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Wei F, Liang X, Shi JC, Luo JN, Qiu LJ, Li XX, Lu LJ, Wen YQ, Feng JY. Pan-Genomic Analysis Identifies the Chinese Strain as a New Subspecies of Xanthomonas fragariae. PLANT DISEASE 2024; 108:45-49. [PMID: 37555725 DOI: 10.1094/pdis-05-23-0933-sc] [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: 08/10/2023]
Abstract
Xanthomonas fragariae is classified as a quarantine pathogen by the European and Mediterranean Plant Protection Organization. It commonly induces typical angular leaf spot (ALS) symptoms in strawberry leaves. X. fragariae strains from China (YL19, SHAQP01, and YLX21) exhibit ALS symptoms in leaves and more severe symptoms of dry cavity rot in strawberry crowns. Conversely, strains from other countries do not cause severe dry cavity rot symptoms in strawberries. After employing multilocus sequence analysis (MLSA), average nucleotide identity (ANI), and amino acid identity (AAI), we determined that Chinese strains of X. fragariae are genetically distinct from other strains and can be considered a new subspecies. Subsequent analysis of 63 X. fragariae genomes published at NCBI using IPGA and EDGAR3.0 revealed the pan-genomic profile, with 1,680 shared genes present in all 63 strains, including 71 virulence-related genes. Additionally, we identified 123 genes exclusive to all the Chinese strains, encompassing 12 virulence-related genes. The qRT-PCR analysis demonstrated that the expression of XopD, XopG1, CE8, GT2, and GH121 out of 12 virulence-related genes of Chinese strains (YL19) exhibited a constant increase in the early stages (6, 24, 54, and 96 hours postinoculation [hpi]) of strawberry leaf infected by YL19. So, the presence of XopD, XopG1, CE8, GT2, and GH121 in Chinese strains may play important roles in the early infection process of Chinese strains. These findings offer novel insights into comprehending the population structure and variation in the pathogenic capacity of X. fragariae.
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Affiliation(s)
- Feng Wei
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China
- Key Laboratory of Protected Horticulture Engineering in Northwest China, Ministry of Agriculture, Yangling 712100, Shaanxi, China
| | - Xia Liang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China
- Key Laboratory of Protected Horticulture Engineering in Northwest China, Ministry of Agriculture, Yangling 712100, Shaanxi, China
| | - Jian-Cheng Shi
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China
- Key Laboratory of Protected Horticulture Engineering in Northwest China, Ministry of Agriculture, Yangling 712100, Shaanxi, China
| | - Jing-Nan Luo
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China
- Key Laboratory of Protected Horticulture Engineering in Northwest China, Ministry of Agriculture, Yangling 712100, Shaanxi, China
| | - Li-Juan Qiu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China
- Key Laboratory of Protected Horticulture Engineering in Northwest China, Ministry of Agriculture, Yangling 712100, Shaanxi, China
| | - Xi-Xuan Li
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China
- Key Laboratory of Protected Horticulture Engineering in Northwest China, Ministry of Agriculture, Yangling 712100, Shaanxi, China
| | - Li-Juan Lu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China
- Key Laboratory of Protected Horticulture Engineering in Northwest China, Ministry of Agriculture, Yangling 712100, Shaanxi, China
| | - Ying-Qiang Wen
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Jia-Yue Feng
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China
- Key Laboratory of Protected Horticulture Engineering in Northwest China, Ministry of Agriculture, Yangling 712100, Shaanxi, China
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Chan DTC, Baldwin GS, Bernstein HC. Revealing the Host-Dependent Nature of an Engineered Genetic Inverter in Concordance with Physiology. BIODESIGN RESEARCH 2023; 5:0016. [PMID: 37849456 PMCID: PMC10432152 DOI: 10.34133/bdr.0016] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 07/17/2023] [Indexed: 10/19/2023] Open
Abstract
Broad-host-range synthetic biology is an emerging frontier that aims to expand our current engineerable domain of microbial hosts for biodesign applications. As more novel species are brought to "model status," synthetic biologists are discovering that identically engineered genetic circuits can exhibit different performances depending on the organism it operates within, an observation referred to as the "chassis effect." It remains a major challenge to uncover which genome-encoded and biological determinants will underpin chassis effects that govern the performance of engineered genetic devices. In this study, we compared model and novel bacterial hosts to ask whether phylogenomic relatedness or similarity in host physiology is a better predictor of genetic circuit performance. This was accomplished using a comparative framework based on multivariate statistical approaches to systematically demonstrate the chassis effect and characterize the performance dynamics of a genetic inverter circuit operating within 6 Gammaproteobacteria. Our results solidify the notion that genetic devices are strongly impacted by the host context. Furthermore, we formally determined that hosts exhibiting more similar metrics of growth and molecular physiology also exhibit more similar performance of the genetic inverter, indicating that specific bacterial physiology underpins measurable chassis effects. The result of this study contributes to the field of broad-host-range synthetic biology by lending increased predictive power to the implementation of genetic devices in less-established microbial hosts.
