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Zhang Z, Zhang G, Zhang X, Zhang H, Xie J, Zeng R, Guo B, Huang L. The complete chloroplast genome sequence and phylogenetic relationship analysis of Eomecon chionantha, one species unique to China. JOURNAL OF PLANT RESEARCH 2024; 137:575-587. [PMID: 38652407 DOI: 10.1007/s10265-024-01539-y] [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: 06/26/2023] [Accepted: 02/29/2024] [Indexed: 04/25/2024]
Abstract
Eomecon chionantha Hance, an endemic species in China, has a long medical history in Chinese ethnic minority medicine and is known for its anti-inflammatory and analgesic effects. However, studies of E. chionantha are lacking. In this study, we investigated the characteristics of the E. chionantha chloroplast genome and determined the taxonomic position of E. chionantha in Papaveraceae via phylogenetic analysis. In addition, we determined molecular markers to identify E. chionantha at the molecular level by comparing the chloroplast genomes of E. chionantha and its closely related species. The complete chloroplast genomic information indicated that E. chionantha chloroplast DNA (178,808 bp) contains 99 protein-coding genes, 8 rRNAs, and 37 tRNAs. Meanwhile, we were able to identify a total of 54 simple sequence repeats through our analysis. Our findings from the phylogenetic analysis suggest that E. chionantha shares a close relationship with four distinct species, namely Macleaya microcarpa, Coreanomecon hylomeconoides, Hylomecon japonica, and Chelidonium majus. Additionally, using the Kimura two-parameter model, we successfully identified five hypervariable regions (ycf4-cemA, ycf3-trnS-GGA, trnC-GCA-petN, rpl32-trnL-UAG, and psbI-trnS-UGA). To the best of our knowledge, this is the first report of the complete chloroplast genome of E. chionantha, providing a scientific reference for further understanding of E. chionantha from the perspective of the chloroplast genome and establishing a solid foundation for the future identification, taxonomic determination and evolutionary analysis of this species.
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Affiliation(s)
- Zhi Zhang
- Key Laboratory of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100193, China
- School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| | - Guoshuai Zhang
- Key Laboratory of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100193, China
| | - Xinke Zhang
- Key Laboratory of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100193, China
| | - Huihui Zhang
- Key Laboratory of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100193, China
| | - Junbo Xie
- Key Laboratory of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100193, China
| | - Rui Zeng
- College of Pharmacy, Southwest Minzu University, Chengdu, 610041, China
| | - Baolin Guo
- Key Laboratory of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100193, China.
| | - Linfang Huang
- Key Laboratory of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100193, China.
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Yilmaz S, Batuman O. Co-Infection of Tomato Brown Rugose Fruit Virus and Pepino Mosaic Virus in Grocery Tomatoes in South Florida: Prevalence and Genomic Diversity. Viruses 2023; 15:2305. [PMID: 38140546 PMCID: PMC10748365 DOI: 10.3390/v15122305] [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: 11/01/2023] [Revised: 11/21/2023] [Accepted: 11/21/2023] [Indexed: 12/24/2023] Open
Abstract
Tomato brown rugose fruit virus (ToBRFV) is an economically important seed and mechanically transmitted pathogen of significant importance to tomato production around the globe. Synergistic interaction with pepino mosaic virus (PepMV), another seed and mechanically transmitted virus, and long-distance dissemination of these two viruses via contaminated tomato fruits through global marketing were previously suggested. In 2019, we detected both viruses in several grocery store-purchased tomatoes in South Florida, USA. In this study, to identify potential sources of inoculum, co-infection status, prevalence, and genomic diversity of these viruses, we surveyed symptomatic and asymptomatic imported tomatoes sold in ten different groceries in four cities in South Florida. According to the product labels, all collected tomatoes originated from Canada, Mexico, or repacking houses in the United States. With high prevalence levels, 86.5% of the collected samples were infected with ToBRFV, 90% with PepMV alone, and 73% were mixed-infected. The phylogenetic study showed no significant correlations between ToBRFV genomic diversity and the tomato label origin. Phylogenetic analysis of PepMV isolates revealed the prevalence of the PepMV strains, Chilean (CH2) and recombinant (US2). The results of this study highlight the continual presence of PepMV and ToBRFV in imported tomatoes in Florida grocery stores.
