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Kutsuwada Y, Tomotake S, Tsuda H, Watanabe K, Matsumoto A, Iwamoto S, Mizuno N. NSPlex: an efficient method to analyze non-specific peaks amplified using commercial STR kits. Int J Legal Med 2024:10.1007/s00414-024-03234-y. [PMID: 38613626 DOI: 10.1007/s00414-024-03234-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 04/08/2024] [Indexed: 04/15/2024]
Abstract
Commercial short tandem repeat (STR) kits exclusively contain human-specific primers; however, various non-human organisms with high homology to the STR kit's primer sequences can cause cross-reactivity. Owing to the proprietary nature of the primers in STR kits, the origins and sequences of most non-specific peaks (NSPs) remain unclear. Such NSPs can complicate data interpretation between the casework and reference samples; thus, we developed "NSPlex", an efficient method to discover the biological origins of NSPs. We used leftover STR kit amplicons after capillary electrophoresis and performed advanced bioinformatics analyses using next-generation sequencing followed by BLAST nucleotide searches. Using our method, we could successfully identify NSP generated from PCR amplicons of a sample mixture of human DNA and DNA extracted from matcha powder (finely ground powder of green tea leaves and previously known as a potential source of NSP). Our results showed our method is efficient for NSP analysis without the need for the primer information as in commercial STR kits.
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Affiliation(s)
- Yukinobu Kutsuwada
- DNA Center Kashiwa Branch, Criminal Identification Division, National Police Agency, 6-3-1 Kashiwanoha, Kashiwa, Chiba, 277-0882, Japan.
- Division of Human Genetics, Center for Molecular Medicine, Jichi Medical University, Tochigi, Japan.
| | - Sho Tomotake
- Forensic Science Laboratory, Okayama Prefectural Police Headquarter, Okayama, Japan
| | - Hidetoshi Tsuda
- Division of Human Genetics, Center for Molecular Medicine, Jichi Medical University, Tochigi, Japan
| | - Kazuhisa Watanabe
- Division of Human Genetics, Center for Molecular Medicine, Jichi Medical University, Tochigi, Japan
| | - Ayumi Matsumoto
- Division of Human Genetics, Center for Molecular Medicine, Jichi Medical University, Tochigi, Japan
| | - Sadahiko Iwamoto
- Division of Human Genetics, Center for Molecular Medicine, Jichi Medical University, Tochigi, Japan
| | - Natsuko Mizuno
- Fourth Biology Section, First Department of Forensic Science, National Research Institute of Police Science, Chiba, Japan
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Luo Y, Cheng Y, Liu L, Fu D. The complete mitogenome of the pond wolf spider Pardosa pseudoannulata, with phylogenetic implications for the Lycosidae. Mitochondrial DNA B Resour 2024; 9:475-478. [PMID: 38617814 PMCID: PMC11011225 DOI: 10.1080/23802359.2024.2337791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Accepted: 03/27/2024] [Indexed: 04/16/2024] Open
Abstract
The pond wolf spider Pardosa pseudoannulata Bösenberg & Strand, 1906 (Araneae: Lycosidae) is an important predator of agricultural pests in southern, eastern and southeastern Asia. Here, we report the complete mitogenome of this spider reconstructed from Illumina sequencing data. The circular mitogenome length is 14,533 bp with the nucleotide composition A (33.3%), C (8.2%), G (15.2%), and T (43.3%). The P. pseudoannulata mitogenome comprises 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes, and a control region. Phylogenetic analyses of Lycosidae mitogenomes supported the monophyly of the subfamily Pardosinae and the two genera Pardosa and Alopecosa, and indicated the polyphyly of the subfamily Lycosinae and the paraphyly of its type genus Lycosa. In this study, P. pseudoannulata is the closest relative to P. pusiola. These results provide useful genetic information for future studies on the diversity, phylogeny, and evolution for wolf spiders.
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Affiliation(s)
- Yufa Luo
- School of Life and Environmental Sciences, Key Laboratory of Wetland Biodiversity of the Jianhu Basin of Shaoxing, Shaoxing University, Shaoxing, Zhejiang, China
| | - Ying Cheng
- School of Life and Environmental Sciences, Key Laboratory of Wetland Biodiversity of the Jianhu Basin of Shaoxing, Shaoxing University, Shaoxing, Zhejiang, China
| | - Lijuan Liu
- School of Life and Environmental Sciences, Key Laboratory of Wetland Biodiversity of the Jianhu Basin of Shaoxing, Shaoxing University, Shaoxing, Zhejiang, China
| | - Dan Fu
- School of Life and Environmental Sciences, Key Laboratory of Wetland Biodiversity of the Jianhu Basin of Shaoxing, Shaoxing University, Shaoxing, Zhejiang, China
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Durango-Manrique YS, López-Rubio A, Gutiérrez LA, Isaza JP, Gómez GF. Mitochondrial genome comparison and phylogenetic position of Fannia pusio among the Calyptratae flies. Heliyon 2024; 10:e27697. [PMID: 38524611 PMCID: PMC10958369 DOI: 10.1016/j.heliyon.2024.e27697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 02/07/2024] [Accepted: 03/05/2024] [Indexed: 03/26/2024] Open
Abstract
Fannia pusio, the chicken dung fly species, remains unexplored despite its forensic, sanitary, and veterinary importance in the Nearctic and Neotropical regions. In this study, we obtained the complete mitochondrial genome of Fannia pusio for the first time using next-generation sequencing. We compared it with previously published mitogenomes of the genus from the Palearctic region, and its phylogenetic position was studied based on the concatenated protein-coding genes (PCGs) dataset of Calyptratae flies. The circular mitochondrial genome of F. pusio is 16,176 bp in length, with a high A + T content (78.3%), whose gene synteny, codon usage analysis, and amino acid frequency are similar to previously reported Fannia mitogenomes. All PCGs underwent purifying selection except the nad2 gene. Interspecific K2P distances of PCGs of Fannia yielded an average of 12.4% (8.1%-21.1%). The Fannia genus is monophyletic and closely related to Muscidae based on molecular data. Further taxonomic sampling is required to deep into the phylogenetic relationships of the originally proposed species-groups and subgroups within the genus. These results provide a valuable dataset for studying the mitochondrial genome evolution and a resource for the taxonomy and systematics of Fannia.
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Affiliation(s)
- Yesica S Durango-Manrique
- Grupo de investigación Bioforense, Facultad de Derecho y Ciencias Forenses, Tecnológico de Antioquia, Institución Universitaria, Medellín, Colombia
| | - Andrés López-Rubio
- Grupo de investigación Bioforense, Facultad de Derecho y Ciencias Forenses, Tecnológico de Antioquia, Institución Universitaria, Medellín, Colombia
| | - Lina A Gutiérrez
- Grupo Biología de Sistemas, Escuela de Ciencias de La Salud, Facultad de Medicina, Universidad Pontificia Bolivariana, Medellín, Colombia
| | - Juan P Isaza
- Grupo Biología de Sistemas, Escuela de Ciencias de La Salud, Facultad de Medicina, Universidad Pontificia Bolivariana, Medellín, Colombia
| | - Giovan F Gómez
- Universidad Nacional de Colombia - Sede de La Paz - Dirección Académica, Escuela de Pregrados - Km 9 vía Valledupar - La Paz, La Paz, Colombia
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Lanh PT, Duong BT, Thu HT, Hoa NT, Quyen DV. Comprehensive analysis of the microbiome in Apis cerana honey highlights honey as a potential source for the isolation of beneficial bacterial strains. PeerJ 2024; 12:e17157. [PMID: 38560453 PMCID: PMC10981410 DOI: 10.7717/peerj.17157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Accepted: 03/04/2024] [Indexed: 04/04/2024] Open
Abstract
Background Honey is a nutritious food made by bees from nectar and sweet deposits of flowering plants and has been used for centuries as a natural remedy for wound healing and other bacterial infections due to its antibacterial properties. Honey contains a diverse community of bacteria, especially probiotic bacteria, that greatly affect the health of bees and their consumers. Therefore, understanding the microorganisms in honey can help to ensure the quality of honey and lead to the identification of potential probiotic bacteria. Methods Herein, the bacteria community in honey produced by Apis cerana was investigated by applying the next-generation sequencing (NGS) method for the V3-V4 hypervariable regions of the bacterial 16S rRNA gene. In addition, lactic acid bacteria (LAB) in the honey sample were also isolated and screened for in vitro antimicrobial activity. Results The results showed that the microbiota of A. cerana honey consisted of two major bacterial phyla, Firmicutes (50%; Clostridia, 48.2%) and Proteobacteria (49%; Gammaproteobacteria, 47.7%). Among the 67 identified bacterial genera, the three most predominant genera were beneficial obligate anaerobic bacteria, Lachnospiraceae (48.14%), followed by Gilliamella (26.80%), and Enterobacter (10.16%). Remarkably, among the identified LAB, Lactobacillus kunkeei was found to be the most abundant species. Interestingly, the isolated L. kunkeei strains exhibited antimicrobial activity against some pathogenic bacteria in honeybees, including Klebsiella spp., Escherichia coli, Enterococcus faecalis, Pseudomonas aeruginosa and Staphylococcus aureus. This underscores the potential candidacy of L. kunkeei for developing probiotics for medical use. Taken together, our results provided new insights into the microbiota community in the A. cerana honey in Hanoi, Vietnam, highlighting evidence that honey can be an unexplored source for isolating bacterial strains with potential probiotic applications in honeybees and humans.