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Affiliation(s)
- Dennis Tin Chat Chan
- Faculty of Biosciences, Fisheries and Economics, UiT, The Arctic University of Norway, 9019 Tromsø, Norway
| | - Geoff S. Baldwin
- Department of Life Sciences, Imperial College London, South Kensington, London SW7 2AZ, UK
- Imperial College Centre for Synthetic Biology, Imperial College London, South Kensington, London SW7 2AZ, UK
| | - Hans C. Bernstein
- Faculty of Biosciences, Fisheries and Economics, UiT, The Arctic University of Norway, 9019 Tromsø, Norway
- The Arctic Centre for Sustainable Energy, UiT, The Arctic University of Norway, 9019 Tromsø, Norway
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Wei F, Wang D, Fan S, Shi J, Cai X, Li Y, Ma Y, Wen Y, Feng J. Complete Genome Sequence Resource for Xanthomonas fragariae Causing Crown Infection Pockets in Strawberry. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2022; 35:170-173. [PMID: 34645282 DOI: 10.1094/mpmi-05-21-0123-a] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Xanthomonas fragariae is a global quarantine pathogen, which typically inflicts angular leaf spots. In the present study, we report a new 4.11-Mb high-quality genome sequence of X. fragariae YL19. YL19 can cause the typical angular leaf spot symptoms on strawberry plants in China as well as crown infection pocket symptoms. This new symptom has not been reported in other X. fragariae. Compared with typical X. fragariae strains, including PD885, NBC2815, PD5205, Fap21, and Fap29, the genome and plasmid in YL19 were smaller in size, lacking 109 coding genes, and have more carbohydrate-active enzyme and secondary metabolism genes. The YL19 genome ought to clarify the molecular mechanisms of genome evolution, host adaptation, and pathological process of X. fragariae and help improve strawberry management strategies.[Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Feng Wei
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China
- Key Laboratory of Protected Horticulture Engineering in Northwest China, Ministry of Agriculture, Yangling 712100, Shaanxi, China
| | - Danjuan Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China
- Key Laboratory of Protected Horticulture Engineering in Northwest China, Ministry of Agriculture, Yangling 712100, Shaanxi, China
| | - Sihao Fan
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China
- Key Laboratory of Protected Horticulture Engineering in Northwest China, Ministry of Agriculture, Yangling 712100, Shaanxi, China
| | - Jiancheng Shi
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China
- Key Laboratory of Protected Horticulture Engineering in Northwest China, Ministry of Agriculture, Yangling 712100, Shaanxi, China
| | - Xiaolin Cai
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China
- Key Laboratory of Protected Horticulture Engineering in Northwest China, Ministry of Agriculture, Yangling 712100, Shaanxi, China
| | - Yulian Li
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China
- Key Laboratory of Protected Horticulture Engineering in Northwest China, Ministry of Agriculture, Yangling 712100, Shaanxi, China
| | - Yangyang Ma
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China
- Key Laboratory of Protected Horticulture Engineering in Northwest China, Ministry of Agriculture, Yangling 712100, Shaanxi, China
| | - Yingqiang Wen
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Jiayue Feng
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China
- Key Laboratory of Protected Horticulture Engineering in Northwest China, Ministry of Agriculture, Yangling 712100, Shaanxi, China
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Draft Genome Sequences of Two Xanthomonas fragariae Strains. Microbiol Resour Announc 2021; 10:10/16/e00138-21. [PMID: 33888499 PMCID: PMC8063642 DOI: 10.1128/mra.00138-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Xanthomonas fragariae is the causal agent of angular leaf spot of strawberry. Short-read sequences were generated for two X. fragariae strains with different virulence phenotypes on the Illumina HiSeq 2000 platform. The genome sequences will contribute to a better understanding of pathogen evolution and the genes contributing to virulence in X. fragariae. Xanthomonas fragariae is the causal agent of angular leaf spot of strawberry. Short-read sequences were generated for two X. fragariae strains with different virulence phenotypes on the Illumina HiSeq 2000 platform. These genome sequences will contribute to a better understanding of pathogen evolution and the genes contributing to virulence in X. fragariae.
