1
|
Gutiérrez RM, de Oliveira RR, Ribeiro THC, de Oliveira KKP, Silva JVN, Alves TC, do Amaral LR, de Souza Gomes M, de Souza Gomes M, Chalfun-Junior A. Unveiling the phenology and associated floral regulatory pathways of Humulus lupulus L. in subtropical conditions. PLANTA 2024; 259:150. [PMID: 38727772 DOI: 10.1007/s00425-024-04428-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Accepted: 05/01/2024] [Indexed: 05/23/2024]
Abstract
MAIN CONCLUSION The hop phenological cycle was described in subtropical condition of Brazil showing that flowering can happen at any time of year and this was related to developmental molecular pathways. Hops are traditionally produced in temperate regions, as it was believed that vernalization was necessary for flowering. Nevertheless, recent studies have revealed the potential for hops to flower in tropical and subtropical climates. In this work, we observed that hops in the subtropical climate of Minas Gerais, Brazil grow and flower multiple times throughout the year, independently of the season, contrasting with what happens in temperate regions. This could be due to the photoperiod consistently being inductive, with daylight hours below the described threshold (16.5 h critical). We observed that when the plants reached 7-9 nodes, the leaves began to transition from heart-shaped to trilobed-shaped, which could be indicative of the juvenile to adult transition. This could be related to the fact that the 5th node (in plants with 10 nodes) had the highest expression of miR156, while two miR172s increased in the 20th node (in plants with 25 nodes). Hop flowers appeared later, in the 25th or 28th nodes, and the expression of HlFT3 and HlFT5 was upregulated in plants between 15 and 20 nodes, while the expression of HlTFL3 was upregulated in plants with 20 nodes. These results indicate the role of axillary meristem age in regulating this process and suggest that the florigenic signal should be maintained until the hop plants bloom. In addition, it is possible that the expression of TFL is not sufficient to inhibit flowering in these conditions and promote branching. These findings suggest that the reproductive transition in hop under inductive photoperiodic conditions could occur in plants between 15 and 20 nodes. Our study sheds light on the intricate molecular mechanisms underlying hop floral development, paving the way for potential advancements in hop production on a global scale.
Collapse
Affiliation(s)
- Robert Márquez Gutiérrez
- Laboratory of Plant Molecular Physiology, Plant Physiology Sector, Institute of Biology, Federal University of Lavras, Lavras, MG, Brazil
| | - Raphael Ricon de Oliveira
- Laboratory of Plant Molecular Physiology, Plant Physiology Sector, Institute of Biology, Federal University of Lavras, Lavras, MG, Brazil
| | - Thales Henrique Cherubino Ribeiro
- Laboratory of Plant Molecular Physiology, Plant Physiology Sector, Institute of Biology, Federal University of Lavras, Lavras, MG, Brazil
| | - Kellen Kauanne Pimenta de Oliveira
- Laboratory of Plant Molecular Physiology, Plant Physiology Sector, Institute of Biology, Federal University of Lavras, Lavras, MG, Brazil
| | - João Victor Nunes Silva
- Institute of Genetics and Biochemistry (INGEB), Laboratory of Bioinformatics and Molecular Analysis (LBAM), Federal University of Uberlândia (UFU), Campus Patos de Minas, Patos de Minas, Minas Gerais, Brazil
| | - Tamires Caixeta Alves
- Institute of Genetics and Biochemistry (INGEB), Laboratory of Bioinformatics and Molecular Analysis (LBAM), Federal University of Uberlândia (UFU), Campus Patos de Minas, Patos de Minas, Minas Gerais, Brazil
| | - Laurence Rodrigues do Amaral
- Institute of Genetics and Biochemistry (INGEB), Laboratory of Bioinformatics and Molecular Analysis (LBAM), Federal University of Uberlândia (UFU), Campus Patos de Minas, Patos de Minas, Minas Gerais, Brazil
| | - Marcos de Souza Gomes
- Institute of Genetics and Biochemistry (INGEB), Laboratory of Bioinformatics and Molecular Analysis (LBAM), Federal University of Uberlândia (UFU), Campus Patos de Minas, Patos de Minas, Minas Gerais, Brazil
| | - Matheus de Souza Gomes
- Institute of Genetics and Biochemistry (INGEB), Laboratory of Bioinformatics and Molecular Analysis (LBAM), Federal University of Uberlândia (UFU), Campus Patos de Minas, Patos de Minas, Minas Gerais, Brazil
| | - Antonio Chalfun-Junior
- Laboratory of Plant Molecular Physiology, Plant Physiology Sector, Institute of Biology, Federal University of Lavras, Lavras, MG, Brazil.
| |
Collapse
|
2
|
Rivarez MPS, Faure C, Svanella-Dumas L, Pecman A, Tušek-Žnidaric M, Schönegger D, De Jonghe K, Blouin A, Rasmussen DA, Massart S, Ravnikar M, Kutnjak D, Marais A, Candresse T. Diversity and Pathobiology of an Ilarvirus Unexpectedly Detected in Diverse Plants and Global Sequencing Data. PHYTOPATHOLOGY 2023; 113:1729-1744. [PMID: 37399026 DOI: 10.1094/phyto-12-22-0465-v] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
High-throughput sequencing (HTS) and sequence mining tools revolutionized virus detection and discovery in recent years, and implementing them with classical plant virology techniques results in a powerful approach to characterize viruses. An example of a virus discovered through HTS is Solanum nigrum ilarvirus 1 (SnIV1) (Bromoviridae), which was recently reported in various solanaceous plants from France, Slovenia, Greece, and South Africa. It was likewise detected in grapevines (Vitaceae) and several Fabaceae and Rosaceae plant species. Such a diverse set of source organisms is atypical for ilarviruses, thus warranting further investigation. In this study, modern and classical virological tools were combined to accelerate the characterization of SnIV1. Through HTS-based virome surveys, mining of sequence read archive datasets, and a literature search, SnIV1 was further identified from diverse plant and non-plant sources globally. SnIV1 isolates showed relatively low variability compared with other phylogenetically related ilarviruses. Phylogenetic analyses showed a distinct basal clade of isolates from Europe, whereas the rest formed clades of mixed geographic origin. Furthermore, systemic infection of SnIV1 in Solanum villosum and its mechanical and graft transmissibility to solanaceous species were demonstrated. Near-identical SnIV1 genomes from the inoculum (S. villosum) and inoculated Nicotiana benthamiana were sequenced, thus partially fulfilling Koch's postulates. SnIV1 was shown to be seed-transmitted and potentially pollen-borne, has spherical virions, and possibly induces histopathological changes in infected N. benthamiana leaf tissues. Overall, this study provides information to better understand the diversity, global presence, and pathobiology of SnIV1; however, its possible emergence as a destructive pathogen remains uncertain. [Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.
Collapse
Affiliation(s)
- Mark Paul Selda Rivarez
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, 1000, Slovenia
| | - Chantal Faure
- University of Bordeaux, INRAE, UMR 1332 Biologie du Fruit et Pathologie, Villenave d'Ornon, 33882, France
| | - Laurence Svanella-Dumas
- University of Bordeaux, INRAE, UMR 1332 Biologie du Fruit et Pathologie, Villenave d'Ornon, 33882, France
| | - Anja Pecman
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, 1000, Slovenia
| | - Magda Tušek-Žnidaric
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, 1000, Slovenia
| | - Deborah Schönegger
- University of Bordeaux, INRAE, UMR 1332 Biologie du Fruit et Pathologie, Villenave d'Ornon, 33882, France
| | - Kris De Jonghe
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food, Merelbeke, 9820, Belgium
| | - Arnaud Blouin
- Plant Pathology Laboratory, TERRA-Gembloux Agro-Bio Tech, University of Liège, Gembloux, 5030, Belgium
| | - David A Rasmussen
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, 27606, U.S.A
| | - Sebastien Massart
- Plant Pathology Laboratory, TERRA-Gembloux Agro-Bio Tech, University of Liège, Gembloux, 5030, Belgium
| | - Maja Ravnikar
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, 1000, Slovenia
| | - Denis Kutnjak
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, 1000, Slovenia
| | - Armelle Marais
- University of Bordeaux, INRAE, UMR 1332 Biologie du Fruit et Pathologie, Villenave d'Ornon, 33882, France
| | - Thierry Candresse
- University of Bordeaux, INRAE, UMR 1332 Biologie du Fruit et Pathologie, Villenave d'Ornon, 33882, France
| |
Collapse
|
3
|
Awasthi P, Mishra AK, Kocábek T, Nath VS, Mishra S, Hazzouri KM, Sudalaimuthuasari N, Stajner N, Jakše J, Krofta K, Hájek T, Amiri KM. CRISPR/Cas9-mediated mutagenesis of the mediator complex subunits MED5a and MED5b genes impaired secondary metabolite accumulation in hop (Humulus lupulus). PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 201:107851. [PMID: 37354728 DOI: 10.1016/j.plaphy.2023.107851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 06/15/2023] [Accepted: 06/17/2023] [Indexed: 06/26/2023]
Abstract
Hop (Humulus lupulus L.) is an important commercial crop known for the biosynthesis of valuable specialized secondary metabolites in glandular trichomes (lupulin glands), which are used for the brewing industry. To achieve burgeoning market demands is the essentiality of comprehensive understanding of the mechanisms of biosynthesis of secondary metabolites in hop. Over the past year, several studies using structural biology and functional genomics approaches have shown that Mediator (MED) serves as an integrative hub for RNAP II-mediated transcriptional regulation of various physiological and cellular processes, including involvement of MED5a and MED5b in hyperaccumulation of phenylpropanoid in A. thaliana. In the present work, an unprecedented attempt was made to generate Hlmed5a/med5b double loci mutant lines in hop using a CRISPR/Cas9-based genome editing system. The Hlmed5a/med5b double loci mutant lines showed reduced expression of structural genes of the flavonoid, humulone, and terpenoid biosynthetic pathways, which was more pronounced in the lupulin gland compared to leaf tissue and was consistent with their reduced accumulation. Phenotypic and anatomical observations revealed that Hlmed5a/med5b double loci mutant line exhibited robust growth, earlier flowering, earlier cone maturity, reduced cone size, variations in floral structure patterns, and distorted lupulin glands without any remarkable changes in leaf morphology, intensity of leaf color, and chlorophyll content. Comparative transcriptome analysis of leaf and lupulin gland tissues indicates that the expression of enzymatic genes related to secondary metabolite biosynthesis, phytohormone biosynthesis, floral organs, flowering time, and trichome development, including other genes related to starch and sucrose metabolism and defense mechanisms, were differentially modulated in the Hlmed5a/med5b lines. The combined results from functional and transcriptomic analyses illuminates the pivotal function of HlMED5a and HlMED5b in homeostasis of secondary meatbolites accumulation in hop.
Collapse
Affiliation(s)
- Praveen Awasthi
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Zygmunta Noskowskiego 12/14, 61-704, Poznań, Poland
| | - Ajay Kumar Mishra
- Khalifa Centre for Genetic Engineering and Biotechnology, United Arab Emirates University, P.O. Box. Al Ain 15551, United Arab Emirates.
| | - Tomáš Kocábek
- Biology Centre, Czech Academy of Sciences, Institute of Plant Molecular Biology, Branišovská 31, 370 05, České Budějovice, Czech Republic
| | - Vishnu Sukumari Nath
- Khalifa Centre for Genetic Engineering and Biotechnology, United Arab Emirates University, P.O. Box. Al Ain 15551, United Arab Emirates
| | - Sagarika Mishra
- Khalifa Centre for Genetic Engineering and Biotechnology, United Arab Emirates University, P.O. Box. Al Ain 15551, United Arab Emirates
| | - Khaled M Hazzouri
- Khalifa Centre for Genetic Engineering and Biotechnology, United Arab Emirates University, P.O. Box. Al Ain 15551, United Arab Emirates
| | - Naganeeswaran Sudalaimuthuasari
- Khalifa Centre for Genetic Engineering and Biotechnology, United Arab Emirates University, P.O. Box. Al Ain 15551, United Arab Emirates
| | - Natasa Stajner
- Department of Agronomy, Biotechnical Faculty, University of Ljubljana, 1000, Ljubljana, Slovenia
| | - Jernej Jakše
- Department of Agronomy, Biotechnical Faculty, University of Ljubljana, 1000, Ljubljana, Slovenia
| | - Karel Krofta
- Hop Research Institute, Co. Ltd., Kadaňská 2525, 438 46, Žatec, Czech Republic
| | - Tomáš Hájek
- University of South Bohemia, Faculty of Science, Branišovská 1716/31c, 370 05, České Budějovice, Czech Republic
| | - Khaled Ma Amiri
- Khalifa Centre for Genetic Engineering and Biotechnology, United Arab Emirates University, P.O. Box. Al Ain 15551, United Arab Emirates.
| |
Collapse
|
4
|
Padgitt-Cobb LK, Pitra NJ, Matthews PD, Henning JA, Hendrix DA. An improved assembly of the "Cascade" hop ( Humulus lupulus) genome uncovers signatures of molecular evolution and refines time of divergence estimates for the Cannabaceae family. HORTICULTURE RESEARCH 2023; 10:uhac281. [PMID: 36818366 PMCID: PMC9930403 DOI: 10.1093/hr/uhac281] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 12/22/2022] [Indexed: 06/16/2023]
Abstract
We present a chromosome-level assembly of the Cascade hop (Humulus lupulus L. var. lupulus) genome. The hop genome is large (2.8 Gb) and complex, and early attempts at assembly were fragmented. Recent advances have made assembly of the hop genome more tractable, transforming the extent of investigation that can occur. The chromosome-level assembly of Cascade was developed by scaffolding the previously reported Cascade assembly generated with PacBio long-read sequencing and polishing with Illumina short-read DNA sequencing. We developed gene models and repeat annotations and used a controlled bi-parental mapping population to identify significant sex-associated markers. We assessed molecular evolution in gene sequences, gene family expansion and contraction, and time of divergence from Cannabis sativa and other closely related plant species using Bayesian inference. We identified the putative sex chromosome in the female genome based on significant sex-associated markers from the bi-parental mapping population. While the estimate of repeat content (~64%) is similar to the estimate for the hemp genome, syntenic blocks in hop contain a greater percentage of LTRs. Hop is enriched for disease resistance-associated genes in syntenic gene blocks and expanded gene families. The Cascade chromosome-level assembly will inform cultivation strategies and serve to deepen our understanding of the hop genomic landscape, benefiting hop researchers and the Cannabaceae genomics community.