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Affiliation(s)
- Pham T. Lanh
- Laboratory of Molecular Microbiology, Institute of Biotechnology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
- University of Science and Technology of Hanoi, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Bui T.T. Duong
- Laboratory of Molecular Microbiology, Institute of Biotechnology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Ha T. Thu
- Laboratory of Molecular Microbiology, Institute of Biotechnology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Nguyen T. Hoa
- Laboratory of Molecular Microbiology, Institute of Biotechnology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Dong Van Quyen
- Laboratory of Molecular Microbiology, Institute of Biotechnology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
- University of Science and Technology of Hanoi, Vietnam Academy of Science and Technology, Hanoi, Vietnam
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He B, Liu Z, Wang X, Li M, Lin X, Xiao Q, Hu J. Dosage and exposure time effects of two micro(nono)plastics on arbuscular mycorrhizal fungal diversity in two farmland soils planted with pepper (Capsicum annuum L.). Sci Total Environ 2024; 917:170216. [PMID: 38278273 DOI: 10.1016/j.scitotenv.2024.170216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Revised: 01/02/2024] [Accepted: 01/14/2024] [Indexed: 01/28/2024]
Abstract
As emerging environmental pollutants, micro(nano)plastics (MPs) like polyethylene terephthalate (PET) and low-density polyethylene (LDPE) have adverse effects on terrestrial biota and ecosystem function. However, the performance and roles of soil arbuscular mycorrhizal (AM) fungi in MPs-contaminated vegetable fields are poorly understood. Thus, a 120-day pot experiment was conducted to test the impacts of two input levels of either PET (~13 μm) or LDPE (~500 nm) on AM fungal diversity and pepper (Capsicum annuum L.) growth in two farmland soils collected from Nanjing (NJ) and Chongqing (CQ), respectively. In the vast majority of cases, 1 % rather than 0.1 % of both MPs greatly decreased the observed richness, Shannon and Simpson's indices, and Pielou's evenness of AM fungi, and decreased mycorrhizal colonization, root and shoot biomasses, fruit yield, and leaf superoxide dismutase, peroxidase, and catalase activities of pepper, while increased leaf malondialdehyde content. From day 40 to 120, the inhibition of either diversity or vitality of AM fungi by 1 % and 0.1 % of MPs gradually increased and weakened, respectively. Compared with PET, LDPE with substantially smaller particle size was more toxic to mycorrhization at day 40, but no longer at day 120. Almost all plant parameters significantly correlated to mycorrhizal colonization, which significantly correlated to both Shannon and Simpson's indices of AM fungi, and soil pH, available P and K concentrations, and alkaline phosphatase activity. All diversity indices of AM fungi clearly negatively correlated to soil pH from 4.4 to 5.6 for the NJ soil and from 5.3 to 6.5 for the CQ soil, and also positively to mineral N and negatively to available P concentrations for the NJ and CQ soils, respectively. Thus, the study emphasized that high input of MPs significantly inhibited soil AM fungal diversity and vitality and thereby vegetable growth via changing soil pH and major nutrient availability.
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Affiliation(s)
- Baiping He
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; School of Biology, Food and Environment, Hefei University, Hefei 230601, China
| | - Zihao Liu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xin Wang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Minghui Li
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Xiangui Lin
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Qingqing Xiao
- School of Biology, Food and Environment, Hefei University, Hefei 230601, China.
| | - Junli Hu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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Ryder D, Stone D, Minardi D, Riley A, Avant J, Cross L, Soeffker M, Davidson D, Newman A, Thomson P, Darby C, van Aerle R. De novo assembly and annotation of the Patagonian toothfish (Dissostichus eleginoides) genome. BMC Genomics 2024; 25:233. [PMID: 38438840 PMCID: PMC10910785 DOI: 10.1186/s12864-024-10141-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 02/19/2024] [Indexed: 03/06/2024] Open
Abstract
BACKGROUND Patagonian toothfish (Dissostichus eleginoides) is an economically and ecologically important fish species in the family Nototheniidae. Juveniles occupy progressively deeper waters as they mature and grow, and adults have been caught as deep as 2500 m, living on or in just above the southern shelves and slopes around the sub-Antarctic islands of the Southern Ocean. As apex predators, they are a key part of the food web, feeding on a variety of prey, including krill, squid, and other fish. Despite its importance, genomic sequence data, which could be used for more accurate dating of the divergence between Patagonian and Antarctic toothfish, or establish whether it shares adaptations to temperature with fish living in more polar or equatorial climes, has so far been limited. RESULTS A high-quality D. eleginoides genome was generated using a combination of Illumina, PacBio and Omni-C sequencing technologies. To aid the genome annotation, the transcriptome derived from a variety of toothfish tissues was also generated using both short and long read sequencing methods. The final genome assembly was 797.8 Mb with a N50 scaffold length of 3.5 Mb. Approximately 31.7% of the genome consisted of repetitive elements. A total of 35,543 putative protein-coding regions were identified, of which 50% have been functionally annotated. Transcriptomics analysis showed that approximately 64% of the predicted genes (22,617 genes) were found to be expressed in the tissues sampled. Comparative genomics analysis revealed that the anti-freeze glycoprotein (AFGP) locus of D. eleginoides does not contain any AFGP proteins compared to the same locus in the Antarctic toothfish (Dissostichus mawsoni). This is in agreement with previously published results looking at hybridization signals and confirms that Patagonian toothfish do not possess AFGP coding sequences in their genome. CONCLUSIONS We have assembled and annotated the Patagonian toothfish genome, which will provide a valuable genetic resource for ecological and evolutionary studies on this and other closely related species.
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Affiliation(s)
- David Ryder
- Centre for Environment, Fisheries and Aquaculture Science (Cefas), Lowestoft, Suffolk, UK.
| | - David Stone
- Centre for Environment, Fisheries and Aquaculture Science (Cefas), Lowestoft, Suffolk, UK
| | - Diana Minardi
- Centre for Environment, Fisheries and Aquaculture Science (Cefas), Lowestoft, Suffolk, UK
| | - Ainsley Riley
- Centre for Environment, Fisheries and Aquaculture Science (Cefas), Lowestoft, Suffolk, UK
| | - Justin Avant
- Centre for Environment, Fisheries and Aquaculture Science (Cefas), Lowestoft, Suffolk, UK
| | - Lisa Cross
- Centre for Environment, Fisheries and Aquaculture Science (Cefas), Lowestoft, Suffolk, UK
| | - Marta Soeffker
- Centre for Environment, Fisheries and Aquaculture Science (Cefas), Lowestoft, Suffolk, UK
- Collaborative Centre for Sustainable Use of the Seas, University of East Anglia, Norwich, UK
| | | | | | | | - Chris Darby
- Centre for Environment, Fisheries and Aquaculture Science (Cefas), Lowestoft, Suffolk, UK
| | - Ronny van Aerle
- Centre for Environment, Fisheries and Aquaculture Science (Cefas), Lowestoft, Suffolk, UK
- Centre for Sustainable Aquaculture Futures , University of Exeter, Exeter, UK
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Peng C, Liao D, Liu K, Wang X, Guo W. The complete chloroplast genome sequence of Calanthe sieboldii (orchidaceae). Mitochondrial DNA B Resour 2024; 9:314-317. [PMID: 38450411 PMCID: PMC10913714 DOI: 10.1080/23802359.2024.2324927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 02/24/2024] [Indexed: 03/08/2024] Open
Abstract
Calanthe sieboldii Decne. ex Regel is a terrestrial orchid with high ornamental and commercial value. In the present study, the chloroplast genome of C. sieboldii was characterized using Illumina technology. The chloroplast genome is 158,345 bp in length with a total AT content of 63.28%. There are 127 genes, comprising 37 tRNA genes, 82 protein-coding genes, and 8 rRNA genes. Phylogenetic relationship analysis was performed using common protein-coding genes extracted from 13 chloroplast genomes of Orchidaceae. It was revealed that C. sieboldi was sister to C. hancockii and closely clustered with C. aristulifera and C. henryi. These findings provide valuable genomic resources that are helpful for further phylogenetic and evolutionary studies of Calanthe.
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Affiliation(s)
- Cuiying Peng
- Hunan Academy of Forestry, Changsha, P. R. China
| | - Dezhi Liao
- Hunan Academy of Forestry, Changsha, P. R. China
| | - Kun Liu
- Jindong Forest Farm of Yongzhou City, Yongzhou, P. R. China
| | - Xujun Wang
- Hunan Academy of Forestry, Changsha, P. R. China
| | - Wei Guo
- Taishan Academy of Forestry Sciences, Taian, P. R. China
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Veneri C, Brandtner D, Mancini P, Bonanno Ferraro G, Iaconelli M, Del Giudice C, Ciccaglione AR, Bruni R, Equestre M, Marcantonio C, Suffredini E, La Rosa G. Detection and full genomic sequencing of rare hepatitis E virus genotype 4d in Italian wastewater, undetected by clinical surveillance. Sci Total Environ 2024; 913:169698. [PMID: 38160838 DOI: 10.1016/j.scitotenv.2023.169698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 12/22/2023] [Accepted: 12/24/2023] [Indexed: 01/03/2024]
Abstract
Hepatitis E is a liver disease caused by the hepatitis E virus (HEV), primarily transmitted through contaminated water or food. There are four different HEV genotypes in humans, with genotypes 1 and 2 being the most widespread. Genotypes 3 and 4 are found in animals and can also infect humans. Genotype 4 is prevalent in Asia, mainly in China. In Italy, only one outbreak of HEV-4 has been documented, which occurred in 2011, involving five patients. In 2013, HEV G4 was also detected in a pig farm. Since then, no further evidence of HEV genotype 4 has been found in the country. This study describes the first detection of HEV genotype 4, subtype d, in wastewater in central Italy, despite a lack of any clinical case reported in the area. By using a multiplex PCR protocol and two sequencing strategies, Illumina and ONT, the virus's complete genome was sequenced and characterized as subtype 4d. These findings shed light on the potential of environmental surveillance for infectious agents to improve our understanding of epidemiology and support public health efforts.
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Affiliation(s)
- C Veneri
- National Center for Water Safety (CeNSiA), Istituto Superiore di Sanità, Rome, Italy
| | - D Brandtner
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - P Mancini
- National Center for Water Safety (CeNSiA), Istituto Superiore di Sanità, Rome, Italy
| | - G Bonanno Ferraro
- National Center for Water Safety (CeNSiA), Istituto Superiore di Sanità, Rome, Italy
| | - M Iaconelli
- National Center for Water Safety (CeNSiA), Istituto Superiore di Sanità, Rome, Italy
| | - C Del Giudice
- National Center for Water Safety (CeNSiA), Istituto Superiore di Sanità, Rome, Italy
| | - A R Ciccaglione
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - R Bruni
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - M Equestre
- Department of Neurosciences, Istituto Superiore di Sanità, 00161 Rome, Italy
| | - C Marcantonio
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - E Suffredini
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, Rome, Italy
| | - G La Rosa
- National Center for Water Safety (CeNSiA), Istituto Superiore di Sanità, Rome, Italy.
