cornell University, Ithaca, NY 14853, USA
| | - Jose Blanca
- Institute for the Conservation and Breeding of Agricultural Biodiversity (COMAV-UPV), Universitat Politècnica de València, Valencia 46022, Spain
| | - Zhonghua Zhang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Sanwen Huang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518124, China
| | - Yong Xu
- National Engineering Research Center for Vegetables, Beijing Academy of Agriculture and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing 100097, China
| | - Yiqun Weng
- U.S. Department of Agriculture-Agricultural Research Service, Vegetable Crops Research Unit, Madison, WI 53706, USA
- Department of Horticulture, University of Wisconsin, Madison, WI 53706, USA
| | - Michael Mazourek
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
| | - Umesh K Reddy
- Department of Biology, West Virginia State University, Institute, WV 25112, USA
| | - Kaori Ando
- U.S. Department of Agriculture-Agricultural Research Service, Crop Improvement and Protection Research Unit, Salinas, CA 93905, USA
| | - James D McCreight
- U.S. Department of Agriculture-Agricultural Research Service, Crop Improvement and Protection Research Unit, Salinas, CA 93905, USA
| | - Arthur A Schaffer
- Plant Science Institute, Agricultural Research Organization, The Volcani Center, P.O.B. 6, Bet-Dagan 50250, Israel
| | - Joseph Burger
- Plant Science Institute, Agricultural Research Organization, Newe Yaar Research Center, Ramat Yishai 30095, Israel
| | - Yaakov Tadmor
- Plant Science Institute, Agricultural Research Organization, Newe Yaar Research Center, Ramat Yishai 30095, Israel
| | - Nurit Katzir
- Plant Science Institute, Agricultural Research Organization, Newe Yaar Research Center, Ramat Yishai 30095, Israel
| | - Xuemei Tang
- Boyce Thompson Institute, Cornell University, Ithaca, NY 14853, USA
| | - Yang Liu
- Boyce Thompson Institute, Cornell University, Ithaca, NY 14853, USA
- Horticulture Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
| | - James J Giovannoni
- Boyce Thompson Institute, Cornell University, Ithaca, NY 14853, USA
- U.S. Department of Agriculture-Agricultural Research Service, Robert W. Holley Center for Agriculture and Health, Ithaca, NY 14853, USA
| | - Kai-Shu Ling
- U.S. Department of Agriculture-Agricultural Research Service, U.S. Vegetable Laboratory, 2700 Savannah Highway, Charleston, SC 29414, USA
| | - W Patrick Wechter
- U.S. Department of Agriculture-Agricultural Research Service, U.S. Vegetable Laboratory, 2700 Savannah Highway, Charleston, SC 29414, USA
| | - Amnon Levi
- U.S. Department of Agriculture-Agricultural Research Service, U.S. Vegetable Laboratory, 2700 Savannah Highway, Charleston, SC 29414, USA
| | - Jordi Garcia-Mas
- Centre for Research in Agricultural Genomics CSIC-IRTA-UAB-UB, Barcelona 08193, Spain
- Institut de Recerca i Tecnologia Agroalimentàries, Barcelona 08193, Spain
| | - Rebecca Grumet
- Department of Horticulture, Michigan State University, East Lansing, MI 48824, USA
| | - Zhangjun Fei
- Boyce Thompson Institute, Cornell University, Ithaca, NY 14853, USA
- U.S. Department of Agriculture-Agricultural Research Service, Robert W. Holley Center for Agriculture and Health, Ithaca, NY 14853, USA
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Cook DE, Valle-Inclan JE, Pajoro A, Rovenich H, Thomma BP, Faino L. Long-Read Annotation: Automated Eukaryotic Genome Annotation Based on Long-Read cDNA Sequencing. PLANT PHYSIOLOGY 2019; 179:38-54. [PMID: 30401722 PMCID: PMC6324239 DOI: 10.1104/pp.18.00848] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Accepted: 10/19/2018] [Indexed: 05/16/2023]
Abstract
Single-molecule full-length complementary DNA (cDNA) sequencing can aid genome annotation by revealing transcript structure and alternative splice forms, yet current annotation pipelines do not incorporate such information. Here we present long-read annotation (LoReAn) software, an automated annotation pipeline utilizing short- and long-read cDNA sequencing, protein evidence, and ab initio prediction to generate accurate genome annotations. Based on annotations of two fungal genomes (Verticillium dahliae and Plicaturopsis crispa) and two plant genomes (Arabidopsis [Arabidopsis thaliana] and Oryza sativa), we show that LoReAn outperforms popular annotation pipelines by integrating single-molecule cDNA-sequencing data generated from either the Pacific Biosciences or MinION sequencing platforms, correctly predicting gene structure, and capturing genes missed by other annotation pipelines.
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Affiliation(s)
- David E. Cook
- Laboratory of Phytopathology, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands
| | - Jose Espejo Valle-Inclan
- Laboratory of Phytopathology, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands
| | - Alice Pajoro
- Laboratory of Molecular Biology, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands
| | - Hanna Rovenich
- Laboratory of Phytopathology, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands
| | - Bart P.H.J. Thomma
- Laboratory of Phytopathology, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands
- Author for contact:
| | - Luigi Faino
- Laboratory of Phytopathology, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands
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Sun CH, Yu JQ, Duan X, Wang JH, Zhang QY, Gu KD, Hu DG, Zheng CS. The MADS transcription factor CmANR1 positively modulates root system development by directly regulating CmPIN2 in chrysanthemum. HORTICULTURE RESEARCH 2018; 5:52. [PMID: 30302256 PMCID: PMC6165851 DOI: 10.1038/s41438-018-0061-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Revised: 05/23/2018] [Accepted: 05/28/2018] [Indexed: 05/20/2023]
Abstract
Plant root systems are essential for many physiological processes, including water and nutrient absorption. MADS-box transcription factor (TF) genes have been characterized as the important regulators of root development in plants; however, the underlying mechanism is largely unknown, including chrysanthemum. Here, it was found that the overexpression of CmANR1, a chrysanthemum MADS-box TF gene, promoted both adventitious root (AR) and lateral root (LR) development in chrysanthemum. Whole transcriptome sequencing analysis revealed a series of differentially expressed unigenes (DEGs) in the roots of CmANR1-transgenic chrysanthemum plants compared to wild-type plants. Functional annotation of these DEGs by alignment with Gene Ontology (GO) terms and biochemical pathway Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis indicated that CmANR1 TF exhibited "DNA binding" and "catalytic" activity, as well as participated in "phytohormone signal transduction". Both chromatin immunoprecipitation-polymerase chain reaction (ChIP-PCR) and gel electrophoresis mobility shift assays (EMSA) indicated the direct binding of CmPIN2 to the recognition site CArG-box motif by CmANR1. Finally, a firefly luciferase imaging assay demonstrated the transcriptional activation of CmPIN2 by CmANR1 in vivo. Overall, our results provide novel insights into the mechanisms of MADS-box TF CmANR1 modulation of both AR and LR development, which occurs by directly regulating auxin transport gene CmPIN2 in chrysanthemum.