Collapse
Affiliation(s)
- Lillian K Padgitt-Cobb
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon, USA
| | - Nicholi J Pitra
- Department of Research and Development, Hopsteiner, S.S. Steiner, Inc., 1 West Washington Avenue, Yakima, Washington 98903, USA
| | - Paul D Matthews
- Department of Research and Development, Hopsteiner, S.S. Steiner, Inc., 1 West Washington Avenue, Yakima, Washington 98903, USA
| | | | | |
Collapse
|
5
|
Salihu B, Mustafa B, Pulaj B, Hajdari A. Chemical composition of the essential oil of hops (Humulus lupulus L.) growing wild in Kosovo. MAKEDONSKO FARMACEVTSKI BILTEN 2022. [DOI: 10.33320/maced.pharm.bull.2022.68.04.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Affiliation(s)
- Blerta Salihu
- Department of Biology, Faculty of Mathematical and Natural Science, University of Prishtina “Hasan Prishtina”, Mother Theresa St. 10000 Prishtinë. Kosovo
| | - Bexhet Mustafa
- Department of Biology, Faculty of Mathematical and Natural Science, University of Prishtina “Hasan Prishtina”, Mother Theresa St. 10000 Prishtinë. Kosovo
| | - Bledar Pulaj
- Department of Biology, Faculty of Mathematical and Natural Science, University of Prishtina “Hasan Prishtina”, Mother Theresa St. 10000 Prishtinë. Kosovo
| | - Avni Hajdari
- Department of Biology, Faculty of Mathematical and Natural Science, University of Prishtina “Hasan Prishtina”, Mother Theresa St. 10000 Prishtinë. Kosovo
| |
Collapse
|
6
|
Cottrell MT. A Search for Diastatic Enzymes Endogenous to Humulus lupulus and Produced by Microbes Associated with Pellet Hops Driving “Hop Creep” of Dry Hopped Beer. JOURNAL OF THE AMERICAN SOCIETY OF BREWING CHEMISTS 2022. [DOI: 10.1080/03610470.2022.2084327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
|
7
|
Hirakawa T, Tanno S. In Vitro Propagation of Humulus lupulus through the Induction of Axillary Bud Development. PLANTS 2022; 11:plants11081066. [PMID: 35448794 PMCID: PMC9031650 DOI: 10.3390/plants11081066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 04/11/2022] [Accepted: 04/12/2022] [Indexed: 11/16/2022]
Abstract
Humulus lupulus (hop) is a necessary material for beer brewing. Improved breeding cultivars of hops with enhanced tolerance to environmental stresses, such as drought and heat stress, accompanying climate change have been developed. However, a propagation system, which is needed for the proliferation of new cultivars, is not currently available for hops. In this study, we found that treatment of stem explants with 0.01–0.05 ppm gibberellic acid (GA3) induced the development of axillary buds in the hop cultivar Kirin-2, resulting in the proliferation of shoot branching. Additionally, 0.01 ppm benzyl adenine (BA) enhanced the development of axillary buds formed in response to 0.05 ppm GA3 in various hop cultivars, particularly Nugget. The development of axillary buds was strongly repressed by the application of 0.05 ppm BA at a concentration equal to the 0.05 ppm GA3 concentration, which showed the possibility that a high concentration of cytokinin preferentially prevents the effect of GA3 on the development of axillary buds in hops. These results indicated that combined treatment of stem explants with GA3 and cytokinin at appropriate concentrations is effective for the propagation of proliferated hop cultivars through shoot branching.
Collapse
|
8
|
|
9
|
Patzak J, Henychová A, Matoušek J. Developmental regulation of lupulin gland-associated genes in aromatic and bitter hops (Humulus lupulus L.). BMC PLANT BIOLOGY 2021; 21:534. [PMID: 34773975 PMCID: PMC8590222 DOI: 10.1186/s12870-021-03292-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 10/22/2021] [Indexed: 05/25/2023]
Abstract
BACKGROUND Hop (Humulus lupulus L.) bitter acids are valuable metabolites for the brewing industry. They are biosynthesized and accumulate in glandular trichomes of the female inflorescence (hop cone). The content of alpha bitter acids, such as humulones, in hop cones can differentiate aromatic from bitter hop cultivars. These contents are subject to genetic and environmental control but significantly correlate with the number and size of glandular trichomes (lupulin glands). RESULTS We evaluated the expression levels of 37 genes involved in bitter acid biosynthesis and morphological and developmental differentiation of glandular trichomes to identify key regulatory factors involved in bitter acid content differences. For bitter acid biosynthesis genes, upregulation of humulone synthase genes, which are important for the biosynthesis of alpha bitter acids in lupulin glands, could explain the higher accumulation of alpha bitter acids in bitter hops. Several transcription factors, including HlETC1, HlMYB61 and HlMYB5 from the MYB family, as well as HlGLABRA2, HlCYCB2-4, HlZFP8 and HlYABBY1, were also more highly expressed in the bitter hop cultivars; therefore, these factors may be important for the higher density of lupulin glands also seen in the bitter hop cultivars. CONCLUSIONS Gene expression analyses enabled us to investigate the differences between aromatic and bitter hops. This study confirmed that the bitter acid content in glandular trichomes (lupulin glands) is dependent on the last step of alpha bitter acid biosynthesis and glandular trichome density.
Collapse
Affiliation(s)
- Josef Patzak
- Hop Research Institute Co., Ltd., Kadaňská 2525, 438 01, Žatec, Czech Republic.
| | - Alena Henychová
- Hop Research Institute Co., Ltd., Kadaňská 2525, 438 01, Žatec, Czech Republic
| | - Jaroslav Matoušek
- Biology Centre ASCR v.v.i, Department of Molecular Genetics, Institute of Plant Molecular Biology, Branišovská 31, 37005, České Budějovice, Czech Republic
| |
Collapse
|
10
|
Patzak J, Henychová A, Krofta K, Svoboda P, Malířová I. The Influence of Hop Latent Viroid (HLVd) Infection on Gene Expression and Secondary Metabolite Contents in Hop ( Humulus lupulus L.) Glandular Trichomes. PLANTS (BASEL, SWITZERLAND) 2021; 10:plants10112297. [PMID: 34834660 PMCID: PMC8617911 DOI: 10.3390/plants10112297] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 10/05/2021] [Accepted: 10/21/2021] [Indexed: 05/10/2023]
Abstract
Viroids are small infectious pathogens, composed of a short single-stranded circular RNA. Hop (Humulus lupulus L.) plants are hosts to four viroids from the family Pospiviroidae. Hop latent viroid (HLVd) is spread worldwide in all hop-growing regions without any visible symptoms on infected hop plants. In this study, we evaluated the influence of HLVd infection on the content and the composition of secondary metabolites in maturated hop cones, together with gene expression analyses of involved biosynthesis and regulation genes for Saaz, Sládek, Premiant and Agnus cultivars. We confirmed that the contents of alpha bitter acids were significantly reduced in the range from 8.8% to 34% by viroid infection. New, we found that viroid infection significantly reduced the contents of xanthohumol in the range from 3.9% to 23.5%. In essential oils of Saaz cultivar, the contents of monoterpenes, terpene epoxides and terpene alcohols were increased, but the contents of sesquiterpenes and terpene ketones were decreased. Secondary metabolites changes were supported by gene expression analyses, except essential oils. Last-step biosynthesis enzyme genes, namely humulone synthase 1 (HS1) and 2 (HS2) for alpha bitter acids and O-methytransferase 1 (OMT1) for xanthohumol, were down-regulated by viroid infection. We found that the expression of ribosomal protein L5 (RPL5) RPL5 and the splicing of transcription factor IIIA-7ZF were affected by viroid infection and a disbalance in proteosynthesis can influence transcriptions of biosynthesis and regulatory genes involved in of secondary metabolites biosynthesis. We suppose that RPL5/TFIIIA-7ZF regulatory cascade can be involved in HLVd replication as for other viroids of the family Pospiviroidae.
Collapse
|
11
|
Hong K, Wang L, Johnpaul A, Lv C, Ma C. Key Enzymes Involved in the Synthesis of Hops Phytochemical Compounds: From Structure, Functions to Applications. Int J Mol Sci 2021; 22:9373. [PMID: 34502286 PMCID: PMC8430942 DOI: 10.3390/ijms22179373] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 08/24/2021] [Accepted: 08/26/2021] [Indexed: 12/13/2022] Open
Abstract
Humulus lupulus L. is an essential source of aroma compounds, hop bitter acids, and xanthohumol derivatives mainly exploited as flavourings in beer brewing and with demonstrated potential for the treatment of certain diseases. To acquire a comprehensive understanding of the biosynthesis of these compounds, the primary enzymes involved in the three major pathways of hops' phytochemical composition are herein critically summarized. Hops' phytochemical components impart bitterness, aroma, and antioxidant activity to beers. The biosynthesis pathways have been extensively studied and enzymes play essential roles in the processes. Here, we introduced the enzymes involved in the biosynthesis of hop bitter acids, monoterpenes and xanthohumol derivatives, including the branched-chain aminotransferase (BCAT), branched-chain keto-acid dehydrogenase (BCKDH), carboxyl CoA ligase (CCL), valerophenone synthase (VPS), prenyltransferase (PT), 1-deoxyxylulose-5-phosphate synthase (DXS), 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HDR), Geranyl diphosphate synthase (GPPS), monoterpene synthase enzymes (MTS), cinnamate 4-hydroxylase (C4H), chalcone synthase (CHS_H1), chalcone isomerase (CHI)-like proteins (CHIL), and O-methyltransferase (OMT1). Furthermore, research advancements of each enzyme in terms of reaction conditions, substrate recognition, enzyme structures, and use in engineered microbes are described in depth. Hence, an extensive review of the key enzymes involved in the phytochemical compounds of hops will provide fundamentals for their applications in beer production.
Collapse
Affiliation(s)
| | | | | | - Chenyan Lv
- College of Food Science and Nutritional Engineering, China Agricultural University, 17 Qinghua Donglu Road, Haidian District, Beijing 100083, China; (K.H.); (L.W.); (A.J.)
| | - Changwei Ma
- College of Food Science and Nutritional Engineering, China Agricultural University, 17 Qinghua Donglu Road, Haidian District, Beijing 100083, China; (K.H.); (L.W.); (A.J.)
| |
Collapse
|
12
|
Werrie PY, Deckers S, Fauconnier ML. Brief Insight into the Underestimated Role of Hop Amylases on Beer Aroma Profiles. JOURNAL OF THE AMERICAN SOCIETY OF BREWING CHEMISTS 2021. [DOI: 10.1080/03610470.2021.1937453] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Pierre-Yves Werrie
- Laboratory of Chemistry of Natural Molecules (ULg), University of Liège, Belgium
| | - Sylvie Deckers
- Laboratory of Chemistry of Natural Molecules (ULg), University of Liège, Belgium
| | | |
Collapse
|
13
|
Ren G, Zhang X, Li Y, Ridout K, Serrano-Serrano ML, Yang Y, Liu A, Ravikanth G, Nawaz MA, Mumtaz AS, Salamin N, Fumagalli L. Large-scale whole-genome resequencing unravels the domestication history of Cannabis sativa. SCIENCE ADVANCES 2021; 7:7/29/eabg2286. [PMID: 34272249 PMCID: PMC8284894 DOI: 10.1126/sciadv.abg2286] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Accepted: 06/03/2021] [Indexed: 05/07/2023]
Abstract
Cannabis sativa has long been an important source of fiber extracted from hemp and both medicinal and recreational drugs based on cannabinoid compounds. Here, we investigated its poorly known domestication history using whole-genome resequencing of 110 accessions from worldwide origins. We show that C. sativa was first domesticated in early Neolithic times in East Asia and that all current hemp and drug cultivars diverged from an ancestral gene pool currently represented by feral plants and landraces in China. We identified candidate genes associated with traits differentiating hemp and drug cultivars, including branching pattern and cellulose/lignin biosynthesis. We also found evidence for loss of function of genes involved in the synthesis of the two major biochemically competing cannabinoids during selection for increased fiber production or psychoactive properties. Our results provide a unique global view of the domestication of C. sativa and offer valuable genomic resources for ongoing functional and molecular breeding research.
Collapse
Affiliation(s)
- Guangpeng Ren
- Laboratory for Conservation Biology, Department of Ecology and Evolution, Biophore, University of Lausanne, 1015 Lausanne, Switzerland.
- State Key Laboratory of Grassland Agro-Ecosystems, School of Life Science and Institute of Innovation Ecology, Lanzhou University, Lanzhou 730000, Gansu, China
| | - Xu Zhang
- State Key Laboratory of Grassland Agro-Ecosystems, School of Life Science and Institute of Innovation Ecology, Lanzhou University, Lanzhou 730000, Gansu, China
| | - Ying Li
- State Key Laboratory of Grassland Agro-Ecosystems, School of Life Science and Institute of Innovation Ecology, Lanzhou University, Lanzhou 730000, Gansu, China
| | - Kate Ridout
- Laboratory for Conservation Biology, Department of Ecology and Evolution, Biophore, University of Lausanne, 1015 Lausanne, Switzerland
- Oxford Molecular Diagnostics Centre, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Martha L Serrano-Serrano
- Laboratory for Conservation Biology, Department of Ecology and Evolution, Biophore, University of Lausanne, 1015 Lausanne, Switzerland
| | - Yongzhi Yang
- State Key Laboratory of Grassland Agro-Ecosystems, School of Life Science and Institute of Innovation Ecology, Lanzhou University, Lanzhou 730000, Gansu, China
| | - Ai Liu
- State Key Laboratory of Grassland Agro-Ecosystems, School of Life Science and Institute of Innovation Ecology, Lanzhou University, Lanzhou 730000, Gansu, China
| | - Gudasalamani Ravikanth
- Suri Sehgal Center for Biodiversity and Conservation, Ashoka Trust for Research in Ecology and the Environment, Royal Enclave Srirampura, Jakkur Post, Bangalore 560 064, India
| | - Muhammad Ali Nawaz
- Department of Biological and Environmental Sciences, Qatar University, Doha, Qatar
- Department of Zoology, Quaid-i-Azam University, Islamabad 45320, Pakistan
| | - Abdul Samad Mumtaz
- Department of Plant Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan
| | - Nicolas Salamin
- Department of Computational Biology, Génopode, University of Lausanne, 1015 Lausanne, Switzerland
| | - Luca Fumagalli
- Laboratory for Conservation Biology, Department of Ecology and Evolution, Biophore, University of Lausanne, 1015 Lausanne, Switzerland.