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ullah S, Huda N, Wahab RA, Hamid AAA, Nasir MHM, Mohamad MAN, Ahmad HF, Oyewusi HA, Huyop F. Baseline amplicon sequencing data for the ITS2 region in the green honey of Banggi Island, Sabah. Data Brief 2024; 52:110044. [PMID: 38328502 PMCID: PMC10847015 DOI: 10.1016/j.dib.2024.110044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 01/03/2024] [Accepted: 01/05/2024] [Indexed: 02/09/2024] Open
Abstract
Green honey, was discovered on Banggi Island, Sabah, showing high in essential amino acids and chlorophyll derivatives. Despite its lucrative market potential owing to its distinctive color, uncertainties persist regarding its nature. This study leverages amplicon sequencing by targeting micro- and macro-organisms present in honey environmental DNA (eDNA) using Internal Transcribed Spacer 2 (ITS2) region, enabling the identification of floral and microorganism sources that represent the honey's composition. The investigation into green honey from Banggi Island concerns the prevalence of honey adulteration and authenticity for economic gain. Adulteration methods, such as the addition of sugar syrups, compromise honey purity. Using a sequencing approach would help in determining the geographic origin and verifying the authenticity of the honey. The study aims to identify plant species or microorganisms in honey's eDNA. To authenticate honey, we utilized ITS2 with Illumina sequencing, exploring the diversity of green honey samples. Raw sequence reads obtained for the green honey sample revealed 1,438,627 raw reads, with a GC average of 49.22 %. A total of 44 amplicon sequence variances (ASVs) were identified, including three genera: Zygosaccharomyces with two species, Fraxinus with three species, and the genus Ficaria with only one species. Their respective relative abundances were 98.55%, 0.94%, and 0.51%. Zygosaccharomyces rouxii and Zygosaccharomyces mellis were identified as the pre-dominant yeast species in honey, while the Fraxinus and Ficaria genus represent common plant species in Sabah, particularly in Banggi Island. The dominance of Zygosaccharomyces species aligns with their known prevalence in honey, affirming the reliability of our findings. The presence of Fraxinus and Ficaria in the honey sample correlates with its abundance in the local environment. This amplicon sequencing approach not only contributes to our understanding of green honey composition but also serves as a valuable resource for authenticating honey origin in Malaysia, particularly for green honey from Banggi Island, Sabah. Our study pioneers the application of ITS2 amplicon sequencing for green honey amplicon sequencing, providing valuable insights into its composition and origin. This methodology, with a focus on eDNA, contributes to the authentication and quality determination of honey in Malaysia, addressing the pressing concerns of adulteration and variability in production practices.
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Affiliation(s)
- Saeed ullah
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, 81310 Johor Bahru, Malaysia
| | - Nurul Huda
- Faculty of Sustainable Agriculture, Universiti Malaysia Sabah, 90509 Sandakan, Sabah, Malaysia
| | - Roswanira Ab. Wahab
- Department of Chemistry, Faculty of Science, Universiti Teknologi Malaysia, 81310 Johor Bahru, Malaysia
| | - Azzmer Azzar Abdul Hamid
- Research Unit for Bioinformatics and Computational Biology (RUBIC), Kulliyyah of Science, International Islamic University Malaysia, Bandar Indera Mahkota, 25200 Kuantan, Pahang, Malaysia
| | - Mohd Hamzah Mohd Nasir
- Research Unit for Bioinformatics and Computational Biology (RUBIC), Kulliyyah of Science, International Islamic University Malaysia, Bandar Indera Mahkota, 25200 Kuantan, Pahang, Malaysia
| | - Mohd Azrul Naim Mohamad
- Research Unit for Bioinformatics and Computational Biology (RUBIC), Kulliyyah of Science, International Islamic University Malaysia, Bandar Indera Mahkota, 25200 Kuantan, Pahang, Malaysia
| | - Hajar Fauzan Ahmad
- Faculty of Industrial Sciences and Technology, Universiti Malaysia Pahang Al Sultan Abdullah, 26300 Gambang, Pahang, Malaysia
| | - Habeebat Adekilekun Oyewusi
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, 81310 Johor Bahru, Malaysia
- Department of Biochemistry, School of Science and Computer Studies, Federal Polytechnic Ado Ekiti, Ado Ekiti PMB 5351, Ekiti State, Nigeria
| | - Fahrul Huyop
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, 81310 Johor Bahru, Malaysia
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Zuleger CL, Schwartz RW, Ong IM, Newton MA, Vail DM, Albertini MR. Development of a next-generation sequencing protocol for the canine T cell receptor beta chain repertoire. Vet Immunol Immunopathol 2024; 268:110702. [PMID: 38183837 PMCID: PMC10872364 DOI: 10.1016/j.vetimm.2023.110702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 12/07/2023] [Accepted: 12/09/2023] [Indexed: 01/08/2024]
Abstract
Profiling the T cell receptor (TCR) repertoire using next-generation sequencing has become common in both human and translational research. Companion dogs with spontaneous tumors, including canine melanoma, share several features, e.g., natural occurrence, shared environmental exposures, natural outbred population, and immunocompetence. T cells play an important role in the adaptive immune system by recognizing specific antigens via a surface TCR. As such, understanding the canine T cell response to vaccines, cancer, immunotherapies, and infectious diseases is critically important for both dog and human health. Off-the-shelf commercial reagents, kits and services are readily available for human, non-human primate, and mouse in this context. However, these resources are limited for the canine. In this study, we present a cost-effective protocol for analysis of canine TCR beta chain genes. Workflow can be accomplished in 1-2 days starting with total RNA and resulting in libraries ready for sequencing on Illumina platforms.
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Affiliation(s)
- Cindy L Zuleger
- Carbone Cancer Center, University of Wisconsin-Madison, Madison, WI, United States; Department of Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, United States
| | - Rene Welch Schwartz
- Department of Biostatistics and Medical Informatics, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, United States
| | - Irene M Ong
- Carbone Cancer Center, University of Wisconsin-Madison, Madison, WI, United States; Department of Biostatistics and Medical Informatics, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, United States; Department of Obstetrics and Gynecology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, United States
| | - Michael A Newton
- Carbone Cancer Center, University of Wisconsin-Madison, Madison, WI, United States; Department of Biostatistics and Medical Informatics, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, United States
| | - David M Vail
- Carbone Cancer Center, University of Wisconsin-Madison, Madison, WI, United States; Department of Medical Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, United States
| | - Mark R Albertini
- Carbone Cancer Center, University of Wisconsin-Madison, Madison, WI, United States; Department of Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, United States; Department of Dermatology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, United States; The Medical Service, William S. Middleton Memorial Veterans Hospital, Madison, WI, United States.
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11
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Anuradha C, Chandrasekar A, Backiyarani S, Thangavelu R, Uma S, Selvarajan R. Dataset from transcriptome profiling of Musa resistant and susceptible cultivars in response to Fusarium oxysporum f.sp. cubense race1 and TR4 challenges using Illumina NovaSeq. Data Brief 2024; 52:109803. [PMID: 38370021 PMCID: PMC10873869 DOI: 10.1016/j.dib.2023.109803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 11/05/2023] [Accepted: 11/07/2023] [Indexed: 02/20/2024] Open
Abstract
In this investigation, the study focused on the RNAseq data generated in response to Fusarium oxysporum f.sp. cubense (Foc) race1 (Cavendish infecting strain VCG 0124), targeting both resistant (cv. Rose, AA) and susceptible cultivars (Namarai, AA), and Tropical Race 4 (TR4, strain VCG 01213/16), involving resistant (cv. Rose, AA) and susceptible cultivars (Matti, AA). The respective contrasting cultivars were independently challenged with Foc race1 and TR4, and the root and corm samples were collected in two replications at varying time intervals [0th (control), 2nd, 4th, 6th, and 8th days] in duplicates. The RNA samples underwent stringent quality checks, with all 80 samples meeting the primary parameters, including a satisfactory RNA integrity number (>7). Subsequent library preparation and secondary quality control steps were executed successfully for all samples, paving the way for the sequencing phase. Sequencing generated an extensive amount of data, yielding a range of 10 to 31 million paired-end raw reads per sample, resulting in a cumulative raw data size of 11-50 GB. These raw reads were aligned against the reference genome of Musa acuminata ssp. malaccensis version 2 (DH Pahang), as well as the pathogen genomes of Foc race 1 and Foc TR4, using the HISAT2 alignment tool. The focal point of this study was the investigation of differential gene expression patterns of Musa spp. upon Foc infection. In Foc race1 resistant and susceptible root samples across the designated day intervals, a significant number of genes displayed up-regulation (ranging from 1 to 228) and down-regulation (ranging from 1 to 274). In corm samples, the up-regulated genes ranged from 1 to 149, while down-regulated genes spanned from 3 to 845. For Foc TR4 resistant and susceptible root samples, the expression profiles exhibited a notable up-regulation of genes (ranging from 31 to 964), along with a down-regulation range of 316-1315. In corm samples, up-regulated genes ranged from 57 to 929, while down-regulated genes were observed in the range of 40-936. In addition to the primary analysis, a comprehensive secondary analysis was conducted, including Gene Ontology (GO), euKaryotic Orthologous Groups (KOG) classification, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, and investigations into Simple Sequence Repeats (SSRs), Single Nucleotide Polymorphisms (SNPs), and microRNA (miRNA). The complete dataset was carefully curated and housed at ICAR-NRCB, Trichy, ensuring its accuracy and accessibility for the duration of the study. Further, the raw transcriptome read datasets have been successfully submitted to the National Center for Biotechnology Information - Sequence Read Archive (NCBI-SRA) database, ensuring the accessibility and reproducibility of this valuable dataset for further research endeavors.