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Affiliation(s)
- Cui-Hui Sun
- National Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, Shandong 271018 China
| | - Jian-Qiang Yu
- National Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, Shandong 271018 China
| | - Xi Duan
- Shandong Agricultural and Engineering University, Ji-Nan, Shandong China
| | - Jia-Hui Wang
- National Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, Shandong 271018 China
| | - Quan-Yan Zhang
- National Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, Shandong 271018 China
| | - Kai-Di Gu
- National Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, Shandong 271018 China
| | - Da-Gang Hu
- National Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, Shandong 271018 China
| | - Cheng-Shu Zheng
- National Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, Shandong 271018 China
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Liu X, Cao X, Shi S, Zhao N, Li D, Fang P, Chen X, Qi W, Zhang Z. Comparative RNA-Seq analysis reveals a critical role for brassinosteroids in rose (Rosa hybrida) petal defense against Botrytis cinerea infection. BMC Genet 2018; 19:62. [PMID: 30126371 PMCID: PMC6102922 DOI: 10.1186/s12863-018-0668-x] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Accepted: 08/10/2018] [Indexed: 12/31/2022] Open
Abstract
Background One of the most popular ornamental plants worldwide, roses (Rosa sp.), are very susceptible to Botrytis gray mold disease. The necrotrophic infection of rose petals by B. cinerea causes the collapse and death of these tissues in both the growth and post-harvest stages, resulting in serious economic losses. To understand the molecular basis of rose resistance against B. cinerea, we profiled the petal transcriptome using RNA-Seq technology. Results We identified differentially transcribed genes (DTGs) in petals during B. cinerea infection at 30 h post inoculation (hpi) and/or 48 hpi. Gene ontology term enrichment and pathway analyses revealed that metabolic, secondary metabolite biosynthesis, plant-pathogen interaction, and plant hormone signal transduction pathways were involved. The expression of 370 cell-surface immune receptors was upregulated during infection. In addition, 188 genes encoding transcription factors were upregulated, particularly in the ERF, WRKY, bHLH, MYB, and NAC families, implying their involvement in resistance against B. cinerea. We further identified 325 upregulated DTGs in the hormone signal transduction pathways. Among them, the brassinosteroid (BR)-related genes were the most significantly enriched. To confirm the role of BR in Botrytis resistance, exogenous BR was applied to rose flowers before the inoculation of B. cinerea, which enhanced the defense response in these petals. Conclusions Our global transcriptome profiling provides insights into the complex gene regulatory networks mediating the rose petal response to B. cinerea. We further demonstrated the role of the phytohormone BR in the resistance of petals to necrotrophic fungal pathogens. Electronic supplementary material The online version of this article (10.1186/s12863-018-0668-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Xintong Liu
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, College of Horticulture, China Agricultural University, Yuanmingyuan Xilu 2, Beijing, 100193, China
| | - Xiaoqian Cao
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, College of Horticulture, China Agricultural University, Yuanmingyuan Xilu 2, Beijing, 100193, China
| | - Shaochuan Shi
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, College of Horticulture, China Agricultural University, Yuanmingyuan Xilu 2, Beijing, 100193, China
| | - Na Zhao
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, College of Horticulture, China Agricultural University, Yuanmingyuan Xilu 2, Beijing, 100193, China
| | - Dandan Li
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, College of Horticulture, China Agricultural University, Yuanmingyuan Xilu 2, Beijing, 100193, China
| | - Peihong Fang
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, College of Horticulture, China Agricultural University, Yuanmingyuan Xilu 2, Beijing, 100193, China
| | - Xi Chen
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Weicong Qi
- Institute of Biotechnology, Provincial Key Laboratory of Agrobiology, Jiangsu Academy of Agricultural Sciences, Zhonglingjie 50, Nanjing, 210014, China.
| | - Zhao Zhang
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, College of Horticulture, China Agricultural University, Yuanmingyuan Xilu 2, Beijing, 100193, China.
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Shu Y, Li W, Zhao J, Liu Y, Guo C. Transcriptome sequencing and expression profiling of genes involved in the response to abiotic stress in Medicago ruthenica. Genet Mol Biol 2018; 41:638-648. [PMID: 30004107 PMCID: PMC6136363 DOI: 10.1590/1678-4685-gmb-2017-0284] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Accepted: 01/03/2018] [Indexed: 11/21/2022] Open
Abstract
Medicago ruthenica is a perennial forage legume with the remarkable ability to survive under unfavorable environmental conditions. It has been identified as an excellent species of Medicago that can adapt to various environmental stresses including low temperature, drought, and salinity. To investigate its potential as a genetic resource, we performed transcriptome sequencing and analysis in M. ruthenica under abiotic stresses. We generated >120 million reads from six cDNA libraries, resulting in 79,249 unique transcripts, most of which were highly similar to transcripts from M. truncatula (44,608, 56.3%) and alfalfa (M. sativa, 48,023, 60.6%). Based on gene expression profiles, 2,721 transcripts were identified as abiotic stress responsive genes which were predicted to be mainly involved in phytohormone signaling pathways, transcriptional regulation, and ROS-scavenging. These results suggest that they play critical roles in the response to abiotic stress. In summary, we identified genes in our transcriptome dataset involved in the regulation of the abiotic stress response in M. ruthenica which will provide a valuable resource for the future identification and functional analysis of candidate genes for adaption to unfavorable conditions. The genes identified here could be also useful for improving stress tolerance traits in alfalfa through molecular breeding in the future.
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Affiliation(s)
- Yongjun Shu
- College of Life Science and Technology, Harbin Normal University, Harbin Heilongjiang, China
| | - Wei Li
- College of Life Science and Technology, Harbin Normal University, Harbin Heilongjiang, China
| | - Jinyue Zhao
- College of Life Science and Technology, Harbin Normal University, Harbin Heilongjiang, China
| | - Ying Liu
- College of Life Science and Technology, Harbin Normal University, Harbin Heilongjiang, China
| | - Changhong Guo
- College of Life Science and Technology, Harbin Normal University, Harbin Heilongjiang, China
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31
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Zhang X, Liu Z, Wei G, Yang F, Liu X. In Silico Genome-Wide Analysis Reveals the Potential Links Between Core Genome of Acidithiobacillus thiooxidans and Its Autotrophic Lifestyle. Front Microbiol 2018; 9:1255. [PMID: 29937764 PMCID: PMC6002666 DOI: 10.3389/fmicb.2018.01255] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Accepted: 05/24/2018] [Indexed: 12/27/2022] Open
Abstract
The coinage “pan-genome” was first introduced dating back to 2005, and was used to elaborate the entire gene repertoire of any given species. Core genome consists of genes shared by all bacterial strains studied and is considered to encode essential functions associated with species’ basic biology and phenotypes, yet its relatedness with bacterial lifestyle of the species remains elusive. We performed the pan-genome analysis of sulfur-oxidizing acidophile Acidithiobacillus thiooxidans as a case study to highlight species’ core genome and its relevance with autotrophic lifestyle of bacterial species. The mathematical modeling based on bacterial genomes of A. thiooxidans species, including a novel strain ZBY isolated from Zambian copper mine plus eight other recognized strains, was attempted to extrapolate the expansion of its pan-genome, suggesting that A. thiooxidans pan-genome is closed. Further investigation revealed a common set of genes, many of which were assigned to metabolic profiles, notably with respect to energy metabolism, amino acid metabolism, and carbohydrate metabolism. The predicted metabolic profiles of A. thiooxidans were characterized by the fixation of inorganic carbon, assimilation of nitrogen compounds, and aerobic oxidation of various sulfur species. Notably, several hydrogenase (H2ase)-like genes dispersed in core genome might represent the novel classes due to the potential functional disparities, despite being closely related homologous genes that code for H2ase. Overall, the findings shed light on the distinguishing features of A. thiooxidans genomes on a global scale, and extend the understanding of its conserved core genome pertaining to autotrophic lifestyle.