- Centre Universitaire Romand de Médecine Légale, Centre Hospitalier Universitaire Vaudois et Université de Lausanne, Chemin de la Vulliette 4, 1000 Lausanne 25, Switzerland
| |
Collapse
|
14
|
Purayannur S, Gent DH, Miles TD, Radišek S, Quesada‐Ocampo LM. The hop downy mildew pathogen Pseudoperonospora humuli. MOLECULAR PLANT PATHOLOGY 2021; 22:755-768. [PMID: 33942461 PMCID: PMC8232024 DOI: 10.1111/mpp.13063] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 01/29/2021] [Accepted: 03/14/2021] [Indexed: 06/12/2023]
Abstract
UNLABELLED Pseudoperonospora humuli is an obligate biotrophic oomycete that causes downy mildew, one of the most devastating diseases of cultivated hop, Humulus lupulus. Downy mildew occurs in all production areas of the crop in the Northern Hemisphere and Argentina. The pathogen overwinters in hop crowns and roots, and causes considerable crop loss. Downy mildew is managed by sanitation practices, planting of resistant cultivars, and fungicide applications. However, the scarcity of sources of host resistance and fungicide resistance in pathogen populations complicates disease management. This review summarizes the current knowledge on the symptoms of the disease, life cycle, virulence factors, and management of hop downy mildew, including various forecasting systems available in the world. Additionally, recent developments in genomics and effector discovery, and the future prospects of using such resources in successful disease management are also discussed. TAXONOMY Class: Oomycota; Order: Peronosporales; Family: Peronosporaceae; Genus: Pseudoperonospora; Species: Pseudoperonospora humuli. DISEASE SYMPTOMS The disease is characterized by systemically infected chlorotic shoots called "spikes". Leaf symptoms and signs include angular chlorotic lesions and profuse sporulation on the abaxial side of the leaf. Under severe disease pressure, dark brown discolouration or lesions are observed on cones. Infected crowns have brown to black streaks when cut open. Cultivars highly susceptible to crown rot may die at this phase of the disease cycle without producing shoots. However, foliar symptoms may not be present on plants with systemically infected root systems. INFECTION PROCESS Pathogen mycelium overwinters in buds and crowns, and emerges on infected shoots in spring. Profuse sporulation occurs on infected tissues and sporangia are released and dispersed by air currents. Under favourable conditions, sporangia germinate and produce biflagellate zoospores that infect healthy tissue, thus perpetuating the infection cycle. Though oospores are produced in infected tissues, their role in the infection cycle is not defined. CONTROL Downy mildew on hop is managed by a combination of sanitation practices and timely fungicide applications. Forecasting systems are used to time fungicide applications for successful management of the disease. USEFUL WEBSITES: https://content.ces.ncsu.edu/hop-downy-mildew (North Carolina State University disease factsheet), https://www.canr.msu.edu/resources/michigan-hop-management-guide (Michigan Hop Management Guide), http://uspest.org/risk/models (Oregon State University Integrated Plant Protection Center degree-day model for hop downy mildew), https://www.usahops.org/cabinet/data/Field-Guide.pdf (Field Guide for Integrated Pest Management in Hops).
Collapse
Affiliation(s)
- Savithri Purayannur
- Department of Entomology and Plant PathologyNorth Carolina State UniversityRaleighNorth CarolinaUSA
| | - David H. Gent
- US Department of Agriculture‐Agricultural Research Service, Forage Seed and Cereal Research Unit, and Department of Botany and Plant PathologyOregon State UniversityCorvallisOregonUSA
| | - Timothy D. Miles
- Department of Plant, Soil and Microbial SciencesMichigan State UniversityEast LansingMichiganUSA
| | - Sebastjan Radišek
- Plant Protection DepartmentDiagnostics LaboratorySlovenian Institute for Hop Research and BrewingŽalecSlovenia
| | - Lina M. Quesada‐Ocampo
- Department of Entomology and Plant PathologyNorth Carolina State UniversityRaleighNorth CarolinaUSA
| |
Collapse
|
15
|
Saffar A, Matin MM. Tracing foreign sequences in plant transcriptomes and genomes using OCT4, a POU domain protein. Mol Genet Genomics 2021; 296:677-688. [PMID: 33738520 DOI: 10.1007/s00438-021-01768-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 02/10/2021] [Indexed: 10/21/2022]
Abstract
Contaminations in sequencing data, especially in reference genomes, lead to inevitable errors in downstream analyses. Similarly, presence of contaminants in transcriptomes, misrepresents the molecular basis of various interactions. In this study, we report the presence of a large number of plant transcriptomes contaminated with RNAs encoding POU domain proteins; a family of proteins that has not been reported in plants and fungi. Besides, our findings illustrated that there are four POU domain protein-coding sequences in the reference genome of Rhodamnia argentea. It turned out that the existing foreign fragments are related to arthropods that are considered as plant pests. We also identified two contaminated draft genomes, Humulus lupulus and Cannabis sativa that contained complete rDNA sequences originating from Tetranychus species. As a result, careful screening of sequencing data before releasing them in public databases or checking existing genomes for possible contaminations is recommended.
Collapse
Affiliation(s)
- Adeleh Saffar
- Department of Biology, Faculty of Science, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Maryam M Matin
- Department of Biology, Faculty of Science, Ferdowsi University of Mashhad, Mashhad, Iran.
- Novel Diagnostics and Therapeutics Research Group, Institute of Biotechnology, Ferdowsi University of Mashhad, Mashhad, Iran.
| |
Collapse
|
16
|
Eriksen RL, Padgitt-Cobb LK, Townsend MS, Henning JA. Gene expression for secondary metabolite biosynthesis in hop (Humulus lupulus L.) leaf lupulin glands exposed to heat and low-water stress. Sci Rep 2021; 11:5138. [PMID: 33664420 PMCID: PMC7970847 DOI: 10.1038/s41598-021-84691-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 02/05/2021] [Indexed: 01/31/2023] Open
Abstract
Hops are valued for their secondary metabolites, including bitter acids, flavonoids, oils, and polyphenols, that impart flavor in beer. Previous studies have shown that hop yield and bitter acid content decline with increased temperatures and low-water stress. We looked at physiological traits and differential gene expression in leaf, stem, and root tissue from hop (Humulus lupulus) cv. USDA Cascade in plants exposed to high temperature stress, low-water stress, and a compound treatment of both high temperature and low-water stress for six weeks. The stress conditions imposed in these experiments caused substantial changes to the transcriptome, with significant reductions in the expression of numerous genes involved in secondary metabolite biosynthesis. Of the genes involved in bitter acid production, the critical gene valerophenone synthase (VPS) experienced significant reductions in expression levels across stress treatments, suggesting stress-induced lability in this gene and/or its regulatory elements may be at least partially responsible for previously reported declines in bitter acid content. We also identified a number of transcripts with homology to genes shown to affect abiotic stress tolerance in other plants that may be useful as markers for breeding improved abiotic stress tolerance in hop. Lastly, we provide the first transcriptome from hop root tissue.
Collapse
Affiliation(s)
- Renée L. Eriksen
- grid.512836.b0000 0001 2205 063XUSDA Agricultural Research Service, Forage Seed and Cereal Research Unit, 3450 SW Campus Way, Corvallis, OR 97331 USA
| | - Lillian K. Padgitt-Cobb
- grid.4391.f0000 0001 2112 1969Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR 97331 USA
| | - M. Shaun Townsend
- grid.4391.f0000 0001 2112 1969Department of Crop and Soil Science, Oregon State University, Corvallis, OR 97331 USA
| | - John A. Henning
- grid.512836.b0000 0001 2205 063XUSDA Agricultural Research Service, Forage Seed and Cereal Research Unit, 3450 SW Campus Way, Corvallis, OR 97331 USA
| |
Collapse
|
17
|
Awasthi P, Kocábek T, Mishra AK, Nath VS, Shrestha A, Matoušek J. Establishment of CRISPR/Cas9 mediated targeted mutagenesis in hop (Humulus lupulus). PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2021; 160:1-7. [PMID: 33445042 DOI: 10.1016/j.plaphy.2021.01.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2020] [Accepted: 01/05/2021] [Indexed: 05/28/2023]
Abstract
The CRISPR/Cas9-based targeted genome editing has emerged as a versatile technique, widely employed in plant genome engineering, both to decipher gene function and as an alternative to classical breeding technique for traits improvement in plants. However, to date, no such platform has been developed for hop (Humulus lupulus L.), which is an economically important crop producing valuable secondary metabolites utilized in the brewing and pharmaceutical industries. Here, we present the first report on the successful establishment of efficient CRISPR/Cas9-based genome editing using the visible endogenous marker gene phytoene desaturase (PDS) involved in carotenoid biosynthesis to demonstrate successful genome editing in hop. Agrobacterium tumefaciens-mediated transformation of in vitro generated internodal explants was used for the stable integration of constructs expressing plant codon-optimized Cas9 and a pair of co-expressed guide RNAs to target the distinct genomic sites of the PDS gene of hop. Analysis of RNA-guided genome-editing events, including mutant lines screening and homozygosity assessment using the T7 endonuclease assay showed that 33.3% of transformed plants were successfully edited at the target site, displaying albino and mosaic regenerants. Intriguingly, the detected mutations were ranges of deletions (16 bp to 39 bp) which led to disruption of the exon-intron boundary, few base substitutions, and a 1 bp insertion at 3 bp upstream of the PAM region of the target site. The decrease in chlorophyll a/b, and carotenoid content in the mutant lines further confirmed the functional disruption of the HlPDS gene. Taken together, our results demonstrate that the CRISPR/Cas9 system can precisely edit the targeted genome sequences, which may revolutionize our way to overcome some of the obstacles that have plagued the traits improvement in hop.
Collapse
Affiliation(s)
- Praveen Awasthi
- Biology Centre, Czech Academy of Sciences, Institute of Plant Molecular Biology, Branišovská 31, 370 05, České Budějovice, Czech Republic
| | - Tomáš Kocábek
- Biology Centre, Czech Academy of Sciences, Institute of Plant Molecular Biology, Branišovská 31, 370 05, České Budějovice, Czech Republic
| | - Ajay Kumar Mishra
- Biology Centre, Czech Academy of Sciences, Institute of Plant Molecular Biology, Branišovská 31, 370 05, České Budějovice, Czech Republic.
| | - Vishnu Sukumari Nath
- Biology Centre, Czech Academy of Sciences, Institute of Plant Molecular Biology, Branišovská 31, 370 05, České Budějovice, Czech Republic
| | - Ankita Shrestha
- Biology Centre, Czech Academy of Sciences, Institute of Plant Molecular Biology, Branišovská 31, 370 05, České Budějovice, Czech Republic
| | - Jaroslav Matoušek
- Biology Centre, Czech Academy of Sciences, Institute of Plant Molecular Biology, Branišovská 31, 370 05, České Budějovice, Czech Republic
| |
Collapse
|
18
|
Padgitt-Cobb LK, Kingan SB, Wells J, Elser J, Kronmiller B, Moore D, Concepcion G, Peluso P, Rank D, Jaiswal P, Henning J, Hendrix DA. A draft phased assembly of the diploid Cascade hop (Humulus lupulus) genome. THE PLANT GENOME 2021; 14:e20072. [PMID: 33605092 DOI: 10.1002/tpg2.20072] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 10/03/2020] [Indexed: 05/25/2023]
Abstract
Hop (Humulus lupulus L. var Lupulus) is a diploid, dioecious plant with a history of cultivation spanning more than one thousand years. Hop cones are valued for their use in brewing and contain compounds of therapeutic interest including xanthohumol. Efforts to determine how biochemical pathways responsible for desirable traits are regulated have been challenged by the large (2.8 Gb), repetitive, and heterozygous genome of hop. We present a draft haplotype-phased assembly of the Cascade cultivar genome. Our draft assembly and annotation of the Cascade genome is the most extensive representation of the hop genome to date. PacBio long-read sequences from hop were assembled with FALCON and partially phased with FALCON-Unzip. Comparative analysis of haplotype sequences provides insight into selective pressures that have driven evolution in hop. We discovered genes with greater sequence divergence enriched for stress-response, growth, and flowering functions in the draft phased assembly. With improved resolution of long terminal retrotransposons (LTRs) due to long-read sequencing, we found that hop is over 70% repetitive. We identified a homolog of cannabidiolic acid synthase (CBDAS) that is expressed in multiple tissues. The approaches we developed to analyze the draft phased assembly serve to deepen our understanding of the genomic landscape of hop and may have broader applicability to the study of other large, complex genomes.
Collapse
Affiliation(s)
- Lillian K Padgitt-Cobb
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR, 97331, USA
| | - Sarah B Kingan
- Pacific Biosciences of California, Menlo Park, CA, 94025, USA
| | - Jackson Wells
- Center for Genome Research and Biocomputing, Oregon State University, Corvallis, OR, 97331, USA
| | - Justin Elser
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, 97331, USA
| | - Brent Kronmiller
- Center for Genome Research and Biocomputing, Oregon State University, Corvallis, OR, 97331, USA
| | | | | | - Paul Peluso
- Pacific Biosciences of California, Menlo Park, CA, 94025, USA
| | - David Rank
- Pacific Biosciences of California, Menlo Park, CA, 94025, USA
| | - Pankaj Jaiswal
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, 97331, USA
| | | | - David A Hendrix
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR, 97331, USA
- School of Electrical Engineering and Computer Science, Oregon State University, Corvallis, OR, 97331, USA
| |
Collapse
|
19
|
Purayannur S, Cano LM, Bowman MJ, Childs KL, Gent DH, Quesada-Ocampo LM. The Effector Repertoire of the Hop Downy Mildew Pathogen Pseudoperonospora humuli. Front Genet 2020; 11:910. [PMID: 32849854 PMCID: PMC7432248 DOI: 10.3389/fgene.2020.00910] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 07/22/2020] [Indexed: 01/18/2023] Open
Abstract
Pseudoperonospora humuli is an obligate biotrophic oomycete that causes downy mildew (DM), one of the most destructive diseases of cultivated hop that can lead to 100% crop loss in susceptible cultivars. We used the published genome of P. humuli to predict the secretome and effectorome and analyze the transcriptome variation among diverse isolates and during infection of hop leaves. Mining the predicted coding genes of the sequenced isolate OR502AA of P. humuli revealed a secretome of 1,250 genes. We identified 296 RXLR and RXLR-like effector-encoding genes in the secretome. Among the predicted RXLRs, there were several WY-motif-containing effectors that lacked canonical RXLR domains. Transcriptome analysis of sporangia from 12 different isolates collected from various hop cultivars revealed 754 secreted proteins and 201 RXLR effectors that showed transcript evidence across all isolates with reads per kilobase million (RPKM) values > 0. RNA-seq analysis of OR502AA-infected hop leaf samples at different time points after infection revealed highly expressed effectors that may play a relevant role in pathogenicity. Quantitative RT-PCR analysis confirmed the differential expression of selected effectors. We identified a set of P. humuli core effectors that showed transcript evidence in all tested isolates and elevated expression during infection. These effectors are ideal candidates for functional analysis and effector-assisted breeding to develop DM resistant hop cultivars.