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Affiliation(s)
- C. Anuradha
- ICAR-National Research Centre for Banana, Thogamalai Road, Thayanur Post, Tiruchirappalli 620102, Tamil Nadu, India
| | - A. Chandrasekar
- ICAR-National Research Centre for Banana, Thogamalai Road, Thayanur Post, Tiruchirappalli 620102, Tamil Nadu, India
| | - S. Backiyarani
- ICAR-National Research Centre for Banana, Thogamalai Road, Thayanur Post, Tiruchirappalli 620102, Tamil Nadu, India
| | - R. Thangavelu
- ICAR-National Research Centre for Banana, Thogamalai Road, Thayanur Post, Tiruchirappalli 620102, Tamil Nadu, India
| | - S. Uma
- ICAR-National Research Centre for Banana, Thogamalai Road, Thayanur Post, Tiruchirappalli 620102, Tamil Nadu, India
| | - R. Selvarajan
- ICAR-National Research Centre for Banana, Thogamalai Road, Thayanur Post, Tiruchirappalli 620102, Tamil Nadu, India
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12
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Duarte F, Cordero E, Calderon M, Godinez A, Ross B, Allard M, Gonzalez-Escalona N. Closed genomes of four multidrug resistance Salmonella enterica serotype Infantis isolated in Costa Rica. Microbiol Resour Announc 2024; 13:e0025723. [PMID: 38019019 DOI: 10.1128/mra.00257-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 10/25/2023] [Indexed: 11/30/2023] Open
Abstract
Here, we report the complete genome of four S. enterica Infantis isolated in Costa Rica from human, poultry rinse, and raw chicken meat from 2017 to 2019. All genomes belonged to ST32 and carried a 310-kb plasmid with many antimicrobial resistance genes including the bla CTX-M65 gene.
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Affiliation(s)
- Francisco Duarte
- Costa Rican Institute for Research and Education in Nutrition and Health (INCIENSA), National Reference Center for Microbiological Food Safety , Cartago, Costa Rica
| | - Estela Cordero
- Costa Rican Institute for Research and Education in Nutrition and Health (INCIENSA), National Reference Center for Microbiological Food Safety , Cartago, Costa Rica
| | - Melany Calderon
- Costa Rican Institute for Research and Education in Nutrition and Health (INCIENSA), National Reference Center for Microbiological Food Safety , Cartago, Costa Rica
| | - Adriana Godinez
- Costa Rican Institute for Research and Education in Nutrition and Health (INCIENSA), National Reference Center for Microbiological Food Safety , Cartago, Costa Rica
| | - Bruce Ross
- Latin America Regional Office, Office of Global Policy and Strategy, Food and Drug Administration Santiago , Santiago, Chile
| | - Marc Allard
- Division of Microbiology, Office of Regulatory Science, Center for Food Safety and Applied Nutrition, Food and Drug Administration , College Park, Maryland, USA
| | - Narjol Gonzalez-Escalona
- Division of Microbiology, Office of Regulatory Science, Center for Food Safety and Applied Nutrition, Food and Drug Administration , College Park, Maryland, USA
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13
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Dai X, Chen Q, Wang W, Wang X. The first complete mitochondrial genome of the agricultural pest Micromelalopha sieversi (Staudinger, 1892) (Lepidoptera: Notodontidae). Mitochondrial DNA B Resour 2024; 9:50-54. [PMID: 38197053 PMCID: PMC10776056 DOI: 10.1080/23802359.2023.2301005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 12/27/2023] [Indexed: 01/11/2024] Open
Abstract
Micromelalopha sieversi (Staudinger, 1892) is a significant pest of Poplar trees in China. In this study, we used high-throughput sequencing to sequence the whole mitochondrial genome of M. sieversi. The length of the genome was 15,373 base pairs. The nucleotide composition was 39.8%, 11.5%, 8.0%, and 40.7% for A, C, G, and T, respectively. We used the maximum-likelihood method to construct a molecular phylogenetic tree based on complete mitogenome sequences of 19 Noctuoidea species as ingroups and five Geometroidea species as outgroups. The results indicate that the genus Micromelalopha is closely related to the genus Clostera in family Notodontidae.
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Affiliation(s)
- Xuan Dai
- College of Plant Protection, Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Changsha, China
| | - Qi Chen
- College of Plant Protection, Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Changsha, China
| | - Wei Wang
- Research Center for Wild Animal and Plant Resource Protection and Utilization, Qiongtai Normal University, Haikou, China
| | - Xing Wang
- Research Center for Wild Animal and Plant Resource Protection and Utilization, Qiongtai Normal University, Haikou, China
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14
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Zhao J, Cheng Y, Jiang N, Qiao G, Qin W. Rhizosphere-associated soil microbiome variability in Verticillium wilt-affected Cotinus coggygria. Front Microbiol 2024; 14:1279096. [PMID: 38249458 PMCID: PMC10797040 DOI: 10.3389/fmicb.2023.1279096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 12/07/2023] [Indexed: 01/23/2024] Open
Abstract
Introduction Verticillium wilt is the most devastating soil-borne disease affecting Cotinus coggygria in the progress of urban landscape construction in China. Methods To assess the variability of the rhizosphere-associated soil microbiome in response to Verticillium wilt occurrence, we investigated the microbial diversity, taxonomic composition, biomarker species, and co-occurrence network of the rhizosphere-associated soil in Verticillium wilt-affected C. coggygria using Illumina sequencing. Results The alpha diversity indices of the rhizosphere bacteria in Verticillium wilt-affected plants showed no significant variability compared with those in healthy plants, except for a moderate increase in the Shannon and Invsimpson indices, while the fungal alpha diversity indices were significantly decreased. The abundance of certain dominant or crucial microbial taxa, such as Arthrobacter, Bacillus, Streptomyces, and Trichoderma, displayed significant variations among different soil samples. The bacterial and fungal community structures exhibited distinct variability, as evidenced by the Bray-Curtis dissimilarity matrices. Co-occurrence networks unveiled intricate interactions within the microbial community of Verticillium wilt-affected C. coggygria, with greater edge numbers and higher network density. The phenomenon was more evident in the fungal community, showing increased positive interaction, which may be associated with the aggravation of Verticillium wilt with the aid of Fusarium. The proportions of bacteria involved in membrane transport and second metabolite biosynthesis functions were significantly enriched in the diseased rhizosphere soil samples. Discussion These findings suggested that healthy C. coggygria harbored an obviously higher abundance of beneficial microbial consortia, such as Bacillus, while Verticillium wilt-affected plants may recruit antagonistic members such as Streptomyces in response to Verticillium dahliae infection. This study provides a theoretical basis for understanding the soil micro-ecological mechanism of Verticillium wilt occurrence, which may be helpful in the prevention and control of the disease in C. coggygria from the microbiome perspective.
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Affiliation(s)
- Juan Zhao
- Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Beijing Key Laboratory of Environment Friendly Management on Fruit Diseases and Pests in North China, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Yanli Cheng
- Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- College of Life Sciences, Yangtze University, Jingzhou, Hubei, China
| | - Nan Jiang
- Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- College of Horticulture and Plant Protection, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China
| | - Guanghang Qiao
- Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Beijing Key Laboratory of Environment Friendly Management on Fruit Diseases and Pests in North China, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Wentao Qin
- Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Beijing Key Laboratory of Environment Friendly Management on Fruit Diseases and Pests in North China, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
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15
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De Riseis S, Harmon FG. Identification of transcriptional networks controlling leaf sheath growth in Sorghum bicolor. BMC Res Notes 2024; 17:1. [PMID: 38167203 PMCID: PMC10759570 DOI: 10.1186/s13104-023-06653-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 12/04/2023] [Indexed: 01/05/2024] Open
Abstract
OBJECTIVES The objective of this data set was to identify transcriptional networks that control elongation of seedling leaf sheaths in the C4 grass Sorghum bicolor. One motivation was that leaf sheaths are a primary constituent of stems in grass seedlings; therefore, genes that control growth of this organ are important contributors to successful transition from the seedling stage to the mature plant stage and, ultimately, crop success. Since diurnal rhythms contribute to regulation of signaling networks responsible for growth, a time course representing the late afternoon and early evening was anticipated to pinpoint important control genes for stem growth. Ultimately, the expected outcome was discovery of transcript networks that integrate internal and external signals to fine tune leaf sheath growth and, consequently, plant height. DATA DESCRIPTION The data set is RNAseq profiling of upper leaf sheaths collected from wild type Sorghum bicolor (BTx623 line) plants at four-hour intervals from 12.5 h after dawn to 20 h after dawn. Global transcript levels in leaves were determined by deep sequencing of mRNA from four individual seedlings at each time point. This data set contains sequences representing the spectrum of mRNAs from individual genes. This data set enables detection of significant changes in gene-level expression caused by the progression of the day from late afternoon to the middle of the night. This data set is useful to identify gene expression networks regulating growth in the leaf sheath, an organ that is a major contributor to the sorghum seedling stem and defines seedling height.
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Affiliation(s)
- Samuel De Riseis
- Plant Gene Expression Center, USDA-ARS, Albany, 94710, USA
- Department of Plant & Microbial Biology, University of California, Berkeley, CA, 94720, USA
| | - Frank G Harmon
- Plant Gene Expression Center, USDA-ARS, Albany, 94710, USA.
- Department of Plant & Microbial Biology, University of California, Berkeley, CA, 94720, USA.
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16
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Van Deuren V, Plessers S, Lavigne R, Robben J. Application of Deep Sequencing in Phage Display. Methods Mol Biol 2024; 2738:333-345. [PMID: 37966608 DOI: 10.1007/978-1-0716-3549-0_20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2023]
Abstract
This chapter describes the workflow to implement deep sequencing into standard phage display experiments on protein libraries. By harvesting the power of high throughput of these techniques, it allows for comprehensive analysis of the naïve library and library evolution in response to selection by ligand binding. The mutagenized target region of the protein variants encoded by the phage pool is analyzed by Illumina paired-end sequencing. Sequence data are processed to extract selection-enriched amino acid motifs. In addition, a complementary long-read sequencing approach is proposed enabling the monitoring of display vector stability.
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Affiliation(s)
- Vincent Van Deuren
- Department of Biochemistry, Molecular and Structural Biology, KU Leuven, Leuven, Belgium
| | - Sander Plessers
- Department of Biochemistry, Molecular and Structural Biology, KU Leuven, Leuven, Belgium
| | - Rob Lavigne
- Animal and Human Health Engineering (A2H), Leuven (Arenberg), KU Leuven, Leuven, Belgium
| | - Johan Robben
- Department of Biochemistry, Molecular and Structural Biology, KU Leuven, Leuven, Belgium.