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Affiliation(s)
- Xian Zhang
- Department of Occupational and Environmental Health, Xiangya School of Public Health, Central South University, Changsha, China
| | - Zhenghua Liu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
| | - Guanyun Wei
- College of Life Science, Nanjing Normal University, Nanjing, China
| | - Fei Yang
- Department of Occupational and Environmental Health, Xiangya School of Public Health, Central South University, Changsha, China
| | - Xueduan Liu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China.,Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
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32
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Wei Q, Jiao C, Ding Y, Gao S, Guo L, Chen M, Hu P, Xia S, Ren G, Fei Z. Cellular and molecular characterizations of a slow-growth variant provide insights into the fast growth of bamboo. TREE PHYSIOLOGY 2018; 38:641-654. [PMID: 29077967 DOI: 10.1093/treephys/tpx129] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2017] [Accepted: 09/24/2017] [Indexed: 05/16/2023]
Abstract
Few studies about bamboo naturally occurring mutants have been reported so far. Using an integrated anatomy, mathematics and genomics approach, we systematically characterized the cellular and molecular basis underlying the abnormal internode development of Pseudosasa japonica var. tsutsumiana, a stable variant with dwarf and swollen internodes that are caused by the compressed spiral growth and the swollen cells in the bottom part of the internode. P. japonica var. tsutsumiana is a slow-growth variant with disorderly cell division and cell growth during the fast growth stage. Comparative transcriptome analysis identified a number of genes related to cell growth that were significantly down-regulated in the variant, including those related to auxin, vesicle transport, cytoskeleton organization and cell wall modification, consistent with the thinner cell walls and lower contents of cellulose that were found in the variant, which together with the mechanic force composed by the extrusion pressure from the neighboring fast growth cells and the weight pressure above the growing cells might finally result in the radial and irregular growth of the variant cells. This study provides key candidate genes involved in the fast growth of bamboo from a 'mutant' perspective, and supports a plausible mechanism underlying the dwarf and swollen internodes of P. japonica var. tsutsumiana.
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Affiliation(s)
- Qiang Wei
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
- Bamboo Research Institute, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
| | - Chen Jiao
- Boyce Thompson Institute, Cornell University, Ithaca, NY 14853, USA
| | - Yulong Ding
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
- Bamboo Research Institute, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
| | - Shan Gao
- Boyce Thompson Institute, Cornell University, Ithaca, NY 14853, USA
- College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Lin Guo
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
| | - Ming Chen
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
| | - Pei Hu
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
| | - Sujuan Xia
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
| | - Guodong Ren
- State Key Laboratory of Genetic Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Zhangjun Fei
- Boyce Thompson Institute, Cornell University, Ithaca, NY 14853, USA
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Julve Parreño JM, Huet E, Fernández‐del‐Carmen A, Segura A, Venturi M, Gandía A, Pan W, Albaladejo I, Forment J, Pla D, Wigdorovitz A, Calvete JJ, Gutiérrez C, Gutiérrez JM, Granell A, Orzáez D. A synthetic biology approach for consistent production of plant-made recombinant polyclonal antibodies against snake venom toxins. PLANT BIOTECHNOLOGY JOURNAL 2018; 16:727-736. [PMID: 28850773 PMCID: PMC5814581 DOI: 10.1111/pbi.12823] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Revised: 08/03/2017] [Accepted: 08/23/2017] [Indexed: 05/26/2023]
Abstract
Antivenoms developed from the plasma of hyperimmunized animals are the only effective treatment available against snakebite envenomation but shortage of supply contributes to the high morbidity and mortality toll of this tropical disease. We describe a synthetic biology approach to affordable and cost-effective antivenom production based on plant-made recombinant polyclonal antibodies (termed pluribodies). The strategy takes advantage of virus superinfection exclusion to induce the formation of somatic expression mosaics in agroinfiltrated plants, which enables the expression of complex antibody repertoires in a highly reproducible manner. Pluribodies developed using toxin-binding genetic information captured from peripheral blood lymphocytes of hyperimmunized camels recapitulated the overall binding activity of the immune response. Furthermore, an improved plant-made antivenom (plantivenom) was formulated using an in vitro selected pluribody against Bothrops asper snake venom toxins and has been shown to neutralize a wide range of toxin activities and provide protection against lethal venom doses in mice.
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Affiliation(s)
- Jose Manuel Julve Parreño
- Instituto de Biología Molecular y Celular de Plantas (IBMCP)Agencia Estatal Consejo Superior de Investigaciones CientíficasUniversidad Politécnica de ValenciaValenciaSpain
| | - Estefanía Huet
- Instituto de Biología Molecular y Celular de Plantas (IBMCP)Agencia Estatal Consejo Superior de Investigaciones CientíficasUniversidad Politécnica de ValenciaValenciaSpain
| | - Asun Fernández‐del‐Carmen
- Instituto de Biología Molecular y Celular de Plantas (IBMCP)Agencia Estatal Consejo Superior de Investigaciones CientíficasUniversidad Politécnica de ValenciaValenciaSpain
| | - Alvaro Segura
- Instituto Clodomiro PicadoFacultad de MicrobiologíaUniversidad de Costa RicaSan JoséCosta Rica
| | - Micol Venturi
- Instituto de Biología Molecular y Celular de Plantas (IBMCP)Agencia Estatal Consejo Superior de Investigaciones CientíficasUniversidad Politécnica de ValenciaValenciaSpain
| | - Antoni Gandía
- Instituto de Biología Molecular y Celular de Plantas (IBMCP)Agencia Estatal Consejo Superior de Investigaciones CientíficasUniversidad Politécnica de ValenciaValenciaSpain
| | - Wei‐song Pan
- Instituto de Biología Molecular y Celular de Plantas (IBMCP)Agencia Estatal Consejo Superior de Investigaciones CientíficasUniversidad Politécnica de ValenciaValenciaSpain
| | - Irene Albaladejo
- Instituto de Biología Molecular y Celular de Plantas (IBMCP)Agencia Estatal Consejo Superior de Investigaciones CientíficasUniversidad Politécnica de ValenciaValenciaSpain
| | - Javier Forment
- Instituto de Biología Molecular y Celular de Plantas (IBMCP)Agencia Estatal Consejo Superior de Investigaciones CientíficasUniversidad Politécnica de ValenciaValenciaSpain
| | - Davinia Pla
- Instituto de Biomedicina de ValenciaAgencia Estatal Consejo Superior de Investigaciones CientíficasValenciaSpain
| | | | - Juan J. Calvete
- Instituto de Biomedicina de ValenciaAgencia Estatal Consejo Superior de Investigaciones CientíficasValenciaSpain
| | - Carlos Gutiérrez
- Research Institute of Biomedical and Health SciencesUniversity of Las Palmas de Gran CanariaArucasLas PalmasCanary IslandsSpain
| | - José María Gutiérrez
- Instituto Clodomiro PicadoFacultad de MicrobiologíaUniversidad de Costa RicaSan JoséCosta Rica
| | - Antonio Granell
- Instituto de Biología Molecular y Celular de Plantas (IBMCP)Agencia Estatal Consejo Superior de Investigaciones CientíficasUniversidad Politécnica de ValenciaValenciaSpain
| | - Diego Orzáez
- Instituto de Biología Molecular y Celular de Plantas (IBMCP)Agencia Estatal Consejo Superior de Investigaciones CientíficasUniversidad Politécnica de ValenciaValenciaSpain
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Yadav R, Lone SA, Gaikwad K, Singh NK, Padaria JC. Transcriptome sequence analysis and mining of SSRs in Jhar Ber (Ziziphus nummularia (Burm.f.) Wight & Arn) under drought stress. Sci Rep 2018; 8:2406. [PMID: 29402924 PMCID: PMC5799245 DOI: 10.1038/s41598-018-20548-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Accepted: 01/02/2018] [Indexed: 11/09/2022] Open
Abstract
Ziziphus nummularia (Burm.f.) Wight & Arn., a perennial shrub that thrives in the arid regions, is naturally tolerant to drought. However, there are limited studies on the genomics of drought tolerance in Ziziphus sp. In this study, RNA-sequencing of one month old seedlings treated with PEG 6000 was performed using Roche GS-FLX454 Titanium pyrosequencing. A total of 367,176 raw sequence reads were generated, and upon adapter trimming and quality filtration 351,872 reads were assembled de novo into 32,739 unigenes. Further characterization of the unigenes indicated that 73.25% had significant hits in the protein database. Kyoto encyclopedia of genes and genomes database (KEGG) identified 113 metabolic pathways from the obtained unigenes. A large number of drought-responsive genes were obtained and among them differential gene expression of 16 highly induced genes was validated by qRT-PCR analysis. To develop genic-markers, 3,425 simple sequence repeats (SSRs) were identified in 2,813 unigene sequences. The data generated shall serve as an important reservoir for the identification and characterization of drought stress responsive genes for development of drought tolerant crops.