Collapse
Affiliation(s)
- Savithri Purayannur
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, United States
| | - Liliana M. Cano
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, United States
- Indian River Research and Education Center, Department of Plant Pathology, Institute of Food and Agricultural Sciences, University of Florida, Fort Pierce, FL, United States
| | - Megan J. Bowman
- Department of Plant Biology, Michigan State University, East Lansing, MI, United States
- Ball Horticultural Company, West Chicago, IL, United States
| | - Kevin L. Childs
- Department of Plant Biology, Michigan State University, East Lansing, MI, United States
| | - David H. Gent
- United States Department of Agriculture-Agricultural Research Service, Forage Seed and Cereal Research Unit, Oregon State University, Corvallis, OR, United States
| | - Lina M. Quesada-Ocampo
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, United States
| |
Collapse
|
20
|
Easterling KA, Pitra NJ, Morcol TB, Aquino JR, Lopes LG, Bussey KC, Matthews PD, Bass HW. Identification of tandem repeat families from long-read sequences of Humulus lupulus. PLoS One 2020; 15:e0233971. [PMID: 32502183 PMCID: PMC7274563 DOI: 10.1371/journal.pone.0233971] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Accepted: 05/16/2020] [Indexed: 11/28/2022] Open
Abstract
Hop (Humulus lupulus L.) is known for its use as a bittering agent in beer and has a rich history of cultivation, beginning in Europe and now spanning the globe. There are five wild varieties worldwide, which may have been introgressed with cultivated varieties. As a dioecious species, its obligate outcrossing, non-Mendelian inheritance, and genomic structural variability have confounded directed breeding efforts. Consequently, understanding the hop genome represents a considerable challenge, requiring additional resources. In order to facilitate investigations into the transmission genetics of hop, we report here a tandem repeat discovery pipeline developed using k-mer filtering and dot plot analysis of PacBio long-read sequences from the hop cultivar Apollo. From this we identified 17 new and distinct tandem repeat sequence families, which represent candidates for FISH probe development. For two of these candidates, HuluTR120 and HuluTR225, we produced oligonucleotide FISH probes from conserved regions of and demonstrated their utility by staining meiotic chromosomes from wild hop, var. neomexicanus to address, for example, questions about hop transmission genetics. Collectively, these tandem repeat sequence families represent new resources suitable for development of additional cytogenomic tools for hop research.
Collapse
Affiliation(s)
- Katherine A. Easterling
- Department of Biological Science, Florida State University, Tallahassee, FL, United States America
- Hopsteiner, S.S. Steiner, Inc., New York, New York, United States America
| | - Nicholi J. Pitra
- Hopsteiner, S.S. Steiner, Inc., New York, New York, United States America
| | - Taylan B. Morcol
- Hopsteiner, S.S. Steiner, Inc., New York, New York, United States America
- Department of Biological Sciences, Lehman College, City University of New York, Bronx, New York, United States America
- The Graduate Center, City University of New York, New York, New York, United States America
| | - Jenna R. Aquino
- Department of Biological Science, Florida State University, Tallahassee, FL, United States America
| | - Lauren G. Lopes
- Department of Biological Science, Florida State University, Tallahassee, FL, United States America
| | - Kristin C. Bussey
- Department of Biological Science, Florida State University, Tallahassee, FL, United States America
| | - Paul D. Matthews
- Hopsteiner, S.S. Steiner, Inc., New York, New York, United States America
| | - Hank W. Bass
- Department of Biological Science, Florida State University, Tallahassee, FL, United States America
| |
Collapse
|
21
|
Gent DH, Claassen BJ, Gadoury DM, Grünwald NJ, Knaus BJ, Radišek S, Weldon W, Wiseman MS, Wolfenbarger SN. Population Diversity and Structure of Podosphaera macularis in the Pacific Northwestern United States and Other Populations. PHYTOPATHOLOGY 2020; 110:1105-1116. [PMID: 32091314 DOI: 10.1094/phyto-12-19-0448-r] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Powdery mildew, caused by Podosphaera macularis, is one of the most important diseases of hop. The disease was first reported in the Pacific Northwestern United States, the primary hop-growing region in this country, in the mid-1990s. More recently, the disease has reemerged in newly planted hopyards of the eastern United States, as hop production has expanded to meet demands of local craft brewers. The spread of strains virulent on previously resistant cultivars, the paucity of available fungicides, and the potential introduction of the MAT1-2 mating type to the western United States, all threaten sustainability of hop production. We sequenced the transcriptome of 104 isolates of P. macularis collected throughout the western United States, eastern United States, and Europe to quantify genetic diversity of pathogen populations and elucidate the possible origins of pathogen populations in the western United States. Discriminant analysis of principal components grouped isolates within three to five geographic populations, dependent on stringency of grouping criteria. Isolates from the western United States were phenotyped and categorized into one of three pathogenic races based on disease symptoms generated on differential cultivars. Western U.S. populations were clonal, irrespective of pathogenic race, and grouped with isolates originating from Europe. Isolates originating from wild hop plants in the eastern United States were genetically differentiated from all other populations, whereas isolates from cultivated hop plants in the eastern United States mostly grouped with isolates originating from the west, consistent with origins from nursery sources. Mating types of isolates originating from cultivated western and eastern U.S. hop plants were entirely MAT1-1. In contrast, a 1:1 ratio of MAT1-1 and MAT1-2 was observed with isolates sampled from wild plants or Europe. Within the western United States a set of highly differentiated loci were identified in P. macularis isolates associated with virulence to the powdery mildew R-gene R6. The weight of genetic and phenotypic evidence suggests a European origin of the P. macularis populations in the western United States, followed by spread of the pathogen from the western United States to re-emergent production regions in the eastern United States. Furthermore, R6 compatibility appears to have been selected from an extant isolate within the western United States. Greater emphasis on sanitation measures during propagation and quarantine policies should be considered to limit further spread of novel genotypes of the pathogen, both between and within production areas.
Collapse
Affiliation(s)
- David H Gent
- U.S. Department of Agriculture-Agricultural Research Service, Forage Seed and Cereal Research Unit, Corvallis, OR 97331, U.S.A
| | - Briana J Claassen
- Oregon State University, Department of Botany and Plant Pathology, Corvallis, OR 97331, U.S.A
| | - David M Gadoury
- Plant Pathology and Plant-Microbe Biology Section, Cornell University, New York State Agricultural Experiment Station, Geneva, NY 14456, U.S.A
| | - Niklaus J Grünwald
- U.S. Department of Agriculture-Agricultural Research Service, Horticultural Crops Research Unit, Corvallis, OR 97330, U.S.A
| | - Brian J Knaus
- Oregon State University, Department of Botany and Plant Pathology, Corvallis, OR 97331, U.S.A
| | | | - William Weldon
- Plant Pathology and Plant-Microbe Biology Section, Cornell University, New York State Agricultural Experiment Station, Geneva, NY 14456, U.S.A
| | - Michele S Wiseman
- Oregon State University, Department of Botany and Plant Pathology, Corvallis, OR 97331, U.S.A
| | - Sierra N Wolfenbarger
- Oregon State University, Department of Botany and Plant Pathology, Corvallis, OR 97331, U.S.A
| |
Collapse
|
22
|
Kovalchuk I, Pellino M, Rigault P, van Velzen R, Ebersbach J, Ashnest JR, Mau M, Schranz ME, Alcorn J, Laprairie RB, McKay JK, Burbridge C, Schneider D, Vergara D, Kane NC, Sharbel TF. The Genomics of Cannabis and Its Close Relatives. ANNUAL REVIEW OF PLANT BIOLOGY 2020; 71:713-739. [PMID: 32155342 DOI: 10.1146/annurev-arplant-081519-040203] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Cannabis sativa L. is an important yet controversial plant with a long history of recreational, medicinal, industrial, and agricultural use, and together with its sister genus Humulus, it represents a group of plants with a myriad of academic, agricultural, pharmaceutical, industrial, and social interests. We have performed a meta-analysis of pooled published genomics data, andwe present a comprehensive literature review on the evolutionary history of Cannabis and Humulus, including medicinal and industrial applications. We demonstrate that current Cannabis genome assemblies are incomplete, with ∼10% missing, 10-25% unmapped, and 45S and 5S ribosomal DNA clusters as well as centromeres/satellite sequences not represented. These assemblies are also ordered at a low resolution, and their consensus quality clouds the accurate annotation of complete, partial, and pseudogenized gene copies. Considering the importance of genomics in the development of any crop, this analysis underlines the need for a coordinated effort to quantify the genetic and biochemical diversity of this species.
Collapse
Affiliation(s)
- I Kovalchuk
- Department of Biology, University of Lethbridge, Lethbridge, Alberta T1K 3M4, Canada
| | - M Pellino
- College of Agriculture and Bioresources, University of Saskatchewan, Saskatoon, Saskatchewan S7N 4J8, Canada;
| | - P Rigault
- Gydle Inc., Québec, Québec G1S 1E7, Canada
- Center for Organismal Studies (COS), University of Heidelberg, 69120 Heidelberg, Germany
| | - R van Velzen
- Biosystematics Group, Wageningen University, 6703 BD Wageningen, The Netherlands
- Bedrocan International, 9640 CA Veendam, The Netherlands
| | - J Ebersbach
- Saskatoon Research and Development Centre, Agriculture and Agri-Food Canada, Saskatoon, Saskatchewan S7N 0X2, Canada
| | - J R Ashnest
- College of Agriculture and Bioresources, University of Saskatchewan, Saskatoon, Saskatchewan S7N 4J8, Canada;
| | - M Mau
- College of Agriculture and Bioresources, University of Saskatchewan, Saskatoon, Saskatchewan S7N 4J8, Canada;
| | - M E Schranz
- Biosystematics Group, Wageningen University, 6703 BD Wageningen, The Netherlands
| | - J Alcorn
- College of Pharmacy and Nutrition, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5E5, Canada
| | - R B Laprairie
- College of Pharmacy and Nutrition, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5E5, Canada
- Department of Pharmacology, College of Medicine, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
| | - J K McKay
- College of Agricultural Sciences, Colorado State University, Fort Collins, Colorado 80523, USA
| | - C Burbridge
- School of Environment and Sustainability, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5E5, Canada
| | - D Schneider
- School of Environment and Sustainability, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5E5, Canada
| | - D Vergara
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado 80309, USA
| | - N C Kane
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado 80309, USA
| | - T F Sharbel
- College of Agriculture and Bioresources, University of Saskatchewan, Saskatoon, Saskatchewan S7N 4J8, Canada;
| |
Collapse
|
23
|
Dissection of Dynamic Transcriptome Landscape of Leaf, Bract, and Lupulin Gland in Hop ( Humulus lupulus L.). Int J Mol Sci 2019; 21:ijms21010233. [PMID: 31905722 PMCID: PMC6981390 DOI: 10.3390/ijms21010233] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Revised: 12/22/2019] [Accepted: 12/27/2019] [Indexed: 12/19/2022] Open
Abstract
The hop plant (Humulus lupulus L.) produces several valuable secondary metabolites, such as prenylflavonoid, bitter acids, and essential oils. These compounds are biosynthesized in glandular trichomes (lupulin glands) endowed with pharmacological properties and widely implicated in the beer brewing industry. The present study is an attempt to generate exhaustive information of transcriptome dynamics and gene regulatory mechanisms involved in biosynthesis and regulation of these compounds, developmental changes including trichome development at three development stages, namely leaf, bract, and mature lupulin glands. Using high-throughput RNA-Seq technology, a total of 61.13, 50.01, and 20.18 Mb clean reads in the leaf, bract, and lupulin gland libraries, respectively, were obtained and assembled into 43,550 unigenes. The putative functions were assigned to 30,996 transcripts (71.17%) based on basic local alignment search tool similarity searches against public sequence databases, including GO, KEGG, NR, and COG families, which indicated that genes are principally involved in fundamental cellular and molecular functions, and biosynthesis of secondary metabolites. The expression levels of all unigenes were analyzed in leaf, bract, and lupulin glands tissues of hop. The expression profile of transcript encoding enzymes of BCAA metabolism, MEP, and shikimate pathway was most up-regulated in lupulin glands compared with leaves and bracts. Similarly, the expression levels of the transcription factors and structural genes that directly encode enzymes involved in xanthohumol, bitter acids, and terpenoids biosynthesis pathway were found to be significantly enhanced in lupulin glands, suggesting that production of these metabolites increases after the leaf development. In addition, numerous genes involved in primary metabolism, lipid metabolism, photosynthesis, generation of precursor metabolites/energy, protein modification, transporter activity, and cell wall component biogenesis were differentially regulated in three developmental stages, suggesting their involvement in the dynamics of the lupulin gland development. The identification of differentially regulated trichome-related genes provided a new foundation for molecular research on trichome development and differentiation in hop. In conclusion, the reported results provide directions for future functional genomics studies for genetic engineering or molecular breeding for augmentation of secondary metabolite content in hop.
Collapse
|
24
|
McCallum JL, Nabuurs MH, Gallant ST, Kirby CW, Mills AAS. Phytochemical Characterization of Wild Hops ( Humulus lupulus ssp. lupuloides) Germplasm Resources From the Maritimes Region of Canada. FRONTIERS IN PLANT SCIENCE 2019; 10:1438. [PMID: 31921222 PMCID: PMC6917649 DOI: 10.3389/fpls.2019.01438] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 10/16/2019] [Indexed: 05/06/2023]
Abstract
A survey was conducted in the Maritimes region of eastern Canada to measure the phytochemical diversity of prenylchalcone, soft resins (alpha & beta acids), and flavonol constituents from 30 unique wild-growing populations of hops (Humulus lupulus L.). Based on cone chemometrics, the majority of accessions (63.3%) are native Humulus lupulus ssp. lupoloides, with cones containing both xanthogalenol and 4'-O-methyl xanthohumol as chemotaxonomic indicator molecules. Interestingly, the leaves of all verified Humulus lupulus ssp. lupulus accessions accumulated high proportions (>0.20 total flavonols) of two acylated flavonol derivatives (kaempferol-3-O-(6''-O-malonyl)-β-D-glucopyranoside; quercetin-3-O-(6''-O-malonyl)-β-D-glucopyranoside), both previously unreported from hops leaves. The native lupuloides accessions examined possess only trace amounts of this compound in their leaves (<0.10 total flavonols), suggesting its potential utility as a novel, leaf-derived chemotaxonomic marker for subspecies identification purposes. A leaf-derived taxonomic marker is useful for identifying wild-growing accessions, as leaves are present throughout the entire growing season, whereas cones are only produced late in summer. Additionally, the collection of cones from 10-meter tall wild plants in overgrown riparian habitats is often difficult. The total levels of alpha acids, beta acids, and prenylchalcones in wild-collected Maritimes lupuloides cones are markedly higher than those previously reported for lupuloides individuals in the westernmost extent of its native range and show potentially valuable traits for future cultivar development, while some may be worthy of immediate commercial release. The accessions will be maintained as a core germplasm resource for future cultivar development.