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17
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Cuevas-Ferrando E, Sánchez G, Pérez-Cataluña A. SARS-CoV-2 Detection and Genome Sequencing in Urban Wastewaters. Methods Mol Biol 2024; 2732:119-131. [PMID: 38060121 DOI: 10.1007/978-1-0716-3515-5_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/08/2023]
Abstract
Due to the excretion of SARS-CoV-2 in faeces, the use of wastewater-based epidemiology (WBE) is a useful tool for virus surveillance in large populations. The analysis of this virus includes a concentration step prior to virus detection by RT-qPCR. In addition, the use of massive sequencing allows the detection of specific mutations of clinical importance, as well as the detection of the introduction of new lineages in a specific population. In this chapter, we describe the analysis of SARS-CoV-2 in urban wastewater by the concentration of the samples by precipitation with aluminum chloride, the detection, and quantification of SARS-CoV-2 RNA by RT-qPCR and the genomic sequencing using two different sequencing platforms.
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Affiliation(s)
- Enric Cuevas-Ferrando
- VISAFELab, Department of Preservation and Food Safety Technologies, Institute of Agrochemistry and Food Technology, IATA-CSIC, Valencia, Paterna, Spain
| | - Gloria Sánchez
- VISAFELab, Department of Preservation and Food Safety Technologies, Institute of Agrochemistry and Food Technology, IATA-CSIC, Valencia, Paterna, Spain
| | - Alba Pérez-Cataluña
- VISAFELab, Department of Preservation and Food Safety Technologies, Institute of Agrochemistry and Food Technology, IATA-CSIC, Valencia, Paterna, Spain.
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18
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Dukanovic Rikvold P, Skov Hansen LB, Meyer RL, Jørgensen MR, Tiwari MK, Schlafer S. The Effect of Enzymatic Treatment with Mutanase, Beta-Glucanase, and DNase on a Saliva-Derived Biofilm Model. Caries Res 2023; 58:72-80. [PMID: 38154453 PMCID: PMC10997270 DOI: 10.1159/000535980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 12/17/2023] [Indexed: 12/30/2023] Open
Abstract
INTRODUCTION The dental biofilm matrix is an important determinant of virulence for caries development and comprises a variety of extracellular polymeric substances that contribute to biofilm stability. Enzymes that break down matrix components may be a promising approach to caries control, and in light of the compositional complexity of the dental biofilm matrix, treatment with multiple enzymes may enhance the reduction of biofilm formation compared to single enzyme therapy. The present study investigated the effect of the three matrix-degrading enzymes mutanase, beta-glucanase, and DNase, applied separately or in combinations, on biofilm prevention and removal in a saliva-derived in vitro-grown model. METHODS Biofilms were treated during growth to assess biofilm prevention or after 24 h of growth to assess biofilm removal by the enzymes. Biofilms were quantified by crystal violet staining and impedance-based real-time cell analysis, and the biofilm structure was visualized by confocal microscopy and staining of extracellular DNA (eDNA) and polysaccharides. RESULTS The in vitro model was dominated by Streptococcus spp., as determined by 16S rRNA gene amplicon sequencing. All tested enzymes and combinations had a significant effect on biofilm prevention, with reductions of >90% for mutanase and all combinations including mutanase. Combined application of DNase and beta-glucanase resulted in an additive effect (81.0% ± 1.3% SD vs. 36.9% ± 21.9% SD and 48.2% ± 14.9% SD). For biofilm removal, significant reductions of up to 73.2% ± 5.5% SD were achieved for combinations including mutanase, whereas treatment with DNase had no effect. Glucans, but not eDNA decreased in abundance upon treatment with all three enzymes. CONCLUSION Multi-enzyme treatment is a promising approach to dental biofilm control that needs to be validated in more diverse biofilms.
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Affiliation(s)
- Pernille Dukanovic Rikvold
- Department of Dentistry and Oral Health, Section for Oral Ecology, Cariology, Faculty of Health, Aarhus University, Aarhus, Denmark
- Novozymes A/S, Lyngby, Denmark
| | | | - Rikke Louise Meyer
- Interdisciplinary Nanoscience Center (iNANO), Faculty of Natural Sciences, Aarhus University, Aarhus, Denmark
| | | | | | - Sebastian Schlafer
- Department of Dentistry and Oral Health, Section for Oral Ecology, Cariology, Faculty of Health, Aarhus University, Aarhus, Denmark
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Dai X, Deng LF, Xiao X, Yu XJ, Lv JX, Xiong HY, Ma L, Chen Q, Yang LY, Wang X. First record of the complete mitochondrial genome of Botyodes diniasalis (Walker, 1859) (Lepidoptera: Crambidae). Mitochondrial DNA B Resour 2023; 8:1401-1405. [PMID: 38130731 PMCID: PMC10732176 DOI: 10.1080/23802359.2023.2292745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 12/04/2023] [Indexed: 12/23/2023] Open
Abstract
We performed the first sequencing of the complete mitogenome of Botyodes diniasalis by high-throughput sequencing. A circular DNA molecule of 15,219 bp in size, encoding 2 rRNAs, 22 tRNAs, and 13 PCGs, contains a non-coding AT-rich region. The overall nucleotide composition of the genome is A (39.5%), T (41.3%), C (11.3%), and G (7.8%). Phylogenetic analysis based on mitogenomic data suggest that the species B. diniasalis has a close evolutionary relationship with B. principalis in Margaroniini. The complete mitogenome of B. diniasalis will serve as a valuable resource for future studies on evolution, taxonomy, genetic conservation, and utilization of Botyodes.
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Affiliation(s)
- Xuan Dai
- Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Changsha, China
| | - Long-Fei Deng
- Hanshou County Agriculture and Rural Bureau, Changde, China
| | - Xin Xiao
- Hanshou County Agriculture and Rural Bureau, Changde, China
| | - Xiao-Jun Yu
- Hanshou County Agriculture and Rural Bureau, Changde, China
| | - Jun-Xian Lv
- Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Changsha, China
| | | | - Li Ma
- Hanshou County Agriculture and Rural Bureau, Changde, China
| | - Qi Chen
- Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Changsha, China
| | - Lian-Yong Yang
- Changde Academy of Agricultural and Forestry Sciences, Changde, China
| | - Xing Wang
- Tropical Biodiversity and Bioresource Utilization Laboratory, College of Science, Qiongtai Normal University, Haikou, China
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Moosa F, du Plessis M, Weigand MR, Peng Y, Mogale D, de Gouveia L, Nunes MC, Madhi SA, Zar HJ, Reubenson G, Ismail A, Tondella ML, Cohen C, Walaza S, von Gottberg A, Wolter N. Genomic characterization of Bordetella pertussis in South Africa, 2015-2019. Microb Genom 2023; 9:001162. [PMID: 38117675 PMCID: PMC10763497 DOI: 10.1099/mgen.0.001162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 12/04/2023] [Indexed: 12/22/2023] Open
Abstract
Pertussis remains a public health concern in South Africa, with an increase in reported cases and outbreaks in recent years. Whole genome sequencing was performed on 32 Bordetella pertussis isolates sourced from three different surveillance programmes in South Africa between 2015 and 2019. Genome sequences were characterized using multilocus sequence typing, vaccine antigen genes (ptxP, ptxA, ptxB, prn and fimH) and overall genome structure. All isolates were sequence type 2 and harboured the pertussis toxin promoter allele ptxP3. The dominant genotype was ptxP3-ptxA1-ptxB2-prn2-fimH2 (31/32, 96.9 %), with no pertactin-deficient or other mutations in vaccine antigen genes identified. Amongst 21 isolates yielding closed genome assemblies, eight distinct genome structures were detected, with 61.9 % (13/21) of the isolates exhibiting three predominant structures. Increases in case numbers are probably not due to evolutionary changes in the genome but possibly due to other factors such as the cyclical nature of B. pertussis disease, waning immunity due to the use of acellular vaccines and/or population immunity gaps.
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Affiliation(s)
- Fahima Moosa
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Mignon du Plessis
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Michael R. Weigand
- Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Yanhui Peng
- Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Dineo Mogale
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
| | - Linda de Gouveia
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
| | - Marta C. Nunes
- Department of Science and Technology/National Research Foundation, Vaccine Preventable Diseases, University of the Witwatersrand, Johannesburg, South Africa
| | - Shabir A. Madhi
- South African Medical Research Council Vaccines and Infectious Diseases Analytics Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Wits Infectious Diseases and Oncology Research Institute, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Heather J. Zar
- Department of Pediatrics and Child Health, Red Cross Children’s Hospital, Cape Town, South Africa; MRC Unit on Child and Adolescent Health, University of Cape Town, Cape Town, South Africa
| | - Gary Reubenson
- Rahima Moosa Mother & Child Hospital, Department of Pediatrics & Child Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Arshad Ismail
- Sequencing Core Facility, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- Department of Biochemistry and Microbiology, Faculty of Science, Engineering and Agriculture, University of Venda, Thohoyandou 0950, South Africa
- Institute for Water and Wastewater Technology, Durban University of Technology, Durban 4000, South Africa
| | - M. Lucia Tondella
- Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Cheryl Cohen
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Sibongile Walaza
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Anne von Gottberg
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Nicole Wolter
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
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Zhang E, Lu Y, Zhao R, Yin X, Zhang J, Yu B, Yao M, Liao Z, Lan X. Endophytic bacterial community structure and diversity of the medicinal plant Mirabilis himalaica from different locations. Braz J Microbiol 2023; 54:2991-3003. [PMID: 37921953 PMCID: PMC10689605 DOI: 10.1007/s42770-023-01149-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 10/06/2023] [Indexed: 11/05/2023] Open
Abstract
Endophytic bacteria play important roles in medicinal plant growth, abiotic stress, and metabolism. Mirabilis himalaica (Edgew.) Heimerl is known for its medicinal value as Tibetan traditional plant; however, little is known about the endophytic bacteria associated with this plant in different geographic conditions and vegetal tissues. To compare the endophytic bacterial community associated with this plant in different geographic conditions and vegetal tissues, we collected the leaves, stems, and roots of M. himalaica from five locations, Nongmu college (NM), Gongbujiangda (GB), Zhanang County (ZL), Lang County (LX), and Sangri County (SR), and sequenced the 16S rRNA V5-V7 region with the Illumina sequencing method. A total of 522,450 high-quality sequences and 4970 operational taxonomic units (OTUs) were obtained. The different tissues from different locations harbored unique bacterial assemblages. Proteobacteria and Actinobacteria were the dominant phyla in all the samples, while the dominant genera changed based on the different tissues. The endophytic bacterial structures in the leaf and stem tissues were different compared to root tissues. Redundancy analysis (RDA) showed that the endophytic bacterial community was significantly correlated with pH, available phosphorus (AP), total phosphorus (TP), total nitrogen (TN), and soil organic matter (SOM). These findings suggested that the geographic conditions, climate type, ecosystem type, and tissues determined the endophytic bacterial composition and relative abundances. This conclusion could facilitate an understanding of the relationship and ecological function of the endophytic bacteria associated with M. himalaica and provide valuable information for artificial planting of M. himalaica and identifying and applying functional endophytic bacteria.