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Affiliation(s)
- Radha Yadav
- Biotechnology and Climate Change Group, National Research Centre on Plant Biotechnology (ICAR-NRCPB), New Delhi, 110012, India
| | - Showkat Ahmad Lone
- Biotechnology and Climate Change Group, National Research Centre on Plant Biotechnology (ICAR-NRCPB), New Delhi, 110012, India
- Department of Agricultural Microbiology, Faculty of Agricultural Sciences, Aligarh Muslim University, Aligarh, 202002, India
| | - Kishor Gaikwad
- Biotechnology and Climate Change Group, National Research Centre on Plant Biotechnology (ICAR-NRCPB), New Delhi, 110012, India
| | - Nagendra Kumar Singh
- Biotechnology and Climate Change Group, National Research Centre on Plant Biotechnology (ICAR-NRCPB), New Delhi, 110012, India
| | - Jasdeep Chatrath Padaria
- Biotechnology and Climate Change Group, National Research Centre on Plant Biotechnology (ICAR-NRCPB), New Delhi, 110012, India.
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Shu Y, Li W, Zhao J, Zhang S, Xu H, Liu Y, Guo C. Transcriptome sequencing analysis of alfalfa reveals CBF genes potentially playing important roles in response to freezing stress. Genet Mol Biol 2017; 40:824-833. [PMID: 29111565 PMCID: PMC5738619 DOI: 10.1590/1678-4685-gmb-2017-0053] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2017] [Accepted: 06/23/2017] [Indexed: 12/31/2022] Open
Abstract
Alfalfa (Medicago sativa L.) is an important perennial forage, with high nutritional value, which is widely grown in the world. Because of low freezing tolerance, its distribution and production are threatened and limited by winter weather. To understand the complex regulation mechanisms of freezing tolerance in alfalfa, we performed transcriptome sequencing analysis under cold (4 °C) and freezing (-8 °C) stresses. More than 66 million reads were generated, and we identified 5767 transcripts differentially expressed in response to cold and/or freezing stresses. These results showed that these genes were mainly classified as response to stress, transcription regulation, hormone signaling pathway, antioxidant, nodule morphogenesis, etc., implying their important roles in response to cold and freezing stresses. Furthermore, nine CBF transcripts differentially expressed were homologous to CBF genes of Mt-FTQTL6 site, conferring freezing tolerance in M. truncatula, which indicated that a genetic mechanism controlling freezing tolerance was conservative between M. truncatula and M. sativa. In summary, this transcriptome dataset highlighted the gene regulation response to cold and/or freezing stresses in alfalfa, which provides a valuable resource for future identification and functional analysis of candidate genes in determining freezing tolerance.
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Affiliation(s)
- Yongjun Shu
- College of Life Science and Technology, Harbin Normal University, Harbin Heilongjiang, China
| | - Wei Li
- College of Life Science and Technology, Harbin Normal University, Harbin Heilongjiang, China
| | - Jinyue Zhao
- College of Life Science and Technology, Harbin Normal University, Harbin Heilongjiang, China
| | - Sijia Zhang
- College of Life Science and Technology, Harbin Normal University, Harbin Heilongjiang, China
| | - Hanyun Xu
- College of Life Science and Technology, Harbin Normal University, Harbin Heilongjiang, China
| | - Ying Liu
- College of Life Science and Technology, Harbin Normal University, Harbin Heilongjiang, China
| | - Changhong Guo
- College of Life Science and Technology, Harbin Normal University, Harbin Heilongjiang, China
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Simon S, Sagasser S, Saccenti E, Brugler MR, Schranz ME, Hadrys H, Amato G, DeSalle R. Comparative transcriptomics reveal developmental turning points during embryogenesis of a hemimetabolous insect, the damselfly Ischnura elegans. Sci Rep 2017; 7:13547. [PMID: 29051502 PMCID: PMC5648782 DOI: 10.1038/s41598-017-13176-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Accepted: 09/21/2017] [Indexed: 11/12/2022] Open
Abstract
Identifying transcriptional changes during embryogenesis is of crucial importance for unravelling evolutionary, molecular and cellular mechanisms that underpin patterning and morphogenesis. However, comparative studies focusing on early/embryonic stages during insect development are limited to a few taxa. Drosophila melanogaster is the paradigm for insect development, whereas comparative transcriptomic studies of embryonic stages of hemimetabolous insects are completely lacking. We reconstructed the first comparative transcriptome covering the daily embryonic developmental progression of the blue-tailed damselfly Ischnura elegans (Odonata), an ancient hemimetabolous representative. We identified a "core" set of 6,794 transcripts - shared by all embryonic stages - which are mainly involved in anatomical structure development and cellular nitrogen compound metabolic processes. We further used weighted gene co-expression network analysis to identify transcriptional changes during Odonata embryogenesis. Based on these analyses distinct clusters of transcriptional active sequences could be revealed, indicating that embryos at different development stages have their own transcriptomic profile according to the developmental events and leading to sequential reprogramming of metabolic and developmental genes. Interestingly, a major change in transcriptionally active sequences is correlated with katatrepsis (revolution) during mid-embryogenesis, a 180° rotation of the embryo within the egg and specific to hemimetabolous insects.
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Affiliation(s)
- Sabrina Simon
- Biosystematics Group, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands.
- Sackler Institute for Comparative Genomics, American Museum of Natural History, Central Park West and 79th St., New York, NY, 10024, USA.