Collapse
Affiliation(s)
- Jason L. McCallum
- Agriculture and Agri-Food Canada, Charlottetown Research and Development Centre, Charlottetown, Canada
| | | | | | | | | |
Collapse
|
25
|
Yamashiro T, Shiraishi A, Satake H, Nakayama K. Draft genome of Tanacetum cinerariifolium, the natural source of mosquito coil. Sci Rep 2019; 9:18249. [PMID: 31796833 PMCID: PMC6890757 DOI: 10.1038/s41598-019-54815-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Accepted: 11/20/2019] [Indexed: 11/09/2022] Open
Abstract
Pyrethrum (Tanacetum cinerariifolium), which is a perennial Asteraceae plant with white daisy-like flowers, is the original source of mosquito coils and is known for the biosynthesis of the pyrethrin class of natural insecticides. However, the molecular basis of the production of pyrethrins by T. cinerariifolium has yet to be fully elucidated. Here, we present the 7.1-Gb draft genome of T. cinerariifolium, consisting of 2,016,451 scaffolds and 60,080 genes predicted with high confidence. Notably, analyses of transposable elements (TEs) indicated that TEs occupy 33.84% of the genome sequence. Furthermore, TEs of the sire and oryco clades were found to be enriched in the T. cinerariifolium-specific evolutionary lineage, occupying a total of 13% of the genome sequence, a proportion approximately 8-fold higher than that in other plants. InterProScan analysis demonstrated that biodefense-related toxic proteins (e.g., ribosome inactivating proteins), signal transduction-related proteins (e.g., histidine kinases), and metabolic enzymes (e.g., lipoxygenases, acyl-CoA dehydrogenases/oxygenases, and P450s) are also highly enriched in the T. cinerariifolium genome. Molecular phylogenetic analysis detected a variety of enzymes with genus-specific multiplication, including both common enzymes and others that appear to be specific to pyrethrin biosynthesis. Together, these data identify possible novel components of the pyrethrin biosynthesis pathway and provide new insights into the unique genomic features of T. cinerariifolium.
Collapse
Affiliation(s)
- Takanori Yamashiro
- Dainihon Jochugiku Co., Ltd., 1-1-11 Daikoku-cho, Toyonaka, Osaka, 561-0827, Japan
| | - Akira Shiraishi
- Bioorganic Research Institute, Suntory Foundation for Life Sciences, Kyoto, 619-0284, Japan
| | - Honoo Satake
- Bioorganic Research Institute, Suntory Foundation for Life Sciences, Kyoto, 619-0284, Japan.
| | - Koji Nakayama
- Dainihon Jochugiku Co., Ltd., 1-1-11 Daikoku-cho, Toyonaka, Osaka, 561-0827, Japan.
| |
Collapse
|
26
|
Fathi E, Majdi M, Dastan D, Maroufi A. The spatio-temporal expression of some genes involved in the biosynthetic pathways of terpenes/phenylpropanoids in yarrow (Achillea millefolium). PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2019; 142:43-52. [PMID: 31272034 DOI: 10.1016/j.plaphy.2019.06.036] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Revised: 06/18/2019] [Accepted: 06/28/2019] [Indexed: 06/09/2023]
Abstract
Yarrow (Achillea millefolium) is a medicinal plant from the Asteracea which biosynthesize different secondary metabolites especially terpenes and phenylpropanoids. To improve our understanding of the regulatory mechanisms behind the biosynthesis of these compounds we analyzed the expression of some genes associated with the biosynthesis of terpenes and phenylpropanoids in different tissues and in response to trans-cinnamic acid (tCA) as an inhibitor of PAL activity. Isolation and expression analysis of DXR, GPPS, PAL and CHS genes together with linalool synthase (LIS) as monoterpene synthase was conducted in different developmental stages of leaves, flowers and in response to trans-cinnamic acid (tCA). Differential expression of these genes observed in different tissues. tCA up-regulated the biosynthetic genes of monterpenes and down-regulated the biosynthetic genes of phenylpropanoids. Gene expression analysis in intact leaves and leaves without glandular trichomes showed that DXR, LIS, PAL and CHS are highly expressed in glandular trichomes while GPPS expressed ubiquitously. Analysis of essential oils composition showed that sesquiterpenes and monoterpenes are main compounds; in which from 57 identified compounds the highest were germacreneD (% 11.5), guaiol (%10.38), spatulenol (%8.73) and caryophyllene oxide (%7.48).
Collapse
Affiliation(s)
- Ehsan Fathi
- Department of Agronomy and Plant Breeding, University of Kurdistan, Sanandaj, Iran
| | - Mohammad Majdi
- Department of Agronomy and Plant Breeding, University of Kurdistan, Sanandaj, Iran; (b)Research Center for Medicinal Plant Breeding and Development, University of Kurdistan, Sanandaj, Iran.
| | - Dara Dastan
- Department of Pharmacognosy and Pharmaceutical Biotechnology, School of Pharmacy, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Asad Maroufi
- Department of Agronomy and Plant Breeding, University of Kurdistan, Sanandaj, Iran
| |
Collapse
|
27
|
Svara A, Jakse J, Radisek S, Javornik B, Stajner N. Temporal and spatial assessment of defence responses in resistant and susceptible hop cultivars during infection with Verticillium nonalfalfae. JOURNAL OF PLANT PHYSIOLOGY 2019; 240:153008. [PMID: 31326713 DOI: 10.1016/j.jplph.2019.153008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Revised: 06/21/2019] [Accepted: 07/01/2019] [Indexed: 06/10/2023]
Abstract
Hop (Humulus lupulus L.) is an important industrial plant providing ingredients for brewing and pharmaceutical industry worldwide. Its intensive production is challenged by numerous diseases. One of the most lethal and difficult to control is verticillium wilt, a vascular disease caused by the fungal pathogen Verticillium nonalfalfae. The disease can be successfully controlled by the host resistance. Despite various studies that already researched resistance mechanisms of hops, only limited number of resistance genes and markers that could be utilized for efficient resistance breeding has been identified. In this study we aimed to follow fungus colonization pattern and the differential expression of selected genes during pre-symptomatic period of susceptible (Celeia) and resistant (Wye Target) hop cultivars. Results of gene expressions and fungal colonisation of compatible and incompatible interactions with V. nonalfalfae suggest that the hop plant is challenged already at the very early fungal colonisation stages. In total, nine out of 17 gene targets investigated in our study resulted in differential expression between inoculated and control plants of susceptible and resistant cultivars. The difference was the most evident in stems at an early stage of colonisation (6 dpi), showing relatively stronger changes in targeted gene expression to infection in the resistant cultivar than in the susceptible one. Analysed gene targets are involved in the overall defence response processes of nucleic acid binding, signalling, protein ubiquitination, cell oxidative burst, hydroxylation, peroxidation, alternative splicing, and metabolite biosynthesis. The up-regulation of some genes (e.g. glycine-rich RNA-binding family protein, protein phosphatase, cysteine-rich receptor-like protein kinase, zinc finger CCCH domain-containing protein 40, cinnamic acid 4-hydroxylase, class III peroxidase, putative MAPK2, peroxiredoxin-2F) upon infection in incompatible interactions might reflect defence activation, restriction of disease spreading throughout the plant and successful response of resistant genotype.
Collapse
Affiliation(s)
- A Svara
- Department of Biosystems, KU Leuven, W. De Croylaan 42, 3001 Leuven, Belgium.
| | - J Jakse
- Department of Agronomy, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, 1000 Ljubljana, Slovenia.
| | - S Radisek
- Plant Protection Department, Slovenian Institute of Hop Research and Brewing, Cesta Žalskega tabora 2, 3310 Žalec, Slovenia.
| | - B Javornik
- Department of Agronomy, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, 1000 Ljubljana, Slovenia.
| | - N Stajner
- Department of Agronomy, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, 1000 Ljubljana, Slovenia.
| |
Collapse
|
28
|
Shameer K, Naika MB, Shafi KM, Sowdhamini R. Decoding systems biology of plant stress for sustainable agriculture development and optimized food production. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2019; 145:19-39. [DOI: 10.1016/j.pbiomolbio.2018.12.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2017] [Revised: 10/23/2018] [Accepted: 12/06/2018] [Indexed: 12/13/2022]
|
29
|
Rahman A, Góngora-Castillo E, Bowman MJ, Childs KL, Gent DH, Martin FN, Quesada-Ocampo LM. Genome Sequencing and Transcriptome Analysis of the Hop Downy Mildew Pathogen Pseudoperonospora humuli Reveal Species-Specific Genes for Molecular Detection. PHYTOPATHOLOGY 2019; 109:1354-1366. [PMID: 30939079 DOI: 10.1094/phyto-11-18-0431-r] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Pseudoperonospora humuli is an obligate oomycete pathogen of hop (Humulus lupulus) that causes downy mildew, an important disease in most production regions in the Northern Hemisphere. The pathogen can cause a systemic infection in hop, overwinter in the root system, and infect propagation material. Substantial yield loss may occur owing to P. humuli infection of strobiles (seed cones), shoots, and cone-bearing branches. Fungicide application and cultural practices are the primary methods to manage hop downy mildew. However, effective, sustainable, and cost-effective management of downy mildew can be improved by developing early detection systems to inform on disease risk and timely fungicide application. However, no species-specific diagnostic assays or genomic resources are available for P. humuli. The genome of the P. humuli OR502AA isolate was partially sequenced using Illumina technology and assembled with ABySS. The assembly had a minimum scaffold length of 500 bp and an N50 (median scaffold length of the assembled genome) of 19.2 kbp. A total number of 18,656 genes were identified using MAKER standard gene predictions. Additionally, transcriptome assemblies were generated using RNA-seq and Trinity for seven additional P. humuli isolates. Bioinformatics analyses of next generation sequencing reads of P. humuli and P. cubensis (a closely related sister species) identified 242 candidate species-specific P. humuli genes that could be used as diagnostic molecular markers. These candidate genes were validated using polymerase chain reaction against a diverse collection of isolates from P. humuli, P. cubensis, and other oomycetes. Overall, four diagnostic markers were found to be uniquely present in P. humuli. These candidate markers identified through comparative genomics can be used for pathogen diagnostics in propagation material, such as rhizomes and vegetative cuttings, or adapted for biosurveillance of airborne sporangia, an important source of inoculum in hop downy mildew epidemics.
Collapse
Affiliation(s)
- A Rahman
- 1Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC 27695-7613, U.S.A
| | - E Góngora-Castillo
- 1Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC 27695-7613, U.S.A
- 2Department of Biotechnology, Yucatan Center for Scientific Research, 97205 Mérida, Yucatán, México
| | - M J Bowman
- 3Department of Plant Biology, Michigan State University, East Lansing, MI 48823, U.S.A
| | - K L Childs
- 3Department of Plant Biology, Michigan State University, East Lansing, MI 48823, U.S.A
| | - D H Gent
- 4Forage Seed and Cereal Research Unit, U.S. Department of Agriculture-Agricultural Research Service and Oregon State University, Corvallis 97331, OR, U.S.A
| | - F N Martin
- 5Crop Improvement and Protection Research Station, U.S. Department of Agriculture-Agricultural Research Service, Salinas, CA 93905, U.S.A
| | - L M Quesada-Ocampo
- 1Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC 27695-7613, U.S.A
| |
Collapse
|
30
|
Zhou W, Chen Q, Wang XB, Hughes TO, Liu JJ, Zhang X. De novo assembly of the Platycladus orientalis (L.) Franco transcriptome provides insight into the development and pollination mechanism of female cone based on RNA-Seq data. Sci Rep 2019; 9:10191. [PMID: 31308452 PMCID: PMC6629706 DOI: 10.1038/s41598-019-46696-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Accepted: 07/03/2019] [Indexed: 11/30/2022] Open
Abstract
For seed-bearing plants, the basis of seed and fruit formation is pollination. The normal progression of pollination is through advances in continuous signal exchange and material transfer, which occur mainly in female reproductive organs; thus, the molecular mechanism of development in female reproductive organs is vital for understanding the principle of pollination. However, molecular biology studies on the development of female cones related to pollination are rare and unclear in gymnosperms, especially in Cupressaceae. In this study, Platycladus orientalis, a monotypic genus within Cupressaceae, was chosen to examine female cone transcriptomes at pre-pollination and pollination stages by Illumina paired-end sequencing technology to de novo sequence six libraries with 3 biological replicates. These libraries were used to construct a P. orientalis transcriptome database containing 71,669 unigenes (4,963 upregulated unigenes and 11,747 downregulated unigenes at the pollination stage) for subsequent analysis. Based on the annotations and expression levels, the functions of differentially expressed unigenes and enriched pathways between the developmental processes of female cones were analysed to detail the preliminary development and pollination mechanism of the female cone. Targeted investigations were specifically performed to determine the elementary mechanism of secretion and functioning of the pollination drop, a vital ovule secretion at the pollination stage. Ultimately, the expression of 15 unigenes selected between two stages were further assessed and confirmed using qRT-PCR, which demonstrated reliable data and significant differences in the expression profiles of key genes. As one of the largest available transcriptomic resources of this species, the database is constructed to prospectively adapt to the physiological and genomic data of woody plants. This work provided the first transcriptome profile of P. orientalis female cones at different developmental stages, and will promote the illumination of the pollination mechanism of P. orientalis, and will serve as the basis for in-depth genomic study in the Cupressaceae family. This initiative will arouse the interest and attention of scholars and pave the way for future studies.