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Affiliation(s)
- Erhao Zhang
- The Provincial and Ministerial Co-Founded Collaborative Innovation Center for R & D in Tibet Characteristic Agricultural and Animal Husbandry Resources, The Center for Xizang Chinese (Tibetan) Medicine Resource, Joint Laboratory for Tibetan Materia Medica Resources Scientific Protection and Utilization Research of Tibetan Medical Research Center of Tibet, Tibet Agriculture and Animal Husbandry University, Nyingchi, 860000, Tibet, China
| | - Yazhou Lu
- The Provincial and Ministerial Co-Founded Collaborative Innovation Center for R & D in Tibet Characteristic Agricultural and Animal Husbandry Resources, The Center for Xizang Chinese (Tibetan) Medicine Resource, Joint Laboratory for Tibetan Materia Medica Resources Scientific Protection and Utilization Research of Tibetan Medical Research Center of Tibet, Tibet Agriculture and Animal Husbandry University, Nyingchi, 860000, Tibet, China
| | - Rundong Zhao
- The Provincial and Ministerial Co-Founded Collaborative Innovation Center for R & D in Tibet Characteristic Agricultural and Animal Husbandry Resources, The Center for Xizang Chinese (Tibetan) Medicine Resource, Joint Laboratory for Tibetan Materia Medica Resources Scientific Protection and Utilization Research of Tibetan Medical Research Center of Tibet, Tibet Agriculture and Animal Husbandry University, Nyingchi, 860000, Tibet, China
| | - Xiu Yin
- The Provincial and Ministerial Co-Founded Collaborative Innovation Center for R & D in Tibet Characteristic Agricultural and Animal Husbandry Resources, The Center for Xizang Chinese (Tibetan) Medicine Resource, Joint Laboratory for Tibetan Materia Medica Resources Scientific Protection and Utilization Research of Tibetan Medical Research Center of Tibet, Tibet Agriculture and Animal Husbandry University, Nyingchi, 860000, Tibet, China
| | - Jie Zhang
- College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, 466001, Henan, China
| | - Benxia Yu
- Chongqing Academy of Chinese Materia Medica, Chongqing, 400065, China
| | - Min Yao
- Jiangxi Institute for Drug Control, NMPA Key Laboratory of Quality Evaluation of Traditional Chinese Patent Medicine, Nanchang, 330029, Jiangxi, China
| | - Zhihua Liao
- Key Laboratory of Eco-Environments in the Three Gorges Reservoir Region, Ministry of Education, Chongqing Engineering and Technology Research Center for Sweetpotato, School of Life Sciences, Southwest University, Chongqing, 400715, China
| | - Xiaozhong Lan
- The Provincial and Ministerial Co-Founded Collaborative Innovation Center for R & D in Tibet Characteristic Agricultural and Animal Husbandry Resources, The Center for Xizang Chinese (Tibetan) Medicine Resource, Joint Laboratory for Tibetan Materia Medica Resources Scientific Protection and Utilization Research of Tibetan Medical Research Center of Tibet, Tibet Agriculture and Animal Husbandry University, Nyingchi, 860000, Tibet, China.
- Chongqing Academy of Chinese Materia Medica, Chongqing, 400065, China.
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Braga PRC, Dos Santos CA, Bertani AMDJ, Vieira T, Amarante AF, Reis AD, Sacchi CT, Camargo CH, Ribeiro MG, Borges AS, Tiba-Casas MR. Detection and genomic characterization of a multidrug-resistant Salmonella Newport co-harbouring bla CMY-2, qnrB19 and mcr-9 from the diarrheic faeces of a foal. J Glob Antimicrob Resist 2023; 35:198-201. [PMID: 37805072 DOI: 10.1016/j.jgar.2023.09.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 09/26/2023] [Accepted: 09/28/2023] [Indexed: 10/09/2023] Open
Abstract
OBJECTIVES This study reports the genomic characterization of the multidrug resistant Salmonella Newport strain 195_20 recovered from the diarrheic faeces of a foal in Brazil and co-harbouring the mcr-9, blaCMY-2 and qnrB19 antibiotic resistance genes. METHODS Bacterial isolate positive for mobile colistin resistance gene (mcr-9) was submitted to antimicrobial susceptibility testing by disk diffusion and broth microdilution for colistin and polymyxin B. The isolate was submitted to whole genome sequencing by Illumina technology and Nanopore Sequencing. Conjugation assays, plasmid sizes determined by S1-PFGE and plasmid content were investigated by hybrid assembly after MinIon long reads sequencing. RESULTS Isolate 195_20 was identified as sequence type ST45, resistant to penicillin and cephalosporins (ampicillin, ceftazidime, ceftriaxone and cefotaxime), aminoglycosides (streptomycin and gentamicin), phenicol (chloramphenicol), quinolones and fluoroquinolones (nalidixic acid, ciprofloxacin, and pefloxacin), folate pathway antagonists (sulfonamides and trimethoprim-sulfamethoxazole), and tetracycline. A transferable IncHI2/IncHI2A plasmid sized ca. 262kb was found to carry the mcr-9 gene in a module consisting of IS903-mcr-9-wbuC-IS26. In addition, an 174kb IncC and a 48kb IncN plasmid were also identified in the 195_20 isolate, carrying blaCMY-2 and qnrB19, respectively. CONCLUSIONS Not surprisingly, isolate 195_20 was susceptible to polymyxins, possibly due to absence of qseBC regulatory operon. Presence of mobile colistin resistance (mcr-9), third-generation cephalosporins (blaCMY-2) and quinolone (qnrB19) resistance determinants in zoonotic pathogens from animals in close contact with humans alerts for the possible route of transmission between these different reservoirs.
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Affiliation(s)
- Pollyana Rennó Campos Braga
- Department of Veterinary Clinical Science, School of Veterinary Medicine and Animal Science (FMVZ), São Paulo State University (Unesp), Botucatu, SP, Brazil
| | | | | | | | | | | | | | | | - Marcio Garcia Ribeiro
- Department of Veterinary Clinical Science, School of Veterinary Medicine and Animal Science (FMVZ), São Paulo State University (Unesp), Botucatu, SP, Brazil
| | - Alexandre Secorun Borges
- Department of Veterinary Clinical Science, School of Veterinary Medicine and Animal Science (FMVZ), São Paulo State University (Unesp), Botucatu, SP, Brazil
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Wani AK, Ahmad S, Américo-Pinheiro JHP, Tizro N, Singh R. Building the taxonomic profile of the Riniaie Marwah hot spring of Kishtwar in Jammu and Kashmir: the first high-throughput sequencing-based metagenome study. Iran J Microbiol 2023; 15:723-733. [PMID: 38156301 PMCID: PMC10751607 DOI: 10.18502/ijm.v15i6.14132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/30/2023]
Abstract
Background and Objectives Rinaie Marwah hot spring Kishtwar (RMHSK) is one of the geothermal springs located at 33°51'51″N 75°32'07″E with an elevation of 2134 meters above sea level in Jammu and Kashmir, India. We aimed to study the microbial diversity of this geothermal spring using metagenomics. Materials and Methods In the present study, physiochemical parameters including temperature (65-75°C), pH (6. 9-8. 8), hardness (250 ppm), and mineral content was measured along with the microbial diversity using Illumina MiSeq metagenome-based 16s amplicon sequencing (V3-V4). The sequence reads were classified taxonomically into 31 phyla, 71 classes, 152 orders, 256 families, 410 genus, and 665 species. QIIME 2 (Quantitative Insights into Microbial Ecology), an extensible, powerful, and decentralized analytical tool, was used for taxonomic analysis. Results Bacteroidota (32. 57%) was the dominant phylum, Bacteroidia (32. 51%) the dominant class, Bacteroidales (16. 6%) the dominant order, and Lentimicrobiaceae (14. 23%) was the dominant family per the abundance analysis. Shannon (2. 28) and Chao 1 (87. 0) diversity indices support the existence of higher microbial diversity in RMHSK (50717 OTUs). Conclusion The microbial diversity of RMHSK is reported for the first time through a metagenomic study. Identification of microorganisms with characteristics that are relevant to industries.
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Affiliation(s)
- Atif Khurshid Wani
- Department of Biotechnology, School of Bioengineering and Biosciences, Lovely Professional University, Jalandhar, Punjab, India
| | - Suhail Ahmad
- Department of Remote Sensing and GIS, University of Jammu, Jammu, India
| | - Juliana Heloisa Pinê Américo-Pinheiro
- Department of Forest Science, Soils and Environment, School of Agronomic Sciences, São Paulo State University (UNESP), Botucatu, Brazil
- Department of Environmental Sciences, Graduate Program in Environmental Sciences, Brazil University, São Paulo, Brazil
| | - Nazli Tizro
- Department of the Environment, College of Natural Resources and Environment, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Reena Singh
- Department of Biotechnology, School of Bioengineering and Biosciences, Lovely Professional University, Jalandhar, Punjab, India
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Maurya S, Arya CK, Parmar N, Sathyanarayanan N, Joshi CG, Ramanathan G. Genomic profiling and characteristics of a C1 degrading heterotrophic fresh-water bacterium Paracoccus sp. strain DMF. Arch Microbiol 2023; 206:6. [PMID: 38015256 DOI: 10.1007/s00203-023-03729-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 10/27/2023] [Accepted: 10/30/2023] [Indexed: 11/29/2023]
Abstract
Paracoccus species are metabolically versatile gram-negative, aerobic facultative methylotrophic bacteria showing enormous promise for environmental and bioremediation studies. Here we report, the complete genome analysis of Paracoccus sp. strain DMF (P. DMF) that was isolated from a domestic wastewater treatment plant in Kanpur, India (26.4287 °N, 80.3891 °E) based on its ability to degrade a recalcitrant organic solvent N, N-dimethylformamide (DMF). The results reveal a genome size of 4,202,269 base pairs (bp) with a G + C content of 67.9%. The assembled genome comprises 4141 coding sequences (CDS), 46 RNA sequences, and 2 CRISPRs. Interestingly, catabolic operons related to the conventional marine-based methylated amines (MAs) degradation pathway were functionally annotated within the genome of an obligated aerobic heterotroph that is P. DMF. The genomic data-based characterization presented here for the novel heterotroph P. DMF aims to improve the understanding of the phenotypic gene products, enzymes, and pathways involved with greater emphasis on facultative methylotrophic motility-based latent pathogenicity.