| | - Sven Sagasser
- Ludwig Institute for Cancer Research, Karolinska Institutet, 17177, Stockholm, Sweden
| | - Edoardo Saccenti
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Stippeng 4, 6708 WE, Wageningen, The Netherlands
| | - Mercer R Brugler
- Sackler Institute for Comparative Genomics, American Museum of Natural History, Central Park West and 79th St., New York, NY, 10024, USA
- Biological Sciences Department, NYC College of Technology, City University of New York, 300 Jay Street, Brooklyn, New York, 11201, USA
| | - M Eric Schranz
- Biosystematics Group, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Heike Hadrys
- Sackler Institute for Comparative Genomics, American Museum of Natural History, Central Park West and 79th St., New York, NY, 10024, USA
- ITZ, Ecology&Evolution, University of Veterinary Medicine Hanover, Buenteweg 17d, D-30559, Hannover, Germany
- Yale University, Department of Ecology & Evolutionary Biology, 165 Prospect Street, New Haven, CT, 06511, USA
| | - George Amato
- Sackler Institute for Comparative Genomics, American Museum of Natural History, Central Park West and 79th St., New York, NY, 10024, USA
| | - Rob DeSalle
- Sackler Institute for Comparative Genomics, American Museum of Natural History, Central Park West and 79th St., New York, NY, 10024, USA
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Divya B, Yadav P, Masih P, Singh RK, Mohindra V. In silico characterization of Myogenic Factor 6 transcript of Hilsa, Tenualosa ilisha and putative role of its SNPs with differential growth. Meta Gene 2017. [DOI: 10.1016/j.mgene.2017.06.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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Ventura-López C, Galindo-Torres PE, Arcos FG, Galindo-Sánchez C, Racotta IS, Escobedo-Fregoso C, Llera-Herrera R, Ibarra AM. Transcriptomic information from Pacific white shrimp (Litopenaeus vannamei) ovary and eyestalk, and expression patterns for genes putatively involved in the reproductive process. Gen Comp Endocrinol 2017; 246:164-182. [PMID: 27964922 DOI: 10.1016/j.ygcen.2016.12.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Revised: 12/07/2016] [Accepted: 12/09/2016] [Indexed: 11/27/2022]
Abstract
The increased use of massive sequencing technologies has enabled the identification of several genes known to be involved in different mechanisms associated with reproduction that so far have only been studied in vertebrates and other model invertebrate species. In order to further investigate the genes involved in Litopenaeus vannamei reproduction, cDNA and SSH libraries derived from female eyestalk and gonad were produced, allowing the identification of expressed sequences tags (ESTs) that potentially have a role in the regulation of gonadal maturation. In the present study, different transcripts involved in reproduction were identified and a number of them were characterized as full-length. These transcripts were evaluated in males and females in order to establish their tissue expression profiles during developmental stages (juvenile, subadult and adult), and in the case of females, their possible association with gonad maturation was assessed through expression analysis of vitellogenin. The results indicated that the expression of vitellogenin receptor (vtgr) and minichromosome maintenance (mcm) family members in the female gonad suggest an important role during previtellogenesis. Additionally, the expression profiles of genes such as famet, igfbp and gpcr in brain tissues suggest an interaction between the insulin/insulin-like growth factor signaling pathway (IIS) and methyl farnesoate (MF) biosynthesis for control of reproduction. Furthermore, the specific expression pattern of farnesoic acid O-methyltransferase suggests that final synthesis of MF is carried out in different target tissues, where it is regulated by esterase enzymes under a tissue-specific hormonal control. Finally, the presence of a vertebrate type steroid receptor in hepatopancreas and intestine besides being highly expressed in female gonads, suggest a role of that receptor during sexual maturation.
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Affiliation(s)
- Claudia Ventura-López
- Centro de Investigaciones Biológicas del Noroeste, S.C. (CIBNOR), Av. Instituto Politécnico Nacional No.195, Col. Playa Palo de Santa Rita, La Paz, Baja California Sur 23096, Mexico.
| | - Pavel E Galindo-Torres
- Centro de Investigaciones Biológicas del Noroeste, S.C. (CIBNOR), Av. Instituto Politécnico Nacional No.195, Col. Playa Palo de Santa Rita, La Paz, Baja California Sur 23096, Mexico.
| | - Fabiola G Arcos
- Centro de Investigaciones Biológicas del Noroeste, S.C. (CIBNOR), Av. Instituto Politécnico Nacional No.195, Col. Playa Palo de Santa Rita, La Paz, Baja California Sur 23096, Mexico.
| | - Clara Galindo-Sánchez
- Centro de Investigación Científica y de Educación Superior de Ensenada (CICESE), Carretera Ensenada-Tijuana No. 3918, Zona Playitas, Ensenada, Baja California CP 22860, Mexico.
| | - Ilie S Racotta
- Centro de Investigaciones Biológicas del Noroeste, S.C. (CIBNOR), Av. Instituto Politécnico Nacional No.195, Col. Playa Palo de Santa Rita, La Paz, Baja California Sur 23096, Mexico.
| | - Cristina Escobedo-Fregoso
- Consejo Nacional de Ciencia y Tecnología (CONACYT) - Centro de Investigaciones Biológicas del Noroeste, S.C. (CIBNOR), Av. Instituto Politécnico Nacional 195, Col. Playa Palo de Santa Rita, La Paz, Baja California Sur C.P. 23096, Mexico.
| | - Raúl Llera-Herrera
- Consejo Nacional de Ciencia y Tecnología (CONACYT) - Centro de Investigación en Alimentación y Desarrollo A.C. (CIAD) Unidad Mazatlán, Av. Sábalo-Cerritos s/n. Estero del Yugo, Mazatlán, Sinaloa 82000, Mexico.
| | - Ana M Ibarra
- Centro de Investigaciones Biológicas del Noroeste, S.C. (CIBNOR), Av. Instituto Politécnico Nacional No.195, Col. Playa Palo de Santa Rita, La Paz, Baja California Sur 23096, Mexico.
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Transcriptome Analysis of Mango (Mangifera indica L.) Fruit Epidermal Peel to Identify Putative Cuticle-Associated Genes. Sci Rep 2017; 7:46163. [PMID: 28425468 PMCID: PMC5397871 DOI: 10.1038/srep46163] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Accepted: 03/09/2017] [Indexed: 11/10/2022] Open
Abstract
Mango fruit (Mangifera indica L.) are highly perishable and have a limited shelf life, due to postharvest desiccation and senescence, which limits their global distribution. Recent studies of tomato fruit suggest that these traits are influenced by the expression of genes that are associated with cuticle metabolism. However, studies of these phenomena in mango fruit are limited by the lack of genome-scale data. In order to gain insight into the mango cuticle biogenesis and identify putative cuticle-associated genes, we analyzed the transcriptomes of peels from ripe and overripe mango fruit using RNA-Seq. Approximately 400 million reads were generated and de novo assembled into 107,744 unigenes, with a mean length of 1,717 bp and with this information an online Mango RNA-Seq Database (http://bioinfo.bti.cornell.edu/cgi-bin/mango/index.cgi) which is a valuable genomic resource for molecular research into the biology of mango fruit was created. RNA-Seq analysis suggested that the pathway leading to biosynthesis of the cuticle component, cutin, is up-regulated during overripening. This data was supported by analysis of the expression of several putative cuticle-associated genes and by gravimetric and microscopic studies of cuticle deposition, revealing a complex continuous pattern of cuticle deposition during fruit development and involving substantial accumulation during ripening/overripening.
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Loke KK, Rahnamaie-Tajadod R, Yeoh CC, Goh HH, Mohamed-Hussein ZA, Zainal Z, Ismail I, Mohd Noor N. Transcriptome analysis of Polygonum minus reveals candidate genes involved in important secondary metabolic pathways of phenylpropanoids and flavonoids. PeerJ 2017; 5:e2938. [PMID: 28265493 PMCID: PMC5333554 DOI: 10.7717/peerj.2938] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Accepted: 12/23/2016] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Polygonum minus is an herbal plant in the Polygonaceae family which is rich in ethnomedicinal plants. The chemical composition and characteristic pungent fragrance of Polygonum minus have been extensively studied due to its culinary and medicinal properties. There are only a few transcriptome sequences available for species from this important family of medicinal plants. The limited genetic information from the public expressed sequences tag (EST) library hinders further study on molecular mechanisms underlying secondary metabolite production. METHODS In this study, we performed a hybrid assembly of 454 and Illumina sequencing reads from Polygonum minus root and leaf tissues, respectively, to generate a combined transcriptome library as a reference. RESULTS A total of 34.37 million filtered and normalized reads were assembled into 188,735 transcripts with a total length of 136.67 Mbp. We performed a similarity search against all the publicly available genome sequences and found similarity matches for 163,200 (86.5%) of Polygonum minus transcripts, largely from Arabidopsis thaliana (58.9%). Transcript abundance in the leaf and root tissues were estimated and validated through RT-qPCR of seven selected transcripts involved in the biosynthesis of phenylpropanoids and flavonoids. All the transcripts were annotated against KEGG pathways to profile transcripts related to the biosynthesis of secondary metabolites. DISCUSSION This comprehensive transcriptome profile will serve as a useful sequence resource for molecular genetics and evolutionary research on secondary metabolite biosynthesis in Polygonaceae family. Transcriptome assembly of Polygonum minus can be accessed at http://prims.researchfrontier.org/index.php/dataset/transcriptome.