Collapse
Affiliation(s)
- Wei Zhou
- College of Landscape Architecture and Arts, Northwest A&F University, Yangling, Shaanxi, P.R. China
| | - Qi Chen
- College of Landscape Architecture and Arts, Northwest A&F University, Yangling, Shaanxi, P.R. China
| | - Xiao-Bing Wang
- School of Life Science and Technology, Xinxiang University, Xinxiang, Henan, P.R. China
| | - Tyler O Hughes
- Department of Biology, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Jian-Jun Liu
- College of Landscape Architecture and Arts, Northwest A&F University, Yangling, Shaanxi, P.R. China.
| | - Xin Zhang
- Key Laboratory of Silviculture on the Loess Plateau State Forestry Administration, College of Forestry, Northwest A&F University, Yangling, P.R. China.
| |
Collapse
|
31
|
Sukumari Nath V, Kumar Mishra A, Kumar A, Matoušek J, Jakše J. Revisiting the Role of Transcription Factors in Coordinating the Defense Response Against Citrus Bark Cracking Viroid Infection in Commercial Hop ( Humulus Lupulus L.). Viruses 2019; 11:v11050419. [PMID: 31060295 PMCID: PMC6563305 DOI: 10.3390/v11050419] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Revised: 04/29/2019] [Accepted: 05/03/2019] [Indexed: 01/13/2023] Open
Abstract
Transcription factors (TFs) play a major role in controlling gene expression by intricately regulating diverse biological processes such as growth and development, the response to external stimuli and the activation of defense responses. The systematic identification and classification of TF genes are essential to gain insight into their evolutionary history, biological roles, and regulatory networks. In this study, we performed a global mining and characterization of hop TFs and their involvement in Citrus bark cracking viroid CBCVd infection by employing a digital gene expression analysis. Our systematic analysis resulted in the identification of a total of 3,818 putative hop TFs that were classified into 99 families based on their conserved domains. A phylogenetic analysis classified the hop TFs into several subgroups based on a phylogenetic comparison with reference TF proteins from Arabidopsis thaliana providing glimpses of their evolutionary history. Members of the same subfamily and subgroup shared conserved motif compositions. The putative functions of the CBCVd-responsive hop TFs were predicted using their orthologous counterparts in A. thaliana. The analysis of the expression profiling of the CBCVd-responsive hop TFs revealed a massive differential modulation, and the expression of the selected TFs was validated using qRT-PCR. Together, the comprehensive integrated analysis in this study provides better insights into the TF regulatory networks associated with CBCVd infections in the hop, and also offers candidate TF genes for improving the resistance in hop against viroids.
Collapse
Affiliation(s)
- Vishnu Sukumari Nath
- Department of Molecular Genetics, Institute of Plant Molecular Biology, Biology Centre of the Czech Academy of Sciences, Branišovská 31, 37005 České Budějovice, Czech Republic.
| | - Ajay Kumar Mishra
- Department of Molecular Genetics, Institute of Plant Molecular Biology, Biology Centre of the Czech Academy of Sciences, Branišovská 31, 37005 České Budějovice, Czech Republic.
| | - Atul Kumar
- Department of Molecular Genetics, Institute of Plant Molecular Biology, Biology Centre of the Czech Academy of Sciences, Branišovská 31, 37005 České Budějovice, Czech Republic.
| | - Jaroslav Matoušek
- Department of Molecular Genetics, Institute of Plant Molecular Biology, Biology Centre of the Czech Academy of Sciences, Branišovská 31, 37005 České Budějovice, Czech Republic.
| | - Jernej Jakše
- Department of Agronomy, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, SI-1000 Ljubljana, Slovenia.
| |
Collapse
|
32
|
Holt S, Miks MH, de Carvalho BT, Foulquié-Moreno MR, Thevelein JM. The molecular biology of fruity and floral aromas in beer and other alcoholic beverages. FEMS Microbiol Rev 2019; 43:193-222. [PMID: 30445501 PMCID: PMC6524682 DOI: 10.1093/femsre/fuy041] [Citation(s) in RCA: 119] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Accepted: 11/13/2018] [Indexed: 12/03/2022] Open
Abstract
Aroma compounds provide attractiveness and variety to alcoholic beverages. We discuss the molecular biology of a major subset of beer aroma volatiles, fruity and floral compounds, originating from raw materials (malt and hops), or formed by yeast during fermentation. We introduce aroma perception, describe the most aroma-active, fruity and floral compounds in fruits and their presence and origin in beer. They are classified into categories based on their functional groups and biosynthesis pathways: (1) higher alcohols and esters, (2) polyfunctional thiols, (3) lactones and furanones, and (4) terpenoids. Yeast and hops are the main sources of fruity and flowery aroma compounds in beer. For yeast, the focus is on higher alcohols and esters, and particularly the complex regulation of the alcohol acetyl transferase ATF1 gene. We discuss the release of polyfunctional thiols and monoterpenoids from cysteine- and glutathione-S-conjugated compounds and glucosides, respectively, the primary biological functions of the yeast enzymes involved, their mode of action and mechanisms of regulation that control aroma compound production. Furthermore, we discuss biochemistry and genetics of terpenoid production and formation of non-volatile precursors in Humulus lupulus (hops). Insight in these pathways provides a toolbox for creating innovative products with a diversity of pleasant aromas.
Collapse
Affiliation(s)
- Sylvester Holt
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, B-3001 Leuven-Heverlee, Flanders, Belgium
- Center for Microbiology, VIB, Kasteelpark Arenberg 31, B-3001 Leuven-Heverlee, Flanders, Belgium
| | - Marta H Miks
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, 1799 Copenhagen V, Denmark
- Faculty of Food Science, University of Warmia and Mazury in Olsztyn, Plac Cieszyński 1, 10–726 Olsztyn, Poland
| | - Bruna Trindade de Carvalho
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, B-3001 Leuven-Heverlee, Flanders, Belgium
- Center for Microbiology, VIB, Kasteelpark Arenberg 31, B-3001 Leuven-Heverlee, Flanders, Belgium
| | - Maria R Foulquié-Moreno
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, B-3001 Leuven-Heverlee, Flanders, Belgium
- Center for Microbiology, VIB, Kasteelpark Arenberg 31, B-3001 Leuven-Heverlee, Flanders, Belgium
| | - Johan M Thevelein
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, B-3001 Leuven-Heverlee, Flanders, Belgium
- Center for Microbiology, VIB, Kasteelpark Arenberg 31, B-3001 Leuven-Heverlee, Flanders, Belgium
| |
Collapse
|
33
|
Van Holle A, Muylle H, Ruttink T, Van Landschoot A, Haesaert G, Naudts D, De Keukeleire D, Roldán-Ruiz I. Single Nucleotide Polymorphisms and Biochemical Markers As Complementary Tools To Characterize Hops ( Humulus lupulus L.) in Brewing Practice. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:3761-3771. [PMID: 30896165 DOI: 10.1021/acs.jafc.9b00816] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
In brewing practice, the use of the appropriate hop variety is essential to produce consistent and high-quality beers. Yet, hop batches of the same variety cultivated in different geographical regions can display significant biochemical differences, resulting in specific taste- and aroma-related characteristics in beer. In this study, we illustrate the complementarity of genetic and biochemical fingerprinting methods to fully characterize hop batches. Using genotyping-by-sequencing (GBS), a set of 1 830 polymorphic single nucleotide polymorphism (SNP) markers generated 48 unique genetic fingerprints for a collection of 56 commercial hop varieties. Three groups of varieties, consisting of somaclonal variants, could not be further differentiated using this set of markers. Biochemical marker information offered added value to characterize hop samples from a given variety grown at different geographical locations. We demonstrate the power of combining genetic and biochemical fingerprints for quality control of hop batches in the brewing industry.
Collapse
Affiliation(s)
- Ann Van Holle
- Faculty of Bioengineering Sciences, Department of Plants and Crops , Ghent University , Coupure Links 653 , 9000 Ghent , Belgium
- De Proefbrouwerij , Doornzelestraat 20 , 9080 Lochristi , Belgium
| | - Hilde Muylle
- Flanders Research Institute for Agriculture, Fisheries and Food (ILVO) , Caritasstraat 39 , 9090 Melle , Belgium
| | - Tom Ruttink
- Flanders Research Institute for Agriculture, Fisheries and Food (ILVO) , Caritasstraat 39 , 9090 Melle , Belgium
| | - Anita Van Landschoot
- Faculty of Bioengineering Sciences, Department of Biotechnology , Ghent University , Valentin Vaerwyckweg 1 , 9000 Ghent , Belgium
| | - Geert Haesaert
- Faculty of Bioengineering Sciences, Department of Plants and Crops , Ghent University , Coupure Links 653 , 9000 Ghent , Belgium
| | - Dirk Naudts
- De Proefbrouwerij , Doornzelestraat 20 , 9080 Lochristi , Belgium
| | - Denis De Keukeleire
- Faculty of Pharmaceutical Sciences , Ghent University , c/o Gontrode Heirweg 115 , 9090 Melle , Belgium
| | - Isabel Roldán-Ruiz
- Flanders Research Institute for Agriculture, Fisheries and Food (ILVO) , Caritasstraat 39 , 9090 Melle , Belgium
- Faculty of Sciences, Department of Plant Biotechnology and Bioinformatics , Ghent University , Technologiepark Zwijnaarde 71 , 9052 Zwijnaarde , Belgium
| |
Collapse
|
34
|
Qiao X, Li Q, Yin H, Qi K, Li L, Wang R, Zhang S, Paterson AH. Gene duplication and evolution in recurring polyploidization-diploidization cycles in plants. Genome Biol 2019; 20:38. [PMID: 30791939 PMCID: PMC6383267 DOI: 10.1186/s13059-019-1650-2] [Citation(s) in RCA: 463] [Impact Index Per Article: 92.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Accepted: 02/08/2019] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND The sharp increase of plant genome and transcriptome data provide valuable resources to investigate evolutionary consequences of gene duplication in a range of taxa, and unravel common principles underlying duplicate gene retention. RESULTS We survey 141 sequenced plant genomes to elucidate consequences of gene and genome duplication, processes central to the evolution of biodiversity. We develop a pipeline named DupGen_finder to identify different modes of gene duplication in plants. Genes derived from whole-genome, tandem, proximal, transposed, or dispersed duplication differ in abundance, selection pressure, expression divergence, and gene conversion rate among genomes. The number of WGD-derived duplicate genes decreases exponentially with increasing age of duplication events-transposed duplication- and dispersed duplication-derived genes declined in parallel. In contrast, the frequency of tandem and proximal duplications showed no significant decrease over time, providing a continuous supply of variants available for adaptation to continuously changing environments. Moreover, tandem and proximal duplicates experienced stronger selective pressure than genes formed by other modes and evolved toward biased functional roles involved in plant self-defense. The rate of gene conversion among WGD-derived gene pairs declined over time, peaking shortly after polyploidization. To provide a platform for accessing duplicated gene pairs in different plants, we constructed the Plant Duplicate Gene Database. CONCLUSIONS We identify a comprehensive landscape of different modes of gene duplication across the plant kingdom by comparing 141 genomes, which provides a solid foundation for further investigation of the dynamic evolution of duplicate genes.
Collapse
Affiliation(s)
- Xin Qiao
- Centre of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095 China
| | - Qionghou Li
- Centre of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095 China
| | - Hao Yin
- Centre of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095 China
| | - Kaijie Qi
- Centre of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095 China
| | - Leiting Li
- Centre of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095 China
| | - Runze Wang
- Centre of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095 China
| | - Shaoling Zhang
- Centre of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095 China
| | - Andrew H. Paterson
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA 30605 USA
| |
Collapse
|
35
|
Costa LM, Sakakibara H. Sixty Years of Plant and Cell Physiology. PLANT & CELL PHYSIOLOGY 2019; 60:1-3. [PMID: 30605543 DOI: 10.1093/pcp/pcy244] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Affiliation(s)
| | - Hitoshi Sakakibara
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
- RIKEN Center for Sustainable Resource Sciences, Yokohama, Japan
| |
Collapse
|
36
|
Jiang P, Song T, Jiang W, Wang D, Pu B, Luan C. SNP-Based Kompetitive Allele Specific PCR (KASPTM) Method for the Qualification and Quantification of Hop Varieties. JOURNAL OF THE AMERICAN SOCIETY OF BREWING CHEMISTS 2018. [DOI: 10.1080/03610470.2018.1483702] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Peiji Jiang
- Food Science Department, Sichuan Agricultural University, Sichuan, China
- Traditional Fermentation Engineering (Brewing) Department, China National Research Institute of Food and Fermentation Industries, Beijing, China
| | - Tao Song
- Traditional Fermentation Engineering (Brewing) Department, China National Research Institute of Food and Fermentation Industries, Beijing, China
| | - Wei Jiang
- Traditional Fermentation Engineering (Brewing) Department, China National Research Institute of Food and Fermentation Industries, Beijing, China
| | - Deliang Wang
- Traditional Fermentation Engineering (Brewing) Department, China National Research Institute of Food and Fermentation Industries, Beijing, China
| | - Biao Pu
- Food Science Department, Sichuan Agricultural University, Sichuan, China
| | - Chunguang Luan
- Traditional Fermentation Engineering (Brewing) Department, China National Research Institute of Food and Fermentation Industries, Beijing, China
| |
Collapse
|
37
|
Mishra AK, Duraisamy GS, Khare M, Kocábek T, Jakse J, Bříza J, Patzak J, Sano T, Matoušek J. Genome-wide transcriptome profiling of transgenic hop (Humulus lupulus L.) constitutively overexpressing HlWRKY1 and HlWDR1 transcription factors. BMC Genomics 2018; 19:739. [PMID: 30305019 PMCID: PMC6180420 DOI: 10.1186/s12864-018-5125-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Accepted: 09/27/2018] [Indexed: 01/04/2023] Open
Abstract
Background The hop plant (Humulus lupulus L.) is a valuable source of several secondary metabolites, such as flavonoids, bitter acids, and essential oils. These compounds are widely implicated in the beer brewing industry and are having potential biomedical applications. Several independent breeding programs around the world have been initiated to develop new cultivars with enriched lupulin and secondary metabolite contents but met with limited success due to several constraints. In the present work, a pioneering attempt has been made to overexpress master regulator binary transcription factor complex formed by HlWRKY1 and HlWDR1 using a plant expression vector to enhance the level of prenylflavonoid and bitter acid content in the hop. Subsequently, we performed transcriptional profiling using high-throughput RNA-Seq technology in leaves of resultant transformants and wild-type hop to gain in-depth information about the genome-wide functional changes induced by HlWRKY1 and HlWDR1 overexpression. Results The transgenic WW-lines exhibited an elevated expression of structural and regulatory genes involved in prenylflavonoid and bitter acid biosynthesis pathways. In addition, the comparative transcriptome analysis revealed a total of 522 transcripts involved in 30 pathways, including lipids and amino acids biosynthesis, primary carbon metabolism, phytohormone signaling and stress responses were differentially expressed in WW-transformants. It was apparent from the whole transcriptome sequencing that modulation of primary carbon metabolism and other pathways by HlWRKY1 and HlWDR1 overexpression resulted in enhanced substrate flux towards secondary metabolites pathway. The detailed analyses suggested that none of the pathways or genes, which have a detrimental effect on physiology, growth and development processes, were induced on a genome-wide scale in WW-transgenic lines. Conclusions Taken together, our results suggest that HlWRKY1 and HlWDR1 simultaneous overexpression positively regulates the prenylflavonoid and bitter acid biosynthesis pathways in the hop and thus these transgenes are presented as prospective candidates for achieving enhanced secondary metabolite content in the hop. Electronic supplementary material The online version of this article (10.1186/s12864-018-5125-8) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Ajay Kumar Mishra
- Biology Centre of the Czech Academy of Sciences, Institute of Plant Molecular Biology, Department of Molecular Genetics, Branišovská 31, 37005, České Budějovice, Czech Republic
| | - Ganesh Selvaraj Duraisamy
- Biology Centre of the Czech Academy of Sciences, Institute of Plant Molecular Biology, Department of Molecular Genetics, Branišovská 31, 37005, České Budějovice, Czech Republic
| | - Mudra Khare
- Biology Centre of the Czech Academy of Sciences, Institute of Plant Molecular Biology, Department of Molecular Genetics, Branišovská 31, 37005, České Budějovice, Czech Republic
| | - Tomáš Kocábek
- Biology Centre of the Czech Academy of Sciences, Institute of Plant Molecular Biology, Department of Molecular Genetics, Branišovská 31, 37005, České Budějovice, Czech Republic
| | - Jernej Jakse
- Department of Agronomy, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, SI-1000, Ljubljana, Slovenia
| | - Jindřich Bříza
- Biology Centre of the Czech Academy of Sciences, Institute of Plant Molecular Biology, Department of Molecular Genetics, Branišovská 31, 37005, České Budějovice, Czech Republic
| | - Josef Patzak
- Hop Research Institute, Co. Ltd., Kadaňská 2525, 43846, Žatec, Czech Republic
| | - Teruo Sano
- Faculty of Agriculture and Life Science, Department of Applied Biosciences, Hirosaki University, Hirosaki, Aomori, 036-8561, Japan
| | - Jaroslav Matoušek
- Biology Centre of the Czech Academy of Sciences, Institute of Plant Molecular Biology, Department of Molecular Genetics, Branišovská 31, 37005, České Budějovice, Czech Republic.