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Puławska J, Kałużna M, Warabieda W, Pothier JF, Gétaz M, van der Wolf JM. Transcriptome analysis of Xanthomonas fragariae in strawberry leaves. Sci Rep 2020; 10:20582. [PMID: 33239704 PMCID: PMC7688646 DOI: 10.1038/s41598-020-77612-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 11/09/2020] [Indexed: 11/21/2022] Open
Abstract
Xanthomonas fragariae is a quarantine bacterial pathogen that causes angular leaf spot on strawberry. The aim of our study was to analyse the mechanism of interaction of this bacterium with its host plant at the transcriptome level. For this purpose, mRNAs of X. fragariae growing in Wilbrink’s medium and from infected strawberry cv. Elsanta plants were isolated and sequenced using the Illumina MiSeq platform. The expression profiles of the bacteria in Wilbrink’s medium and in planta were very diverse. Of the 3939 CDSs recorded, 1995 had significantly different expression in planta (966 and 1029 genes were down- and upregulated, respectively). Among the genes showing increased expression in planta, those with eggNOG/COG (evolutionary genealogy of genes: Non-supervised Orthologous Groups/Cluster of Orthologous Groups) categories associated with bacterial cell motility, signal transduction, transport and metabolism of inorganic ions and carbohydrates and transcription were overrepresented. Among the genes with the most increased expression in planta, genes primarily associated with flagella synthesis and chemotaxis were found. It is also interesting to note that out of the 31 genes localized on a plasmid, 16 were expressed differently in planta, which may indicate their potential role in plant–pathogen interactions. Many genes with differentiated expression that were localized on chromosome and plasmid encode proteins of unknown function.
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Affiliation(s)
- Joanna Puławska
- Department of Phytopathology, Research Institute of Horticulture, 96-100, Skierniewice, Poland.
| | - Monika Kałużna
- Department of Phytopathology, Research Institute of Horticulture, 96-100, Skierniewice, Poland
| | - Wojciech Warabieda
- Department of Phytopathology, Research Institute of Horticulture, 96-100, Skierniewice, Poland
| | - Joël F Pothier
- Environmental Genomics and Systems Biology Research Group, Institute for Natural Resource Sciences, Zurich University of Applied Sciences (ZHAW), Wädenswil, Switzerland
| | - Michael Gétaz
- Environmental Genomics and Systems Biology Research Group, Institute for Natural Resource Sciences, Zurich University of Applied Sciences (ZHAW), Wädenswil, Switzerland
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Gétaz M, Puławska J, Smits TH, Pothier JF. Host-Pathogen Interactions between Xanthomonas fragariae and Its Host Fragaria × ananassa Investigated with a Dual RNA-Seq Analysis. Microorganisms 2020; 8:E1253. [PMID: 32824783 PMCID: PMC7465820 DOI: 10.3390/microorganisms8081253] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 08/11/2020] [Accepted: 08/14/2020] [Indexed: 12/31/2022] Open
Abstract
Strawberry is economically important and widely grown, but susceptible to a large variety of phytopathogenic organisms. Among them, Xanthomonas fragariae is a quarantine bacterial pathogen threatening strawberry productions by causing angular leaf spots. Using whole transcriptome sequencing, the gene expression of both plant and bacteria in planta was analyzed at two time points, 12 and 29 days post inoculation, in order to compare the pathogen and host response between the stages of early visible and of well-developed symptoms. Among 28,588 known genes in strawberry and 4046 known genes in X. fragariae expressed at both time points, a total of 361 plant and 144 bacterial genes were significantly differentially expressed, respectively. The identified higher expressed genes in the plants were pathogen-associated molecular pattern receptors and pathogenesis-related thaumatin encoding genes, whereas the more expressed early genes were related to chloroplast metabolism as well as photosynthesis related coding genes. Most X. fragariae genes involved in host interaction, recognition, and pathogenesis were lower expressed at late-phase infection. This study gives a first insight into the interaction of X. fragariae with its host. The strawberry plant changed gene expression in order to consistently adapt its metabolism with the progression of infection.
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Affiliation(s)
- Michael Gétaz
- Environmental Genomics and Systems Biology Research Group, Institute of Natural Resource Sciences, Zurich University of Applied Sciences (ZHAW), CH-8820 Wädenswil, Switzerland; (M.G.); (T.H.S.)
| | - Joanna Puławska
- Department of Phytopathology, Research Institute of Horticulture, 96-100 Skierniewice, Poland;
| | - Theo H.M. Smits
- Environmental Genomics and Systems Biology Research Group, Institute of Natural Resource Sciences, Zurich University of Applied Sciences (ZHAW), CH-8820 Wädenswil, Switzerland; (M.G.); (T.H.S.)
| | - Joël F. Pothier
- Environmental Genomics and Systems Biology Research Group, Institute of Natural Resource Sciences, Zurich University of Applied Sciences (ZHAW), CH-8820 Wädenswil, Switzerland; (M.G.); (T.H.S.)