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Affiliation(s)
- Shiwangi Maurya
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, 208016, India
| | - Chetan Kumar Arya
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, 208016, India
| | - Nidhi Parmar
- Gujarat Biotechnology Research Centre (GBRC), Gandhinagar, Gujarat, 382 011, India
| | - Nitish Sathyanarayanan
- Institute for Stem Cell Science and Regenerative Medicine (inStem), Bangalore, 560065, India
| | - Chaitanya G Joshi
- Gujarat Biotechnology Research Centre (GBRC), Gandhinagar, Gujarat, 382 011, India
| | - Gurunath Ramanathan
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, 208016, India.
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Aminu S, Ascandari A, Laamarti M, Safdi NEH, El Allali A, Daoud R. Exploring microbial worlds: a review of whole genome sequencing and its application in characterizing the microbial communities. Crit Rev Microbiol 2023:1-25. [PMID: 38006569 DOI: 10.1080/1040841x.2023.2282447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 11/06/2023] [Indexed: 11/27/2023]
Abstract
The classical microbiology techniques have inherent limitations in unraveling the complexity of microbial communities, necessitating the pivotal role of sequencing in studying the diversity of microbial communities. Whole genome sequencing (WGS) enables researchers to uncover the metabolic capabilities of the microbial community, providing valuable insights into the microbiome. Herein, we present an overview of the rapid advancements achieved thus far in the use of WGS in microbiome research. There was an upsurge in publications, particularly in 2021 and 2022 with the United States, China, and India leading the metagenomics research landscape. The Illumina platform has emerged as the widely adopted sequencing technology, whereas a significant focus of metagenomics has been on understanding the relationship between the gut microbiome and human health where distinct bacterial species have been linked to various diseases. Additionally, studies have explored the impact of human activities on microbial communities, including the potential spread of pathogenic bacteria and antimicrobial resistance genes in different ecosystems. Furthermore, WGS is used in investigating the microbiome of various animal species and plant tissues such as the rhizosphere microbiome. Overall, this review reflects the importance of WGS in metagenomics studies and underscores its remarkable power in illuminating the variety and intricacy of the microbiome in different environments.
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Affiliation(s)
- Suleiman Aminu
- Chemical and Biochemical Sciences-Green Process Engineering, University Mohammed VI Polytechnic, Ben Guerir, Morocco
- Department of Biochemistry, Ahmadu Bello University, Zaria, Nigeria
| | - AbdulAziz Ascandari
- Chemical and Biochemical Sciences-Green Process Engineering, University Mohammed VI Polytechnic, Ben Guerir, Morocco
| | - Meriem Laamarti
- Faculty of Medical Sciences, University Mohammed VI Polytechnic, Ben Guerir, Morocco
| | - Nour El Houda Safdi
- AgroBioSciences Program, College for Sustainable Agriculture and Environmental Science, University Mohammed VI Polytechnic, Ben Guerir, Morocco
| | - Achraf El Allali
- Bioinformatics Laboratory, College of Computing, University Mohammed VI Polytechnic, Ben Guerir, Morocco
| | - Rachid Daoud
- Chemical and Biochemical Sciences-Green Process Engineering, University Mohammed VI Polytechnic, Ben Guerir, Morocco
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26
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Sanderson H, McCarthy MC, Nnajide CR, Sparrow J, Rubin JE, Dillon JAR, White AP. Identification of plasmids in avian-associated Escherichia coli using nanopore and illumina sequencing. BMC Genomics 2023; 24:698. [PMID: 37990161 PMCID: PMC10664647 DOI: 10.1186/s12864-023-09784-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Accepted: 11/03/2023] [Indexed: 11/23/2023] Open
Abstract
BACKGROUND Avian pathogenic Escherichia coli (APEC) are the causative agents of colibacillosis in chickens, a disease which has significant economic impact on the poultry industry. Large plasmids detected in APEC are known to contribute to strain diversity for pathogenicity and antimicrobial resistance, but there could be other plasmids that are missed in standard analysis. In this study, we determined the impact of sequencing and assembly factors for the detection of plasmids in an E. coli whole genome sequencing project. RESULTS Hybrid assembly (Illumina and Nanopore) combined with plasmid DNA extractions allowed for detection of the greatest number of plasmids in E. coli, as detected by MOB-suite software. In total, 79 plasmids were identified in 19 E. coli isolates. Hybrid assemblies were robust and consistent in quality regardless of sequencing kit used or if long reads were filtered or not. In contrast, long read only assemblies were more variable and influenced by sequencing and assembly parameters. Plasmid DNA extractions allowed for the detection of physically smaller plasmids, but when averaged over 19 isolates did not significantly change the overall number of plasmids detected. CONCLUSIONS Hybrid assembly can be reliably used to detect plasmids in E. coli, especially if researchers are focused on large plasmids containing antimicrobial resistance genes and virulence factors. If the goal is comprehensive detection of all plasmids, particularly if smaller sized vectors are desired for biotechnology applications, the addition of plasmid DNA extractions to hybrid assemblies is prudent. Long read sequencing is sufficient to detect many plasmids in E. coli, however, it is more prone to errors when expanded to analyze a large number of isolates.
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Affiliation(s)
- Haley Sanderson
- Vaccine and Infectious Disease Organization (VIDO), University of Saskatchewan, Saskatoon, SK, Canada
| | - Madeline C McCarthy
- Vaccine and Infectious Disease Organization (VIDO), University of Saskatchewan, Saskatoon, SK, Canada
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, SK, Canada
- Current address: Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada
| | - Chinenye R Nnajide
- Vaccine and Infectious Disease Organization (VIDO), University of Saskatchewan, Saskatoon, SK, Canada
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, SK, Canada
| | - Jessica Sparrow
- Vaccine and Infectious Disease Organization (VIDO), University of Saskatchewan, Saskatoon, SK, Canada
| | - Joseph E Rubin
- Department of Veterinary Microbiology, University of Saskatchewan, Saskatoon, SK, Canada
| | - Jo-Anne R Dillon
- Vaccine and Infectious Disease Organization (VIDO), University of Saskatchewan, Saskatoon, SK, Canada
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, SK, Canada
| | - Aaron P White
- Vaccine and Infectious Disease Organization (VIDO), University of Saskatchewan, Saskatoon, SK, Canada.
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, SK, Canada.
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Zhou Z, Ding L, Liu Z, Fu L, Xu L, Feng L, Yu S, Li P, Zhou Y. The complete mitochondrial genome of Goniurosaurus varius (Squamata: Eublepharidae). Mitochondrial DNA B Resour 2023; 8:1215-1219. [PMID: 38239912 PMCID: PMC10796122 DOI: 10.1080/23802359.2023.2278817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Accepted: 10/29/2023] [Indexed: 01/22/2024] Open
Abstract
The complete mitochondrial genome sequence of Goniurosaurus varius is 17778 bp in length (GenBank accession number OQ992199), containing 13 protein-coding genes, 2 rRNA genes, and 22 tRNA genes. The gene order and orientation are identical to those of other Eublepharidae species in the GenBank database. Seven protein-coding genes (COX2, COX3, ND1, ND2, ND3, ND4 and CYTB) exhibit incomplete stop codon 'T.' Phylogenetic analysis revealed the monophyly of Goniurosaurus and Eublepharidae and suggested that G. varius is closely related to the lineage composed of G. luii and G. liboensis. Distinct from other published Eublepharidae species, G. varius contains an extra non-coding region between tRNA-Thr and tRNA-Pro, which may be formed by gene rearrangements. The complete mitochondrial genome will be helpful for further studies on the population genetics of this species and phylogenetic analyses of Eublepharidae.