| |
Collapse
|
38
|
Kirkendall JA, Mitchell CA, Chadwick LR. The Freshening Power of Centennial Hops. JOURNAL OF THE AMERICAN SOCIETY OF BREWING CHEMISTS 2018. [DOI: 10.1080/03610470.2018.1469081] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
|
39
|
van Velzen R, Holmer R, Bu F, Rutten L, van Zeijl A, Liu W, Santuari L, Cao Q, Sharma T, Shen D, Roswanjaya Y, Wardhani TAK, Kalhor MS, Jansen J, van den Hoogen J, Güngör B, Hartog M, Hontelez J, Verver J, Yang WC, Schijlen E, Repin R, Schilthuizen M, Schranz ME, Heidstra R, Miyata K, Fedorova E, Kohlen W, Bisseling T, Smit S, Geurts R. Comparative genomics of the nonlegume Parasponia reveals insights into evolution of nitrogen-fixing rhizobium symbioses. Proc Natl Acad Sci U S A 2018; 115:E4700-E4709. [PMID: 29717040 PMCID: PMC5960304 DOI: 10.1073/pnas.1721395115] [Citation(s) in RCA: 136] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Nodules harboring nitrogen-fixing rhizobia are a well-known trait of legumes, but nodules also occur in other plant lineages, with rhizobia or the actinomycete Frankia as microsymbiont. It is generally assumed that nodulation evolved independently multiple times. However, molecular-genetic support for this hypothesis is lacking, as the genetic changes underlying nodule evolution remain elusive. We conducted genetic and comparative genomics studies by using Parasponia species (Cannabaceae), the only nonlegumes that can establish nitrogen-fixing nodules with rhizobium. Intergeneric crosses between Parasponia andersonii and its nonnodulating relative Trema tomentosa demonstrated that nodule organogenesis, but not intracellular infection, is a dominant genetic trait. Comparative transcriptomics of P. andersonii and the legume Medicago truncatula revealed utilization of at least 290 orthologous symbiosis genes in nodules. Among these are key genes that, in legumes, are essential for nodulation, including NODULE INCEPTION (NIN) and RHIZOBIUM-DIRECTED POLAR GROWTH (RPG). Comparative analysis of genomes from three Parasponia species and related nonnodulating plant species show evidence of parallel loss in nonnodulating species of putative orthologs of NIN, RPG, and NOD FACTOR PERCEPTION Parallel loss of these symbiosis genes indicates that these nonnodulating lineages lost the potential to nodulate. Taken together, our results challenge the view that nodulation evolved in parallel and raises the possibility that nodulation originated ∼100 Mya in a common ancestor of all nodulating plant species, but was subsequently lost in many descendant lineages. This will have profound implications for translational approaches aimed at engineering nitrogen-fixing nodules in crop plants.
Collapse
Affiliation(s)
- Robin van Velzen
- Laboratory of Molecular Biology, Department of Plant Sciences, Wageningen University, 6708 PB, Wageningen, The Netherlands
| | - Rens Holmer
- Laboratory of Molecular Biology, Department of Plant Sciences, Wageningen University, 6708 PB, Wageningen, The Netherlands
- Bioinformatics Group, Department of Plant Sciences, Wageningen University, 6708 PB, Wageningen, The Netherlands
| | - Fengjiao Bu
- Laboratory of Molecular Biology, Department of Plant Sciences, Wageningen University, 6708 PB, Wageningen, The Netherlands
| | - Luuk Rutten
- Laboratory of Molecular Biology, Department of Plant Sciences, Wageningen University, 6708 PB, Wageningen, The Netherlands
| | - Arjan van Zeijl
- Laboratory of Molecular Biology, Department of Plant Sciences, Wageningen University, 6708 PB, Wageningen, The Netherlands
| | - Wei Liu
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Luca Santuari
- Laboratory of Molecular Biology, Department of Plant Sciences, Wageningen University, 6708 PB, Wageningen, The Netherlands
| | - Qingqin Cao
- Laboratory of Molecular Biology, Department of Plant Sciences, Wageningen University, 6708 PB, Wageningen, The Netherlands
- College of Biological Science and Engineering & Beijing Collaborative Innovation Center for Eco-Environmental Improvement with Forestry and Fruit Trees, Beijing University of Agriculture, Beijing 102206, China
| | - Trupti Sharma
- Laboratory of Molecular Biology, Department of Plant Sciences, Wageningen University, 6708 PB, Wageningen, The Netherlands
| | - Defeng Shen
- Laboratory of Molecular Biology, Department of Plant Sciences, Wageningen University, 6708 PB, Wageningen, The Netherlands
| | - Yuda Roswanjaya
- Laboratory of Molecular Biology, Department of Plant Sciences, Wageningen University, 6708 PB, Wageningen, The Netherlands
| | - Titis A K Wardhani
- Laboratory of Molecular Biology, Department of Plant Sciences, Wageningen University, 6708 PB, Wageningen, The Netherlands
| | - Maryam Seifi Kalhor
- Laboratory of Molecular Biology, Department of Plant Sciences, Wageningen University, 6708 PB, Wageningen, The Netherlands
| | - Joelle Jansen
- Laboratory of Molecular Biology, Department of Plant Sciences, Wageningen University, 6708 PB, Wageningen, The Netherlands
| | - Johan van den Hoogen
- Laboratory of Molecular Biology, Department of Plant Sciences, Wageningen University, 6708 PB, Wageningen, The Netherlands
| | - Berivan Güngör
- Laboratory of Molecular Biology, Department of Plant Sciences, Wageningen University, 6708 PB, Wageningen, The Netherlands
| | - Marijke Hartog
- Laboratory of Molecular Biology, Department of Plant Sciences, Wageningen University, 6708 PB, Wageningen, The Netherlands
| | - Jan Hontelez
- Laboratory of Molecular Biology, Department of Plant Sciences, Wageningen University, 6708 PB, Wageningen, The Netherlands
| | - Jan Verver
- Laboratory of Molecular Biology, Department of Plant Sciences, Wageningen University, 6708 PB, Wageningen, The Netherlands
| | - Wei-Cai Yang
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Elio Schijlen
- Bioscience, Wageningen University and Research, 6708 PB, Wageningen, The Netherlands
| | - Rimi Repin
- Sabah Parks, 88806 Kota Kinabalu, Malaysia
| | - Menno Schilthuizen
- Naturalis Biodiversity Center, 2333 CR, Leiden, The Netherlands
- Institute for Tropical Biology and Conservation, Universiti Malaysia Sabah, 88999 Kota Kinabalu, Malaysia
- Institute for Biology Leiden, Leiden University, 2333 BE, Leiden, The Netherlands
| | - M Eric Schranz
- Biosystematics Group, Department of Plant Sciences, Wageningen University, 6708 PB, Wageningen, The Netherlands
| | - Renze Heidstra
- Laboratory of Molecular Biology, Department of Plant Sciences, Wageningen University, 6708 PB, Wageningen, The Netherlands
| | - Kana Miyata
- Laboratory of Molecular Biology, Department of Plant Sciences, Wageningen University, 6708 PB, Wageningen, The Netherlands
| | - Elena Fedorova
- Laboratory of Molecular Biology, Department of Plant Sciences, Wageningen University, 6708 PB, Wageningen, The Netherlands
| | - Wouter Kohlen
- Laboratory of Molecular Biology, Department of Plant Sciences, Wageningen University, 6708 PB, Wageningen, The Netherlands
| | - Ton Bisseling
- Laboratory of Molecular Biology, Department of Plant Sciences, Wageningen University, 6708 PB, Wageningen, The Netherlands
| | - Sandra Smit
- Bioinformatics Group, Department of Plant Sciences, Wageningen University, 6708 PB, Wageningen, The Netherlands
| | - Rene Geurts
- Laboratory of Molecular Biology, Department of Plant Sciences, Wageningen University, 6708 PB, Wageningen, The Netherlands;
| |
Collapse
|
40
|
Nibert ML, Vong M, Fugate KK, Debat HJ. Evidence for contemporary plant mitoviruses. Virology 2018; 518:14-24. [PMID: 29438872 PMCID: PMC6668999 DOI: 10.1016/j.virol.2018.02.005] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Revised: 02/02/2018] [Accepted: 02/03/2018] [Indexed: 10/18/2022]
Abstract
Mitoviruses have small RNA(+) genomes, replicate in mitochondria, and have been shown to infect only fungi to date. For this report, sequences that appear to represent nearly complete plant mitovirus genomes were recovered from publicly available transcriptome data. Twenty of the refined sequences, 2684-2898 nt long and derived from 10 different species of land plants, appear to encompass the complete coding regions of contemporary plant mitoviruses, which furthermore constitute a monophyletic cluster within genus Mitovirus. Complete coding sequences of several of these viruses were recovered from multiple transcriptome (but not genome) studies of the same plant species and also from multiple plant tissues. Crop plants among implicated hosts include beet and hemp. Other new results suggest that such genuine plant mitoviruses were immediate ancestors to endogenized mitovirus elements now widespread in land plant genomes. Whether these mitoviruses are wholly cryptic with regard to plant health remains to be investigated.
Collapse
Affiliation(s)
- Max L Nibert
- Department of Microbiology & Immunobiology, Harvard Medical School, Boston, MA 02115, USA.
| | - Minh Vong
- Department of Microbiology & Immunobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Karen K Fugate
- Sugarbeet and Potato Research, United States Department of Agriculture (USDA), Agricultural Research Service (ARS), Red River Valley Agricultural Research Center, Fargo, ND 58102, USA
| | - Humberto J Debat
- Instituto de Patología Vegetal, Centro de Investigaciones Agropecuarias, Instituto Nacional de Tecnología Agropecuaria (IPAVE-CIAP-INTA), X5020ICA, Córdoba, Argentina
| |
Collapse
|
41
|
Pisupati R, Vergara D, Kane NC. Diversity and evolution of the repetitive genomic content in Cannabis sativa. BMC Genomics 2018; 19:156. [PMID: 29466945 PMCID: PMC5822635 DOI: 10.1186/s12864-018-4494-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Accepted: 01/24/2018] [Indexed: 01/13/2023] Open
Abstract
Background The repetitive content of the genome, once considered to be “junk DNA”, is in fact an essential component of genomic architecture and evolution. In this study, we used the genomes of three varieties of Cannabis sativa, three varieties of Humulus lupulus and one genotype of Morus notabilis to explore their repetitive content using a graph-based clustering method, designed to explore and compare repeat content in genomes that have not been fully assembled. Results The repetitive content in the C. sativa genome is mainly composed of the retrotransposons LTR/Copia and LTR/Gypsy (14% and 14.8%, respectively), ribosomal DNA (2%), and low-complexity sequences (29%). We observed a recent copy number expansion in some transposable element families. Simple repeats and low complexity regions of the genome show higher intra and inter species variation. Conclusions As with other sequenced genomes, the repetitive content of C. sativa’s genome exhibits a wide range of evolutionary patterns. Some repeat types have patterns of diversity consistent with expansions followed by losses in copy number, while others may have expanded more slowly and reached a steady state. Still, other repetitive sequences, particularly ribosomal DNA (rDNA), show signs of concerted evolution playing a major role in homogenizing sequence variation. Electronic supplementary material The online version of this article (10.1186/s12864-018-4494-3) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Rahul Pisupati
- Department of Biotechnology, Indian Institute of Technology, Kharagpur, 721302, India.,Present address: Gregor Mendel Institute, Dr. Bohr-gasse 3, Vienna, 1030, Austria
| | - Daniela Vergara
- Ecology and Evolutionary Biology, University of Colorado, Boulder, 80302, USA
| | - Nolan C Kane
- Ecology and Evolutionary Biology, University of Colorado, Boulder, 80302, USA.
| |
Collapse
|
42
|
De Keukeleire D. A Happy, Hoppy Odyssey: From a Flavorsome Hobby to a Dream Job. JOURNAL OF THE AMERICAN SOCIETY OF BREWING CHEMISTS 2018. [DOI: 10.1094/asbcj-2017-4795-01] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
|
43
|
Zhang D, Easterling KA, Pitra NJ, Coles MC, Buckler ES, Bass HW, Matthews PD. Non-Mendelian Single-Nucleotide Polymorphism Inheritance and Atypical Meiotic Configurations are Prevalent in Hop. THE PLANT GENOME 2017; 10. [PMID: 29293819 DOI: 10.3835/plantgenome2017.04.0032] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Hop ( L.) breeding programs seek to exploit genetic resources for bitter flavor, aroma, and disease resistance. However, these efforts have been thwarted by segregation distortion including female-biased sex ratios. To better understand the transmission genetics of hop, we genotyped 4512 worldwide accessions of hop, including cultivars, landraces, and over 100 wild accessions using a genotyping-by-sequencing (GBS) approach. From the resulting ∼1.2 million single-nucleotide polymorphisms (SNPs), prequalified GBS markers were validated by inferences in population structures and phylogeny. Analysis of pseudo-testcross (Pt) mapping data from F families revealed mixed patterns of Mendelian and non-Mendelian segregation. Three-dimensional (3D) cytogenetic analysis of late meiotic prophase nuclei from two wild and two cultivated hop revealed conspicuous and prevalent occurrences of multiple, atypical, nondisomic chromosome complexes including autosomes. We used genome-wide association studies (GWAS) and fixation index (F) analysis to demonstrate selection mapping of genetic loci for key traits including sex, bitter acids, and drought tolerance. Among the possible mechanisms underlying the observed segregation distortion from the genomic data analysis, the cytogenetic analysis points to meiotic chromosome behavior as one of the contributing factors. The findings shed light on long-standing questions on the unusual transmission genetics and phenotypic variation in hop, with major implications for breeding, cultivation, and the natural history of .