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Affiliation(s)
- Kok-Keong Loke
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, Bangi, Malaysia
| | | | - Chean-Chean Yeoh
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi, Malaysia
| | - Hoe-Han Goh
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, Bangi, Malaysia
| | - Zeti-Azura Mohamed-Hussein
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, Bangi, Malaysia
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi, Malaysia
| | - Zamri Zainal
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, Bangi, Malaysia
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi, Malaysia
| | - Ismanizan Ismail
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, Bangi, Malaysia
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi, Malaysia
| | - Normah Mohd Noor
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, Bangi, Malaysia
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Complete Genome Sequences of the Neethling-Like Lumpy Skin Disease Virus Strains Obtained Directly from Three Commercial Live Attenuated Vaccines. GENOME ANNOUNCEMENTS 2016; 4:4/6/e01255-16. [PMID: 27834707 PMCID: PMC5105100 DOI: 10.1128/genomea.01255-16] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Lumpy skin disease virus (LSDV) causes an economically important disease in cattle. Here, we report the complete genome sequences of three LSDV strains obtained directly from the live attenuated vaccines: Lumpyvax (MSD Animal Health), Herbivac LS (Deltamune) and Lumpy Skin Disease Vaccine (Onderstepoort Biological Products).
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Zheng Y, Gao S, Padmanabhan C, Li R, Galvez M, Gutierrez D, Fuentes S, Ling KS, Kreuze J, Fei Z. VirusDetect: An automated pipeline for efficient virus discovery using deep sequencing of small RNAs. Virology 2016; 500:130-138. [PMID: 27825033 DOI: 10.1016/j.virol.2016.10.017] [Citation(s) in RCA: 133] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Revised: 10/17/2016] [Accepted: 10/20/2016] [Indexed: 12/14/2022]
Abstract
Accurate detection of viruses in plants and animals is critical for agriculture production and human health. Deep sequencing and assembly of virus-derived small interfering RNAs has proven to be a highly efficient approach for virus discovery. Here we present VirusDetect, a bioinformatics pipeline that can efficiently analyze large-scale small RNA (sRNA) datasets for both known and novel virus identification. VirusDetect performs both reference-guided assemblies through aligning sRNA sequences to a curated virus reference database and de novo assemblies of sRNA sequences with automated parameter optimization and the option of host sRNA subtraction. The assembled contigs are compared to a curated and classified reference virus database for known and novel virus identification, and evaluated for their sRNA size profiles to identify novel viruses. Extensive evaluations using plant and insect sRNA datasets suggest that VirusDetect is highly sensitive and efficient in identifying known and novel viruses. VirusDetect is freely available at http://bioinfo.bti.cornell.edu/tool/VirusDetect/.
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Affiliation(s)
- Yi Zheng
- Boyce Thompson Institute, Ithaca, NY 14853, USA
| | - Shan Gao
- Boyce Thompson Institute, Ithaca, NY 14853, USA; College of Life Sciences, Nankai University, Tianjin 300071, PR China
| | - Chellappan Padmanabhan
- U.S. Vegetable Laboratory, U.S. Department of Agriculture-Agricultural Research Service, Charleston, SC 29414, USA
| | - Rugang Li
- U.S. Vegetable Laboratory, U.S. Department of Agriculture-Agricultural Research Service, Charleston, SC 29414, USA
| | - Marco Galvez
- Virology laboratory, International Potato Center (CIP), Lima, Peru
| | - Dina Gutierrez
- Virology laboratory, International Potato Center (CIP), Lima, Peru
| | - Segundo Fuentes
- Virology laboratory, International Potato Center (CIP), Lima, Peru
| | - Kai-Shu Ling
- U.S. Vegetable Laboratory, U.S. Department of Agriculture-Agricultural Research Service, Charleston, SC 29414, USA
| | - Jan Kreuze
- Virology laboratory, International Potato Center (CIP), Lima, Peru
| | - Zhangjun Fei
- Boyce Thompson Institute, Ithaca, NY 14853, USA; Robert W. Holley Center for Agriculture and Health, U.S. Department of Agriculture-Agricultural Research Service, Ithaca, NY 14853, USA.
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Complete Genome Sequence of Capripoxvirus Strain KSGP 0240 from a Commercial Live Attenuated Vaccine. GENOME ANNOUNCEMENTS 2016; 4:4/5/e01114-16. [PMID: 27795268 PMCID: PMC5073255 DOI: 10.1128/genomea.01114-16] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Capripoxviruses cause economically important diseases in domestic ruminants in regions endemic for these viruses. We report here the complete genome sequence of the KSGP 0240 vaccine strain from the live attenuated vaccine Kenyavac (JOVAC).
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Complete Genome Sequence of the Goatpox Virus Strain Gorgan Obtained Directly from a Commercial Live Attenuated Vaccine. GENOME ANNOUNCEMENTS 2016; 4:4/5/e01113-16. [PMID: 27738031 PMCID: PMC5064104 DOI: 10.1128/genomea.01113-16] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
This is a report of the complete genome sequence of the goatpox virus strain Gorgan, which was obtained directly from a commercial live attenuated vaccine (Caprivac, Jordan Bio-Industries Centre).
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Comparative Genomics of the Extreme Acidophile Acidithiobacillus thiooxidans Reveals Intraspecific Divergence and Niche Adaptation. Int J Mol Sci 2016; 17:ijms17081355. [PMID: 27548157 PMCID: PMC5000751 DOI: 10.3390/ijms17081355] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2016] [Revised: 08/05/2016] [Accepted: 08/11/2016] [Indexed: 11/17/2022] Open
Abstract
Acidithiobacillus thiooxidans known for its ubiquity in diverse acidic and sulfur-bearing environments worldwide was used as the research subject in this study. To explore the genomic fluidity and intraspecific diversity of Acidithiobacillus thiooxidans (A. thiooxidans) species, comparative genomics based on nine draft genomes was performed. Phylogenomic scrutiny provided first insights into the multiple groupings of these strains, suggesting that genetic diversity might be potentially correlated with their geographic distribution as well as geochemical conditions. While these strains shared a large number of common genes, they displayed differences in gene content. Functional assignment indicated that the core genome was essential for microbial basic activities such as energy acquisition and uptake of nutrients, whereas the accessory genome was thought to be involved in niche adaptation. Comprehensive analysis of their predicted central metabolism revealed that few differences were observed among these strains. Further analyses showed evidences of relevance between environmental conditions and genomic diversification. Furthermore, a diverse pool of mobile genetic elements including insertion sequences and genomic islands in all A. thiooxidans strains probably demonstrated the frequent genetic flow (such as lateral gene transfer) in the extremely acidic environments. From another perspective, these elements might endow A. thiooxidans species with capacities to withstand the chemical constraints of their natural habitats. Taken together, our findings bring some valuable data to better understand the genomic diversity and econiche adaptation within A. thiooxidans strains.