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Affiliation(s)
| | - Ozgur Batuman
- Southwest Florida Research and Education Center, Department of Plant Pathology, University of Florida, Immokalee, FL 34142, USA;
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Esmaeilzadeh F, Santosa AI, Çelik A, Koolivand D. Revealing an Iranian Isolate of Tomato Brown Rugose Fruit Virus: Complete Genome Analysis and Mechanical Transmission. Microorganisms 2023; 11:2434. [PMID: 37894095 PMCID: PMC10608917 DOI: 10.3390/microorganisms11102434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 09/11/2023] [Accepted: 09/17/2023] [Indexed: 10/29/2023] Open
Abstract
An analysis of the complete genome sequence of a novel isolate of tomato brown rugose fruit virus (ToBRFV) obtained from tomatoes in Iran and named ToBRFV-Ir is presented in this study. Comprehensive phylogenetic analysis utilizing key viral proteins, including 126 KDa, 183 KDa, movement protein (MP), and coat protein (CP), as well as the complete genome sequence, classified ToBRFV-Ir and 65 isolates from GenBank into three distinct clades. Notably, genetic diversity assessment revealed relatively low variability among the isolates, irrespective of their geographical or clade affiliation. Natural selection analysis based on the complete genome sequence showed that dN/dS values were consistently <1, indicating the prevailing role of negative selection across all populations. Analyses using the Recombination Detection Program and SplitsTree found no evidence of recombination events or signals in the complete genome sequence of the tested isolates. Thus, these results suggest that the genetic composition of ToBRFV remains stable without significant genetic exchange or recombination events occurring. A simple arithmetic comparison of the patristic distances and dates suggested that the time to the most recent common ancestor (TMRCA) of the ToBRFV populations is approximately 0.8 up to 2.7 with the closest tobamoviruses. An evolutionary study of the tested isolates from various countries based on the complete genome suggests Peruvian ancestry. The ToBRF-Ir isolate was successfully transmitted through mechanical inoculations to Solanum lycopersicum and Nicotiana rustica. These findings shed light on the genetic dynamics and transmission mechanisms of ToBRFV, providing valuable insights into its molecular characteristics and potential spread among susceptible plant species.
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Affiliation(s)
- Fereshteh Esmaeilzadeh
- Department of Plant Protection, Faculty of Agriculture, University of Zanjan, Zanjan 45371-38791, Iran (D.K.)
| | - Adyatma Irawan Santosa
- Department of Plant Protection, Faculty of Agriculture, Universitas Gadjah Mada, Yogyakarta 55281, Indonesia
| | - Ali Çelik
- Department of Plant Protection, Faculty of Agriculture, Bolu Abant İzzet Baysal University, Bolu 14030, Turkey
| | - Davoud Koolivand
- Department of Plant Protection, Faculty of Agriculture, University of Zanjan, Zanjan 45371-38791, Iran (D.K.)
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Salem NM, Jewehan A, Aranda MA, Fox A. Tomato Brown Rugose Fruit Virus Pandemic. ANNUAL REVIEW OF PHYTOPATHOLOGY 2023; 61:137-164. [PMID: 37268006 DOI: 10.1146/annurev-phyto-021622-120703] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Tomato brown rugose fruit virus (ToBRFV) is an emerging tobamovirus. It was first reported in 2015 in Jordan in greenhouse tomatoes and now threatens tomato and pepper crops around the world. ToBRFV is a stable and highly infectious virus that is easily transmitted by mechanical means and via seeds, which enables it to spread locally and over long distances. The ability of ToBRFV to infect tomato plants harboring the commonly deployed Tm resistance genes, as well as pepper plants harboring the L resistance alleles under certain conditions, limits the ability to prevent damage from the virus. The fruit production and quality of ToBRFV-infected tomato and pepper plants can be drastically affected, thus significantly impacting their market value. Herein, we review the current information and discuss the latest areas of research on this virus, which include its discovery and distribution, epidemiology, detection, and prevention and control measures, that could help mitigate the ToBRFV disease pandemic.
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Affiliation(s)
- Nida' M Salem
- Department of Plant Protection, School of Agriculture, The University of Jordan, Amman, Jordan;
| | - Ahmad Jewehan
- Applied Plant Genomics Group, Institute of Genetics and Biotechnology, Hungarian University of Agriculture and Life Sciences, Gödöllő, Hungary
| | - Miguel A Aranda
- Centro de Edafología y Biología Aplicada del Segura, Consejo Superior de Investigaciones Científicas (CSIC), Murcia, Spain
| | - Adrian Fox
- Fera Science, Sand Hutton, York, United Kingdom
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
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Pouraziz P, Yousefi M, Santosa AI, Koolivand D. Genetic Variation between Asian and Mediterranean Populations of Cucurbit Aphid-Borne Yellows Virus. Viruses 2023; 15:1714. [PMID: 37632056 PMCID: PMC10457933 DOI: 10.3390/v15081714] [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: 06/26/2023] [Revised: 07/16/2023] [Accepted: 07/17/2023] [Indexed: 08/27/2023] Open
Abstract
Viral symptoms, such as yellowing, leaf deformation, mottling, vein clearing, and reduced yield, were observed in cucurbits in Iran. This study aimed to detect the main suspected causal agent, cucurbit aphid-borne yellows virus (CABYV), in Iran and analyze the genetic diversity among isolates. Two hundred samples were collected from different growing areas between 2019 and 2022. PCR amplification was performed on the P3 and P4 genes. The sequences of 18 Iranian isolates were obtained and deposited in GenBank. Recombination, phylogenetic, and population genetics studies were then carried out for the complete genome and all ORFs sequences, together with other isolates in GenBank. The nucleotide identities of the overlapped ORF3/4 sequences of Iranian isolates were 94.8 to 99.5% among themselves, and with other tested isolates ranging from 94.3 to 99.3%. Phylogenetic trees based on the complete genome and the overlapped ORF3/4 showed two major clades, namely Asian and Mediterranean, and the new isolates from Iran were positioned in both clades. The obtained results also suggest that all the genes and two clades of CABYV populations were under negative selection pressure. Furthermore, rare gene flow between these two clades (FST > 0.33) confirmed the high genetic separation among them.