Collapse
|
44
|
Schluttenhofer C, Yuan L. Challenges towards Revitalizing Hemp: A Multifaceted Crop. TRENDS IN PLANT SCIENCE 2017; 22:917-929. [PMID: 28886910 DOI: 10.1016/j.tplants.2017.08.004] [Citation(s) in RCA: 101] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2017] [Revised: 08/03/2017] [Accepted: 08/09/2017] [Indexed: 05/21/2023]
Abstract
Hemp has been an important crop throughout human history for food, fiber, and medicine. Despite significant progress made by the international research community, the basic biology of hemp plants remains insufficiently understood. Clear objectives are needed to guide future research. As a semi-domesticated plant, hemp has many desirable traits that require improvement, including eliminating seed shattering, enhancing the quantity and quality of stem fiber, and increasing the accumulation of phytocannabinoids. Methods to manipulate the sex of hemp plants will also be important for optimizing yields of seed, fiber, and cannabinoids. Currently, research into trait improvement is hindered by the lack of molecular techniques adapted to hemp. Here we review how addressing these limitations will help advance our knowledge of plant biology and enable us to fully domesticate and maximize the agronomic potential of this promising crop.
Collapse
Affiliation(s)
- Craig Schluttenhofer
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY 40546, USA; The Kentucky Tobacco Research and Development Center, University of Kentucky, Lexington, KY 40546, USA
| | - Ling Yuan
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY 40546, USA; The Kentucky Tobacco Research and Development Center, University of Kentucky, Lexington, KY 40546, USA; South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.
| |
Collapse
|
45
|
Kobayashi M, Ohyanagi H, Takanashi H, Asano S, Kudo T, Kajiya-Kanegae H, Nagano AJ, Tainaka H, Tokunaga T, Sazuka T, Iwata H, Tsutsumi N, Yano K. Heap: a highly sensitive and accurate SNP detection tool for low-coverage high-throughput sequencing data. DNA Res 2017; 24:397-405. [PMID: 28498906 PMCID: PMC5737671 DOI: 10.1093/dnares/dsx012] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Accepted: 04/20/2017] [Indexed: 12/30/2022] Open
Abstract
Recent availability of large-scale genomic resources enables us to conduct so called genome-wide association studies (GWAS) and genomic prediction (GP) studies, particularly with next-generation sequencing (NGS) data. The effectiveness of GWAS and GP depends on not only their mathematical models, but the quality and quantity of variants employed in the analysis. In NGS single nucleotide polymorphism (SNP) calling, conventional tools ideally require more reads for higher SNP sensitivity and accuracy. In this study, we aimed to develop a tool, Heap, that enables robustly sensitive and accurate calling of SNPs, particularly with a low coverage NGS data, which must be aligned to the reference genome sequences in advance. To reduce false positive SNPs, Heap determines genotypes and calls SNPs at each site except for sites at the both ends of reads or containing a minor allele supported by only one read. Performance comparison with existing tools showed that Heap achieved the highest F-scores with low coverage (7X) restriction-site associated DNA sequencing reads of sorghum and rice individuals. This will facilitate cost-effective GWAS and GP studies in this NGS era. Code and documentation of Heap are freely available from https://github.com/meiji-bioinf/heap (29 March 2017, date last accessed) and our web site (http://bioinf.mind.meiji.ac.jp/lab/en/tools.html (29 March 2017, date last accessed)).
Collapse
Affiliation(s)
- Masaaki Kobayashi
- Bioinformatics Laboratory, Department of Life Sciences, School of Agriculture, Meiji University, Kanagawa 214-8571, Japan
| | - Hajime Ohyanagi
- Bioinformatics Laboratory, Department of Life Sciences, School of Agriculture, Meiji University, Kanagawa 214-8571, Japan.,King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - Hideki Takanashi
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan
| | - Satomi Asano
- Bioinformatics Laboratory, Department of Life Sciences, School of Agriculture, Meiji University, Kanagawa 214-8571, Japan
| | - Toru Kudo
- Bioinformatics Laboratory, Department of Life Sciences, School of Agriculture, Meiji University, Kanagawa 214-8571, Japan
| | - Hiromi Kajiya-Kanegae
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan
| | - Atsushi J Nagano
- Faculty of Agriculture, Ryukoku University, Shiga 520-2194, Japan.,PRESTO, Japan Science and Technology Agency, Japan.,Center for Ecological Research, Kyoto University, Shiga 520-2113, Japan
| | - Hitoshi Tainaka
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan
| | | | - Takashi Sazuka
- Bioscience and Biotechnology Center, Nagoya University, Aichi 464-8601, Japan
| | - Hiroyoshi Iwata
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan
| | - Nobuhiro Tsutsumi
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan
| | - Kentaro Yano
- Bioinformatics Laboratory, Department of Life Sciences, School of Agriculture, Meiji University, Kanagawa 214-8571, Japan
| |
Collapse
|
46
|
Kappagantu M, Bullock JM, Nelson ME, Eastwell KC. Hop stunt viroid: Effect on Host (Humulus lupulus) Transcriptome and Its Interactions With Hop Powdery Mildew (Podospheara macularis). MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2017; 30:842-851. [PMID: 28703029 DOI: 10.1094/mpmi-03-17-0071-r] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Viroids are the smallest known plant pathogens that exploit host systems for their replication and cause diseases in many hosts. In this study, the host response of hop plants to Hop stunt viroid (HSVd) infection was studied through transcriptome analysis. RNA sequence analysis of hop leaves infected with HSVd revealed dynamic changes in hop gene expression. Defense-related genes and genes involved in lipid and terpenoid metabolism are the major categories that showed differential expression due to HSVd infection. Additionally, the effect of HSVd on development of hop powdery mildew (Podospheara macularis) (HPM) was studied. Transcriptome analysis followed by quantitative reverse transcription-polymerase chain reaction analysis showed that transcript levels of pathogenesis-related (PR) genes such as PR protein 1, chitinase, and thaumatin-like protein genes are induced in leaves infected with HPM alone. The response in these genes to HPM is significantly down-regulated in leaves with HSVd-HPM mixed infection. These results confirm that HSVd alters host metabolism, physiology, and plant defense responses. Nevertheless, in detached leaf assays, HPM consistently expanded faster on HSVd-negative leaves relative to HSVd-positive leaves. Although HSVd infection suppresses elements associated with the host immunity response, infection by HSVd is antagonistic to HPM infection of hops.
Collapse
Affiliation(s)
- Madhu Kappagantu
- Department of Plant Pathology, Washington State University-IAREC, 24106 N Bunn Road, Prosser 99350, WA, U.S.A
| | - Jeff M Bullock
- Department of Plant Pathology, Washington State University-IAREC, 24106 N Bunn Road, Prosser 99350, WA, U.S.A
| | - Mark E Nelson
- Department of Plant Pathology, Washington State University-IAREC, 24106 N Bunn Road, Prosser 99350, WA, U.S.A
| | - Kenneth C Eastwell
- Department of Plant Pathology, Washington State University-IAREC, 24106 N Bunn Road, Prosser 99350, WA, U.S.A
| |
Collapse
|
47
|
Progar V, Jakše J, Štajner N, Radišek S, Javornik B, Berne S. Comparative transcriptional analysis of hop responses to infection with Verticillium nonalfalfae. PLANT CELL REPORTS 2017; 36:1599-1613. [PMID: 28698905 PMCID: PMC5602066 DOI: 10.1007/s00299-017-2177-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2017] [Accepted: 07/04/2017] [Indexed: 05/13/2023]
Abstract
KEY MESSAGE Dynamic transcriptome profiling revealed excessive, yet ineffective, immune response to V. nonalfalfae infection in susceptible hop, global gene downregulation in shoots of resistant hop and only a few infection-associated genes in roots. Hop (Humulus lupulus L.) production is hampered by Verticillium wilt, a disease predominantly caused by the soil-borne fungus Verticillium nonalfalfae. Only a few hop cultivars exhibit resistance towards it and mechanisms of this resistance have not been discovered. In this study, we compared global transcriptional responses in roots and shoots of resistant and susceptible hop plants infected by a lethal strain of V. nonalfalfae. Time-series differential gene expression profiles between infected and mock inoculated plants were determined and subjected to network-based analysis of functional enrichment. In the resistant hop cultivar, a remarkably low number of genes were differentially expressed in roots in response to V. nonalfalfae infection, while the majority of differentially expressed genes were down-regulated in shoots. The most significantly affected genes were related to cutin biosynthesis, cell wall biogenesis, lateral root development and terpenoid biosynthesis. On the other hand, susceptible hop exhibited a strong defence response in shoots and roots, including increased expression of genes associated with plant responses, such as innate immunity, wounding, jasmonic acid pathway and chitinase activity. Strong induction of defence-associated genes in susceptible hop and a low number of infection-responsive genes in the roots of resistant hop are consistent with previous findings, confirming the pattern of excessive response of the susceptible cultivar, which ultimately fails to protect the plant from V. nonalfalfae. This research offers a multifaceted overview of transcriptional responses of susceptible and resistant hop cultivars to V. nonalfalfae infection and represents a valuable resource in the study of this plant-pathogen interaction.
Collapse
Affiliation(s)
- Vasja Progar
- Department of Agronomy, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Jernej Jakše
- Department of Agronomy, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Nataša Štajner
- Department of Agronomy, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Sebastjan Radišek
- Plant Protection Department, Slovenian Institute of Hop Research and Brewing, Žalec, Slovenia
| | - Branka Javornik
- Department of Agronomy, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Sabina Berne
- Department of Agronomy, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| |
Collapse
|
48
|
Pokorn T, Radišek S, Javornik B, Štajner N, Jakše J. Development of hop transcriptome to support research into host-viroid interactions. PLoS One 2017; 12:e0184528. [PMID: 28886174 PMCID: PMC5590963 DOI: 10.1371/journal.pone.0184528] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2017] [Accepted: 08/25/2017] [Indexed: 01/08/2023] Open
Abstract
Viroids, the smallest known pathogens, unable to encode any proteins, can cause severe diseases in their host plants. One of the proposed mechanisms of their pathogenicity includes silencing the host's genes via viroid-derived small RNAs, which are products of the host's immune response to the viroid's double stranded RNA. Humulus lupulus (hop) plants are hosts to several viroids; two of them, HLVd and CBCVd, are interesting models for studying host-viroid interactions, due to the symptomless infection of the former and severe stunting disease caused by the latter. To study these interactions, we constructed a deep hop NGS transcriptome based on 35 Gb paired-end sequencing data assembled into over 74 Mb of contigs. These transcripts were used for in-silico prediction of target transcripts of vd-sRNA of the two aforementioned viroids, using two different software tools. Prediction models revealed that 1062 and 1387 hop transcripts share nucleotide similarities with HLVd- and CBCVd-derived small RNAs, respectively, so they could be silenced in an RNA interference process. Furthermore, we selected 17 transcripts from 4 groups of targets involved in the metabolism of plant hormones, small RNA biogenesis, transcripts with high complementarity with viroid-derived small RNAs and transcripts targeted by CBCVd-derived small RNAs with high cellular concentrations. Their expression was monitored by reverse transcription quantitative PCR performed using leaf, flower and cone samples. Additionally, the expression of 5 pathogenesis related genes was monitored. Expression analysis confirmed high expression levels of four pathogenesis related genes in leaves of HLVd and CBCVd infected hop plants. Expression fluctuations were observed for the majority of targets, with possible evidence of downregulation of GATA transcription factor by CBCVd- and of linoleate 13S-lipoxygenase by HLVd-derived small RNAs. These results provide a deep transcriptome of hop and the first insights into complex viroid-hop plant interactions.
Collapse
Affiliation(s)
- Tine Pokorn
- Agronomy Department, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Sebastjan Radišek
- Department of Plant Protection, Slovenian Institute of Hop Research and Brewing, Žalec, Slovenia
| | - Branka Javornik
- Agronomy Department, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Nataša Štajner
- Agronomy Department, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Jernej Jakše
- Agronomy Department, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| |
Collapse
|
49
|
Champagne A, Boutry M. A comprehensive proteome map of glandular trichomes of hop (Humulus lupulus
L.) female cones: Identification of biosynthetic pathways of the major terpenoid-related compounds and possible transport proteins. Proteomics 2017; 17. [DOI: 10.1002/pmic.201600411] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Revised: 01/23/2017] [Accepted: 02/09/2017] [Indexed: 11/06/2022]
Affiliation(s)
- Antoine Champagne
- Institut des Sciences de la Vie; Université catholique de Louvain; Louvain-la-Neuve Belgium
| | - Marc Boutry
- Institut des Sciences de la Vie; Université catholique de Louvain; Louvain-la-Neuve Belgium
| |
Collapse
|
50
|
Kawada T, Shiraishi A, Aoyama M, Satake H. Transcriptomes of the Premature and Mature Ovaries of an Ascidian, Ciona intestinalis. Front Endocrinol (Lausanne) 2017; 8:88. [PMID: 28484427 PMCID: PMC5402223 DOI: 10.3389/fendo.2017.00088] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Accepted: 04/05/2017] [Indexed: 01/26/2023] Open
Affiliation(s)
- Tsuyoshi Kawada
- Bioorganic Research Institute, Suntory Foundation for Life Sciences, Kyoto, Japan
| | - Akira Shiraishi
- Bioorganic Research Institute, Suntory Foundation for Life Sciences, Kyoto, Japan
| | - Masato Aoyama
- Faculty of Bioscience, Nara Woman’s University, Nara, Japan
| | - Honoo Satake
- Bioorganic Research Institute, Suntory Foundation for Life Sciences, Kyoto, Japan
- *Correspondence: Honoo Satake,
| |
Collapse
|