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An YM, Song LL, Liu YR, Shu YJ, Guo CH. De Novo Transcriptional Analysis of Alfalfa in Response to Saline-Alkaline Stress. FRONTIERS IN PLANT SCIENCE 2016; 7:931. [PMID: 27458463 PMCID: PMC4931813 DOI: 10.3389/fpls.2016.00931] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2016] [Accepted: 06/11/2016] [Indexed: 05/23/2023]
Abstract
Saline-alkaline stress, caused by high levels of harmful carbonate salts and high soil pH, is a major abiotic stress that affects crop productivity. Alfalfa is a widely cultivated perennial forage legume with some tolerance to biotic and abiotic stresses, especially to saline-alkaline stress. To elucidate the mechanism underlying plant saline-alkaline tolerance, we conducted transcriptome analysis of whole alfalfa seedlings treated with saline-alkaline solutions for 0 day (control), 1 day (short-term treatment), and 7 days (long-term treatment) using ion torrent sequencing technology. A transcriptome database dataset of 53,853 unigenes was generated, and 2,286 and 2,233 genes were differentially expressed in the short-term and long-term treatment, respectively. Gene ontology analysis revealed 14 highly enriched pathways and demonstrated the differential response of metabolic pathways between the short-term and long-term treatment. The expression levels of 109 and 96 transcription factors were significantly altered significantly after 1 day and 7 days of treatment, respectively. Specific responses of peroxidase, flavonoids, and the light pathway component indicated that the antioxidant capacity was one of the central mechanisms of saline-alkaline stress tolerance response in alfalfa. Among the 18 differentially expressed genes examined by real time PCR, the expression levels of eight genes, including inositol transporter, DNA binding protein, raffinose synthase, ferritin, aldo/keto reductase, glutathione S-transferase, xyloglucan endotrans glucosylase, and a NAC transcription factor, exhibited different patterns in response to saline and alkaline stress. The expression levels of the NAC transcription factor and glutathione S-transferase were altered significantly under saline stress and saline-alkaline stress; they were upregulated under saline-alkaline stress and downregulated under salt stress. Physiology assays showed an increased concentration of reactive oxygen species and malondialdehyde and a decreased content of chlorophyll, indicating that anti-oxidation and detoxification play an important role in response to saline-alkaline stress. Overall, the transcriptome analysis provided novel insights into the saline-alkaline stress tolerance response mechanisms in alfalfa.
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Fernandez-Moreno JP, Tzfadia O, Forment J, Presa S, Rogachev I, Meir S, Orzaez D, Aharoni A, Granell A. Characterization of a New Pink-Fruited Tomato Mutant Results in the Identification of a Null Allele of the SlMYB12 Transcription Factor. PLANT PHYSIOLOGY 2016; 171:1821-36. [PMID: 27208285 PMCID: PMC4936558 DOI: 10.1104/pp.16.00282] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Accepted: 05/02/2016] [Indexed: 05/24/2023]
Abstract
The identification and characterization of new tomato (Solanum lycopersicum) mutants affected in fruit pigmentation and nutritional content can provide valuable insights into the underlying biology, as well as a source of new alleles for breeding programs. To date, all characterized pink-pigmented tomato fruit mutants appear to result from low SlMYB12 transcript levels in the fruit skin. Two new mutant lines displaying a pink fruit phenotype (pf1 and pf2) were characterized in this study. In the pf mutants, SlMYB12 transcripts accumulated to wild-type levels but exhibited the same truncation, which resulted in the absence of the essential MYB activation domain coding region. Allelism and complementation tests revealed that both pf mutants were allelic to the y locus and showed the same recessive null allele in homozygosis: Δy A set of molecular and metabolic effects, reminiscent of those observed in the Arabidopsis (Arabidopsis thaliana) myb11 myb12 myb111 triple mutant, were found in the tomato Δy mutants. To our knowledge, these have not been described previously, and our data support the idea of their being null mutants, in contrast to previously described transcriptional hypomorphic pink fruit lines. We detected a reduction in the expression of several flavonol glycosides and some associated glycosyl transferases. Transcriptome analysis further revealed that the effects of the pf mutations extended beyond the flavonoid pathway into the interface between primary and secondary metabolism. Finally, screening for Myb-binding sites in the candidate gene promoter sequences revealed that 141 of the 152 co-down-regulated genes may be direct targets of SlMYB12 regulation.
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Affiliation(s)
- Josefina-Patricia Fernandez-Moreno
- Instituto de Biología Molecular y Celular de Plantas (CSIC-UPV), Ciudad Politécnica de la Innovación, Universidad Politécnica de Valencia, CP 46022 Valencia, Spain (J.-P.F.-M., J.F., S.P., D.O., A.G.);VIB/Ghent University, Bioinformatics and Systems Biology, B-9052 Gent, Belgium (O.T.); andDepartment of Plant Sciences and the Environment, Weizmann Institute of Science, Rehovot 76100, Israel (I.R., S.M., A.A.)
| | - Oren Tzfadia
- Instituto de Biología Molecular y Celular de Plantas (CSIC-UPV), Ciudad Politécnica de la Innovación, Universidad Politécnica de Valencia, CP 46022 Valencia, Spain (J.-P.F.-M., J.F., S.P., D.O., A.G.);VIB/Ghent University, Bioinformatics and Systems Biology, B-9052 Gent, Belgium (O.T.); andDepartment of Plant Sciences and the Environment, Weizmann Institute of Science, Rehovot 76100, Israel (I.R., S.M., A.A.)
| | - Javier Forment
- Instituto de Biología Molecular y Celular de Plantas (CSIC-UPV), Ciudad Politécnica de la Innovación, Universidad Politécnica de Valencia, CP 46022 Valencia, Spain (J.-P.F.-M., J.F., S.P., D.O., A.G.);VIB/Ghent University, Bioinformatics and Systems Biology, B-9052 Gent, Belgium (O.T.); andDepartment of Plant Sciences and the Environment, Weizmann Institute of Science, Rehovot 76100, Israel (I.R., S.M., A.A.)
| | - Silvia Presa
- Instituto de Biología Molecular y Celular de Plantas (CSIC-UPV), Ciudad Politécnica de la Innovación, Universidad Politécnica de Valencia, CP 46022 Valencia, Spain (J.-P.F.-M., J.F., S.P., D.O., A.G.);VIB/Ghent University, Bioinformatics and Systems Biology, B-9052 Gent, Belgium (O.T.); andDepartment of Plant Sciences and the Environment, Weizmann Institute of Science, Rehovot 76100, Israel (I.R., S.M., A.A.)
| | - Ilana Rogachev
- Instituto de Biología Molecular y Celular de Plantas (CSIC-UPV), Ciudad Politécnica de la Innovación, Universidad Politécnica de Valencia, CP 46022 Valencia, Spain (J.-P.F.-M., J.F., S.P., D.O., A.G.);VIB/Ghent University, Bioinformatics and Systems Biology, B-9052 Gent, Belgium (O.T.); andDepartment of Plant Sciences and the Environment, Weizmann Institute of Science, Rehovot 76100, Israel (I.R., S.M., A.A.)
| | - Sagit Meir
- Instituto de Biología Molecular y Celular de Plantas (CSIC-UPV), Ciudad Politécnica de la Innovación, Universidad Politécnica de Valencia, CP 46022 Valencia, Spain (J.-P.F.-M., J.F., S.P., D.O., A.G.);VIB/Ghent University, Bioinformatics and Systems Biology, B-9052 Gent, Belgium (O.T.); andDepartment of Plant Sciences and the Environment, Weizmann Institute of Science, Rehovot 76100, Israel (I.R., S.M., A.A.)
| | - Diego Orzaez
- Instituto de Biología Molecular y Celular de Plantas (CSIC-UPV), Ciudad Politécnica de la Innovación, Universidad Politécnica de Valencia, CP 46022 Valencia, Spain (J.-P.F.-M., J.F., S.P., D.O., A.G.);VIB/Ghent University, Bioinformatics and Systems Biology, B-9052 Gent, Belgium (O.T.); andDepartment of Plant Sciences and the Environment, Weizmann Institute of Science, Rehovot 76100, Israel (I.R., S.M., A.A.)
| | - Aspah Aharoni
- Instituto de Biología Molecular y Celular de Plantas (CSIC-UPV), Ciudad Politécnica de la Innovación, Universidad Politécnica de Valencia, CP 46022 Valencia, Spain (J.-P.F.-M., J.F., S.P., D.O., A.G.);VIB/Ghent University, Bioinformatics and Systems Biology, B-9052 Gent, Belgium (O.T.); andDepartment of Plant Sciences and the Environment, Weizmann Institute of Science, Rehovot 76100, Israel (I.R., S.M., A.A.)
| | - Antonio Granell
- Instituto de Biología Molecular y Celular de Plantas (CSIC-UPV), Ciudad Politécnica de la Innovación, Universidad Politécnica de Valencia, CP 46022 Valencia, Spain (J.-P.F.-M., J.F., S.P., D.O., A.G.);VIB/Ghent University, Bioinformatics and Systems Biology, B-9052 Gent, Belgium (O.T.); andDepartment of Plant Sciences and the Environment, Weizmann Institute of Science, Rehovot 76100, Israel (I.R., S.M., A.A.)