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Affiliation(s)
- Parastoo Pouraziz
- Department of Plant Protection, Faculty of Agriculture, University of Zanjan, Zanjan 45371-38111, Iran (D.K.)
| | - Milad Yousefi
- Department of Plant Protection, Faculty of Agriculture, University of Zanjan, Zanjan 45371-38111, Iran (D.K.)
| | - Adyatma Irawan Santosa
- Department of Plant Protection, Faculty of Agriculture, Universitas Gadjah Mada, Yogyakarta 55281, Indonesia
| | - Davoud Koolivand
- Department of Plant Protection, Faculty of Agriculture, University of Zanjan, Zanjan 45371-38111, Iran (D.K.)
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Çelik A, Morca AF, Coşkan S, Santosa AI. Global Population Structure of Apple Mosaic Virus (ApMV, Genus Ilarvirus). Viruses 2023; 15:1221. [PMID: 37376521 DOI: 10.3390/v15061221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Revised: 05/02/2023] [Accepted: 05/09/2023] [Indexed: 06/29/2023] Open
Abstract
The gene sequence data for apple mosaic virus (ApMV) in NCBI GenBank were analyzed to determine the phylogeny and population structure of the virus at a global level. The phylogenies of the movement protein (MP) and coat protein (CP) genes, encoded by RNA3, were shown to be identical and consisted of three lineages but did not closely correlate with those of P1 and P2, suggesting the presence of recombinant isolates. Recombination Detection Program (RDP v.4.56) detected significant recombination signal in the P1 region of K75R1 (KY883318) and Apple (HE574162) and the P2 region of Apple (HE574163) and CITH GD (MN822138). Observation on several diversity parameters suggested that the isolates in group 3 had higher divergence among them, compared to isolates in groups 1 and 2. The neutrality tests assigned positive values to P1, indicating that only this region experiencing balanced or contracting selection. Comparisons of the three phylogroups demonstrated high Fixation index (FST) values and confirmed genetic separation and the lack of gene flow among them. Additionally, ±500 bp of partial MP + 'intergenic region' + partial CP coding regions of two Turkish isolates from apple and seven from hazelnut were sequenced and determined that their phylogenetic positions fell within group 1 and 3, respectively.
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Affiliation(s)
- Ali Çelik
- Department of Plant Protection, Faculty of Agriculture, Bolu Abant İzzet Baysal University, 14030 Bolu, Türkiye
- Scientifical Industrial and Technological Application and Research Center, Bolu Abant İzzet Baysal University, 14030 Bolu, Türkiye
| | - Ali Ferhan Morca
- Directorate of Central Plant Protection Research Institute, Gayret Mah. Fatih Sultan Mehmet Bulv., Yenimahalle, 06172 Ankara, Türkiye
| | - Sevgi Coşkan
- Directorate of Central Plant Protection Research Institute, Gayret Mah. Fatih Sultan Mehmet Bulv., Yenimahalle, 06172 Ankara, Türkiye
| | - Adyatma Irawan Santosa
- Department of Plant Protection, Faculty of Agriculture, Universitas Gadjah Mada, Jl. Flora No. 1, Sleman, Yogyakarta 55281, Indonesia
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Topkaya Ş, Çelik A, Santosa AI, Jones RAC. Molecular Analysis of the Global Population of Potato Virus S Redefines Its Phylogeny, and Has Crop Biosecurity Implications. Viruses 2023; 15:v15051104. [PMID: 37243190 DOI: 10.3390/v15051104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 04/20/2023] [Accepted: 04/28/2023] [Indexed: 05/28/2023] Open
Abstract
In 2020, 264 samples were collected from potato fields in the Turkish provinces of Bolu, Afyon, Kayseri and Niğde. RT-PCR tests, with primers which amplified its coat protein (CP), detected potato virus S (PVS) in 35 samples. Complete CP sequences were obtained from 14 samples. Phylogenetic analysis using non-recombinant sequences of (i) the 14 CP's, another 8 from Tokat province and 73 others from GenBank; and (ii) 130 complete ORF, RdRp and TGB sequences from GenBank, found that they fitted within phylogroups, PVSI, PVSII or PVSIII. All Turkish CP sequences were in PVSI, clustering within five subclades. Subclades 1 and 4 were in three to four provinces, whereas 2, 3 and 5 were in one province each. All four genome regions were under strong negative selection constraints (ω = 0.0603-0.1825). Considerable genetic variation existed amongst PVSI and PVSII isolates. Three neutrality test methods showed PVSIII remained balanced whilst PVSI and PVSII underwent population expansion. The high fixation index values assigned to all PVSI, PVSII and PVSIII comparisons supported subdivision into three phylogroups. As it spreads more readily by aphid and contact transmission, and may elicit more severe symptoms in potato, PVSII spread constitutes a biosecurity threat for countries still free from it.