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Smits THM. The importance of genome sequence quality to microbial comparative genomics. BMC Genomics 2019; 20:662. [PMID: 31429698 PMCID: PMC6701015 DOI: 10.1186/s12864-019-6014-5] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2019] [Accepted: 08/05/2019] [Indexed: 12/16/2022] Open
Abstract
The quality of microbial genome sequences has been a concern ever since the emergence of genome sequencing. The quality of the genome assemblies is dependent on the sequencing technology used and the aims for which the sequence was generated. Novel sequencing and bioinformatics technologies are not intrinsically better than the older technologies, although they are generally more efficient. In this correspondence, the importance for comparative genomics of additional manual assembly efforts over autoassembly and careful annotation is emphasized.
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Affiliation(s)
- Theo H M Smits
- Environmental Genomics and Systems Biology Research Group, Institute of Natural Resource Sciences (IUNR), Zurich University of Applied Sciences ZHAW, Wädenswil, Switzerland.
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8
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mRNA extraction of Xanthomonas fragariae in strawberry and validation of reference genes for the RT-qPCR for study of bacterial gene expression. Mol Biol Rep 2019; 46:5723-5733. [PMID: 31368022 DOI: 10.1007/s11033-019-05006-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Accepted: 07/26/2019] [Indexed: 01/11/2023]
Abstract
This is the first study which describes a unique procedure of isolating of high-quality, intact RNA from strawberry leaves of Xanthomonas fragariae, three most suitable reference genes, crucial for the normalization of RT-qPCR data for this pathogen and accurate expression analysis of target genes. In our study, various mathematic algorithms: NormFinder geNorm, BestKeeper, the delta CT method, RefFinder were adopted for validation of most stable reference genes from nine candidate genes (ffh, glyA, gyrA, gyrB, proC, pykA, recA, rpoB, rpoD). The analyses allowing to select three most suitable pioneer reference genes, gyrB, ffh, and pykA, that we recommend for the normalization of RT-qPCR data and for the study of the expression of target genes in Xf. Moreover, their combination as references allowed for an accurate expression analysis and computation of the fold change of the flhF and iroN2 genes in Xf. These two genes are important for the success of the colonization of plant tissue and pathogenicity and sequences of primers designed to study these genes, are presented.
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Gétaz M, Krijger M, Rezzonico F, Smits THM, van der Wolf JM, Pothier JF. Genome-based population structure analysis of the strawberry plant pathogen Xanthomonas fragariae reveals two distinct groups that evolved independently before its species description. Microb Genom 2018; 4:e000189. [PMID: 29874158 PMCID: PMC6113873 DOI: 10.1099/mgen.0.000189] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Accepted: 05/11/2018] [Indexed: 11/18/2022] Open
Abstract
Xanthomonas fragariae is a quarantine organism in Europe, causing angular leaf spots on strawberry plants. It is spreading worldwide in strawberry-producing regions due to import of plant material through trade and human activities. In order to resolve the population structure at the strain level, we have employed high-resolution molecular typing tools on a comprehensive strain collection representing global and temporal distribution of the pathogen. Clustered regularly interspaced short palindromic repeat regions (CRISPRs) and variable number of tandem repeats (VNTRs) were identified within the reference genome of X. fragariae LMG 25863 as a potential source of variation. Strains from our collection were whole-genome sequenced and used in order to identify variable spacers and repeats for discriminative purpose. CRISPR spacer analysis and multiple-locus VNTR analysis (MLVA) displayed a congruent population structure, in which two major groups and a total of four subgroups were revealed. The two main groups were genetically separated before the first X. fragariae isolate was described and are potentially responsible for the worldwide expansion of the bacterial disease. Three primer sets were designed for discriminating CRISPR-associated markers in order to streamline group determination of novel isolates. Overall, this study describes typing methods to discriminate strains and monitor the pathogen population structure, more especially in the view of a new outbreak of the pathogen.
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Affiliation(s)
- Michael Gétaz
- Environmental Genomics and Systems Biology Research Group, Institute of Natural Resource Sciences, Zurich University of Applied Sciences (ZHAW), CH-8820 Wädenswil, Switzerland
| | - Marjon Krijger
- Wageningen University and Research, Wageningen, the Netherlands
| | - Fabio Rezzonico
- Environmental Genomics and Systems Biology Research Group, Institute of Natural Resource Sciences, Zurich University of Applied Sciences (ZHAW), CH-8820 Wädenswil, Switzerland
| | - Theo H. M. Smits
- Environmental Genomics and Systems Biology Research Group, Institute of Natural Resource Sciences, Zurich University of Applied Sciences (ZHAW), CH-8820 Wädenswil, Switzerland
| | | | - Joël F. Pothier
- Environmental Genomics and Systems Biology Research Group, Institute of Natural Resource Sciences, Zurich University of Applied Sciences (ZHAW), CH-8820 Wädenswil, Switzerland
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