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Jo Y, Choi H, Cho WK. Genome Sequence of Dengue virus 3 from the Pythium insidiosum Transcriptomes. Front Microbiol 2016; 7:926. [PMID: 27379056 PMCID: PMC4908670 DOI: 10.3389/fmicb.2016.00926] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2016] [Accepted: 05/31/2016] [Indexed: 12/25/2022] Open
Affiliation(s)
- Yeonhwa Jo
- Department of Agricultural Biotechnology, College of Agriculture and Life Sciences, Seoul National University Seoul, Republic of Korea
| | - Hoseong Choi
- Department of Agricultural Biotechnology, College of Agriculture and Life Sciences, Seoul National University Seoul, Republic of Korea
| | - Won K Cho
- Department of Agricultural Biotechnology, College of Agriculture and Life Sciences, Seoul National UniversitySeoul, Republic of Korea; The Taejin Genome InstituteHoengseong, Republic of Korea
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49
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Jing X, White TA, Luan J, Jiao C, Fei Z, Douglas AE. Evolutionary conservation of candidate osmoregulation genes in plant phloem sap-feeding insects. INSECT MOLECULAR BIOLOGY 2016; 25:251-258. [PMID: 26896054 DOI: 10.1111/imb.12215] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The high osmotic pressure generated by sugars in plant phloem sap is reduced in phloem-feeding aphids by sugar transformations and facilitated water flux in the gut. The genes mediating these osmoregulatory functions have been identified and validated empirically in the pea aphid Acyrthosiphon pisum: sucrase 1 (SUC1), a sucrase in glycoside hydrolase family 13 (GH13), and aquaporin 1 (AQP1), a member of the Drosophila integral protein (DRIP) family of aquaporins. Here, we describe molecular analysis of GH13 and AQP genes in phloem-feeding representatives of the four phloem-feeding groups: aphids (Myzus persicae), coccids (Planococcus citri), psyllids (Diaphorina citri, Bactericera cockerelli) and whiteflies (Bemisia tabaci MEAM1 and MED). A single candidate GH13-SUC gene and DRIP-AQP gene were identified in the genome/transcriptome of most insects tested by the criteria of sequence motif and gene expression in the gut. Exceptionally, the psyllid Ba. cockerelli transcriptome included a gut-expressed Pyrocoelia rufa integral protein (PRIP)-AQP, but has no DRIP-AQP transcripts, suggesting that PRIP-AQP is recruited for osmoregulatory function in this insect. This study indicates that phylogenetically related SUC and AQP genes may generally mediate osmoregulatory functions in these diverse phloem-feeding insects, and provides candidate genes for empirical validation and development as targets for osmotic disruption of pest species.
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Affiliation(s)
- X Jing
- Department of Entomology, Cornell University, Ithaca, NY, USA
| | - T A White
- Lancaster Environment Centre, Lancaster University, Lancaster, UK
| | - J Luan
- Department of Entomology, Cornell University, Ithaca, NY, USA
| | - C Jiao
- Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, NY, USA
| | - Z Fei
- Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, NY, USA
| | - A E Douglas
- Department of Entomology, Cornell University, Ithaca, NY, USA
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
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50
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Chen J, Zheng Y, Qin L, Wang Y, Chen L, He Y, Fei Z, Lu G. Identification of miRNAs and their targets through high-throughput sequencing and degradome analysis in male and female Asparagus officinalis. BMC PLANT BIOLOGY 2016; 16:80. [PMID: 27068118 PMCID: PMC4828810 DOI: 10.1186/s12870-016-0770-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Accepted: 04/06/2016] [Indexed: 05/03/2023]
Abstract
BACKGROUND MicroRNAs (miRNAs), a class of non-coding small RNAs (sRNAs), regulate various biological processes. Although miRNAs have been identified and characterized in several plant species, miRNAs in Asparagus officinalis have not been reported. As a dioecious plant with homomorphic sex chromosomes, asparagus is regarded as an important model system for studying mechanisms of plant sex determination. RESULTS Two independent sRNA libraries from male and female asparagus plants were sequenced with Illumina sequencing, thereby generating 4.13 and 5.88 million final clean reads, respectively. Both libraries predominantly contained 24-nt sRNAs, followed by 21-nt sRNAs. Further analysis identified 154 conserved miRNAs, which belong to 26 families, and 39 novel miRNA candidates seemed to be specific to asparagus. Comparative profiling revealed that 63 miRNAs exhibited significant differential expression between male and female plants, which was confirmed by real-time quantitative PCR analysis. Among them, 37 miRNAs were significantly up-regulated in the female library, whereas the others were preferentially expressed in the male library. Furthermore, 40 target mRNAs representing 44 conserved and seven novel miRNAs were identified in asparagus through high-throughput degradome sequencing. Functional annotation showed that these target mRNAs were involved in a wide range of developmental and metabolic processes. CONCLUSIONS We identified a large set of conserved and specific miRNAs and compared their expression levels between male and female asparagus plants. Several asparagus miRNAs, which belong to the miR159, miR167, and miR172 families involved in reproductive organ development, were differentially expressed between male and female plants, as well as during flower development. Consistently, several predicted targets of asparagus miRNAs were associated with floral organ development. These findings suggest the potential roles of miRNAs in sex determination and reproductive developmental processes in asparagus.
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Affiliation(s)
- Jingli Chen
- />Key Laboratory of Horticultural Plant Growth, Development and Biotechnology, Agricultural Ministry of China, Department of Horticulture, Zhejiang University, Hangzhou, 310058 PR China
| | - Yi Zheng
- />Boyce Thompson Institute for Plant Research, Cornell University, Tower Road, Ithaca, New York 14853 USA
| | - Li Qin
- />Key Laboratory of Horticultural Plant Growth, Development and Biotechnology, Agricultural Ministry of China, Department of Horticulture, Zhejiang University, Hangzhou, 310058 PR China
| | - Yan Wang
- />Key Laboratory of Horticultural Plant Growth, Development and Biotechnology, Agricultural Ministry of China, Department of Horticulture, Zhejiang University, Hangzhou, 310058 PR China
| | - Lifei Chen
- />Key Laboratory of Horticultural Plant Growth, Development and Biotechnology, Agricultural Ministry of China, Department of Horticulture, Zhejiang University, Hangzhou, 310058 PR China
| | - Yanjun He
- />Key Laboratory of Horticultural Plant Growth, Development and Biotechnology, Agricultural Ministry of China, Department of Horticulture, Zhejiang University, Hangzhou, 310058 PR China
| | - Zhangjun Fei
- />Boyce Thompson Institute for Plant Research, Cornell University, Tower Road, Ithaca, New York 14853 USA
- />USDA Robert W. Holley Center for Agriculture and Health, Tower Road Ithaca, New York, 14853 USA
| | - Gang Lu
- />Key Laboratory of Horticultural Plant Growth, Development and Biotechnology, Agricultural Ministry of China, Department of Horticulture, Zhejiang University, Hangzhou, 310058 PR China
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