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Affiliation(s)
- Şerife Topkaya
- Department of Plant Protection, Faculty of Agriculture, Tokat Gaziosmanpasa University, Tokat 60250, Turkey
| | - Ali Çelik
- Department of Plant Protection, Faculty of Agriculture, Bolu Abant İzzet Baysal University, Bolu 14030, Turkey
| | - Adyatma Irawan Santosa
- Department of Plant Protection, Faculty of Agriculture, Universitas Gadjah Mada, Yogyakarta 55281, Indonesia
| | - Roger A C Jones
- The UWA Institute of Agriculture, The University of Western Australia, Crawley, WA 6009, Australia
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Abou Kubaa R, Amoia SS, Altamura G, Minafra A, Chiumenti M, Cillo F. Nanopore Technology Applied to Targeted Detection of Tomato Brown Rugose Fruit Virus Allows Sequencing of Related Viruses and the Diagnosis of Mixed Infections. PLANTS (BASEL, SWITZERLAND) 2023; 12:999. [PMID: 36903859 PMCID: PMC10005216 DOI: 10.3390/plants12050999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 02/10/2023] [Accepted: 02/17/2023] [Indexed: 06/18/2023]
Abstract
Tomato (Solanum lycopersicum) plants from a commercial glasshouse were identified with symptoms compatible with a tomato brown rugose fruit virus (ToBRFV) infection. Reverse transcription-PCR and quantitative PCR confirmed the presence of ToBRFV. Subsequently, the same RNA sample and a second from tomato plants infected with a similar tobamovirus, tomato mottle mosaic virus (ToMMV), were extracted and processed for high-throughput sequencing with the Oxford Nanopore Technology (ONT). For the targeted detection of ToBRFV, the two libraries were synthesized by using six ToBRFV sequence-specific primers in the reverse transcription step. This innovative target enrichment technology enabled deep coverage sequencing of ToBRFV, with 30% of the total reads mapping to the target virus genome and 57% mapping to the host genome. The same set of primers applied to the ToMMV library generated 5% of the total reads mapping to the latter virus, indicating that sequencing of similar, non-target viral sequences was also allowed. Further, the complete genome of pepino mosaic virus (PepMV) was also sequenced from the ToBRFV library, thus suggesting that, even using multiple sequence-specific primers, a low rate of off-target sequencing can usefully provide additional information on unexpected viral species coinfecting the same samples in an individual assay. These results demonstrate that targeted nanopore sequencing can specifically identify viral agents and has sufficient sensitivity towards non-target organisms to provide evidence of mixed virus infections.
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Affiliation(s)
- Raied Abou Kubaa
- Institute for Sustainable Plant Protection—National Research Council, 70126 Bari, Italy
| | - Serafina Serena Amoia
- Institute for Sustainable Plant Protection—National Research Council, 70126 Bari, Italy
- Department of Soil, Plant and Food Sciences, University of Bari Aldo Moro, 70126 Bari, Italy
| | - Giuseppe Altamura
- Institute for Sustainable Plant Protection—National Research Council, 70126 Bari, Italy
- Research, Experimentation and Education Centre in Agriculture (CRSFA) “Basile Caramia”, Via Cisternino 281, 70010 Locorotondo, Italy
| | - Angelantonio Minafra
- Institute for Sustainable Plant Protection—National Research Council, 70126 Bari, Italy
| | - Michela Chiumenti
- Institute for Sustainable Plant Protection—National Research Council, 70126 Bari, Italy
| | - Fabrizio Cillo
- Institute for Sustainable Plant Protection—National Research Council, 70126 Bari, Italy
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