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Affiliation(s)
- Zhengyan Zhou
- College of Life Science and bioengineering, Shenyang University, Shenyang, China
| | - Lin Ding
- College of Life Science and bioengineering, Shenyang University, Shenyang, China
| | - Ziyi Liu
- College of Life Science and bioengineering, Shenyang University, Shenyang, China
| | - Longming Fu
- College of Life Science and bioengineering, Shenyang University, Shenyang, China
| | - Lanying Xu
- College of Life Science and bioengineering, Shenyang University, Shenyang, China
| | - Lin Feng
- College of Life Science and bioengineering, Shenyang University, Shenyang, China
| | - Sufan Yu
- College of Life Science and bioengineering, Shenyang University, Shenyang, China
| | - Pipeng Li
- Institute of Herpetology, Shenyang Normal University, Shenyang, China
| | - Yu Zhou
- College of Life Science, Shenyang Normal University, Shenyang, China
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Tulloch LB, Carvalho S, Lima M, Wall RJ, Tinti M, Pinto EG, MacLean L, Wyllie S. RES-Seq-a barcoded library of drug-resistant Leishmania donovani allowing rapid assessment of cross-resistance and relative fitness. mBio 2023; 14:e0180323. [PMID: 37929970 PMCID: PMC10746238 DOI: 10.1128/mbio.01803-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Accepted: 10/02/2023] [Indexed: 11/07/2023] Open
Abstract
Visceral leishmaniasis (VL) is a parasitic disease endemic across multiple regions of the world and is fatal if untreated. New therapeutic options with diverse mechanisms of actions (MoAs) are required to consolidate progress toward control of this disease and combat drug resistance. Here, we describe the development of a scalable resistance library screen (RES-Seq) as a tool to facilitate the identification and prioritization of anti-leishmanial compounds acting via novel MoA. We have amassed a large collection of Leishmania donovani cell lines resistant to frontline drugs and compounds in the VL pipeline, with resistance-conferring mutations fully characterized. New phenotypic hits screened against this highly curated panel of resistant lines can determine cross-resistance and potentially shared MoA. The ability to efficiently identify compounds acting via previously established MoA is vital to maintain diversity within drug development portfolios. To expedite screening, short identifier DNA barcodes were introduced into resistant clones enabling pooling and simultaneous screening of multiple cell lines. Illumina sequencing of barcodes enables the growth kinetics and relative fitness of multiple cell lines under compound selection to be tracked. Optimal conditions allowing discrimination of resistant and sensitive clones were established (3× and 10× EC50 for 3 days) and applied to screening of a complex library with VL preclinical and clinical drug candidates. RES-Seq is set to play an important role in ensuring that anti-leishmanial compounds exploiting diverse mechanisms of action are developed, ultimately providing options for future drug combination strategies.IMPORTANCEVisceral leishmaniasis (VL) remains the third largest parasitic killer worldwide, responsible for 20,000-30,000 deaths each year. Control and ultimate elimination of VL will require a range of therapeutic options with diverse mechanisms of action to combat drug resistance. One approach to ensure that compounds in development exploit diverse mechanisms of action is to screen them against highly curated cell lines resistant to drugs already in the VL pipeline. The identification of cross-resistant cell lines indicates that test compounds are likely acting via previously established mechanisms. Current cross-resistance screens are limited by the requirement to profile individual resistant cell lines one at a time. Here, we introduce unique DNA barcodes into multiple resistant cell lines to facilitate parallel profiling. Utilizing the power of Illumina sequencing, growth kinetics and relative fitness under compound selection can be monitored revolutionizing our ability to identify and prioritize compounds acting via novel mechanisms.
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Affiliation(s)
- Lindsay B. Tulloch
- Wellcome Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Sandra Carvalho
- Wellcome Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Marta Lima
- Wellcome Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Richard J. Wall
- Wellcome Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Michele Tinti
- Wellcome Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Erika G. Pinto
- Drug Discovery Unit, Wellcome Centre for Anti-infectives Research, University of Dundee, Dundee, United Kingdom
| | - Lorna MacLean
- Drug Discovery Unit, Wellcome Centre for Anti-infectives Research, University of Dundee, Dundee, United Kingdom
| | - Susan Wyllie
- Wellcome Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dundee, United Kingdom
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29
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Liu B, Wang Y, Zhang H, Zhou Y, Zhang C, Yang N, Wang W. The Variations of Microbial Diversity and Community Structure Along Different Stream Orders in Wuyi Mountains. Microb Ecol 2023; 86:2330-2343. [PMID: 37222804 DOI: 10.1007/s00248-023-02240-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Accepted: 05/08/2023] [Indexed: 05/25/2023]
Abstract
The surface water is an important habitat for freshwater microorganisms, but there is a lack of understanding of the pattern of microbial diversity and structure in stream continuums of small subtropical forest watersheds. Therefore, this study aimed to understand the variations in microbial diversity and community structure along stream orders (1-5) in the small subtropical forest catchments of the Wuyi Mountains. Using GIS software, 20 streams were chosen and classified into 5 orders. Illumina sequencing was used to analyze the dynamics of microbial communities, along with stream orders and hydro-chemical properties of stream water were also determined. Our results indicated that the bacterial and fungal richness (ACE index) was higher in low-order (1 and 2 orders) streams than in high-order (3, 4, and 5 orders) streams, with the highest value in the order 2 streams (P < 0.05). The water temperature and dissolved oxygen were positively correlated with fungal richness (P < 0.05). The bacterial rare taxa had a significant correlation with the abundance taxa (P < 0.05). The relative abundances of Bacteroidetes, Actinobacteria, and Chytridiomycota microbial phyla were significantly different among different order streams (P < 0.05). Using the neutral community model, we found that the fungal community structure was significantly shaped by hydro-chemical properties, while the bacterial community structure was largely regulated by stochastic processes. Our findings suggest that variations in microbial community structure in subtropical headwaters are largely shaped by the water temperature and dissolved oxygen.
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Affiliation(s)
- Boran Liu
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, 210037, Jiangsu, China
- National Observation and Research Station of Fujian Wuyishan Forest Ecosystem, Wuyishan, 354300, Fujian, China
| | - Yuchao Wang
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, 210037, Jiangsu, China
- National Observation and Research Station of Fujian Wuyishan Forest Ecosystem, Wuyishan, 354300, Fujian, China
| | - Huiguang Zhang
- National Observation and Research Station of Fujian Wuyishan Forest Ecosystem, Wuyishan, 354300, Fujian, China
- Wuyishan National Park Research and Monitoring Center, Wuyishan, 354300, Fujian, China
| | - Yan Zhou
- National Observation and Research Station of Fujian Wuyishan Forest Ecosystem, Wuyishan, 354300, Fujian, China
- Wuyishan National Park Research and Monitoring Center, Wuyishan, 354300, Fujian, China
| | - Chenhui Zhang
- National Observation and Research Station of Fujian Wuyishan Forest Ecosystem, Wuyishan, 354300, Fujian, China
- Wuyishan National Park Research and Monitoring Center, Wuyishan, 354300, Fujian, China
| | - Nan Yang
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, 210037, Jiangsu, China.
| | - Weifeng Wang
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, 210037, Jiangsu, China.
- National Observation and Research Station of Fujian Wuyishan Forest Ecosystem, Wuyishan, 354300, Fujian, China.
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Bushra R, Ahmed I, Li JL, Lian Z, Li S, Ali A, Uzair B, Amin A, Ehsan M, Liu YH, Li WJ. Untapped rich microbiota of mangroves of Pakistan: diversity and community compositions. Folia Microbiol (Praha) 2023:10.1007/s12223-023-01095-3. [PMID: 37843797 DOI: 10.1007/s12223-023-01095-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 09/11/2023] [Indexed: 10/17/2023]
Abstract
The mangrove ecosystem is the world's fourth most productive ecosystem in terms of service value and offering rich biological resources. Microorganisms play vital roles in these ecological processes, thus researching the mangroves-microbiota is crucial for a deeper comprehension of mangroves dynamics. Amplicon sequencing that targeted V4 region of 16S rRNA gene was employed to profile the microbial diversities and community compositions of 19 soil samples, which were collected from the rhizosphere of 3 plant species (i.e., Avicennia marina, Ceriops tagal, and Rhizophora mucronata) in the mangrove forests of Lasbela coast, Pakistan. A total of 67 bacterial phyla were observed from three mangroves species, and these taxa were classified into 188 classes, 453 orders, 759 families, and 1327 genera. We found that Proteobacteria (34.9-38.4%) and Desulfobacteria (7.6-10.0%) were the dominant phyla followed by Chloroflexi (6.6-7.3%), Gemmatimonadota (5.4-6.8%), Bacteroidota (4.3-5.5%), Planctomycetota (4.4-4.9%) and Acidobacteriota (2.7-3.4%), Actinobacteriota (2.5-3.3%), and Crenarchaeota (2.5-3.3%). After considering the distribution of taxonomic groups, we prescribe that the distinctions in bacterial community composition and diversity are ascribed to the changes in physicochemical attributes of the soil samples (i.e., electrical conductivity (ECe), pH, total organic matter (OM), total organic carbon (OC), available phosphorus (P), and extractable potassium (CaCO3). The findings of this study indicated a high-level species diversity in Pakistani mangroves. The outcomes may also aid in the development of effective conservation policies for mangrove ecosystems, which have been hotspots for anthropogenic impacts in Pakistan. To our knowledge, this is the first microbial research from a Pakistani mangrove forest.
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Affiliation(s)
- Rabia Bushra
- National Culture Collection of Pakistan (NCCP), Land Resources Research Institute (LRRI), National Agriculture Research Center (NARC), Islamabad 45500, Pakistan
- Department of Biological Sciences, International Islamic University, Islamabad 44000, Pakistan
| | - Iftikhar Ahmed
- National Culture Collection of Pakistan (NCCP), Land Resources Research Institute (LRRI), National Agriculture Research Center (NARC), Islamabad 45500, Pakistan.
| | - Jia-Ling Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Zhenghan Lian
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Shuai Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Ahmad Ali
- National Culture Collection of Pakistan (NCCP), Land Resources Research Institute (LRRI), National Agriculture Research Center (NARC), Islamabad 45500, Pakistan
| | - Bushra Uzair
- Department of Biological Sciences, International Islamic University, Islamabad 44000, Pakistan
| | - Arshia Amin
- Department of Bioinformatics and Biosciences, Capital University of Science and Technology, Islamabad 45500, Pakistan
| | | | - Yong-Hong Liu
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, People's Republic of China
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China.
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, People's Republic of China.
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Cui S, Du J, Zhu L, Xin D, Xin Y, Zhang J. Analysis of Microbial Diversity in South Shetland Islands and Antarctic Peninsula Soils Based on Illumina High-Throughput Sequencing and Cultivation-Dependent Techniques. Microorganisms 2023; 11:2517. [PMID: 37894176 PMCID: PMC10609098 DOI: 10.3390/microorganisms11102517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 10/04/2023] [Accepted: 10/06/2023] [Indexed: 10/29/2023] Open
Abstract
To assess the diversity of bacterial taxa in Antarctic soils and obtain novel microbial resources, 15 samples from 3 sampling sites (DIS5, GWS7, FPS10) of South Shetland Islands and 2 sampling sites (APS18, CIS17) of Antarctic Peninsula were collected. High-throughput sequencing (HTS) of 16S rRNA genes within these samples was conducted on an Illumina Miseq platform. A total of 140,303 16S rRNA gene reads comprising 802 operational taxonomic units (OTUs) were obtained. After taxonomic classification, 25 phyla, 196 genera, and a high proportion of unidentified taxa were detected, among which seven phyla and 99 genera were firstly detected in Antarctica. The bacterial communities were dominated by Actinomycetota (40.40%), Pseudomonadota (17.14%), Bacteroidota (10.55%) and Chloroflexota (10.26%). Based on the HTS analyses, cultivation-dependent techniques were optimized to identify the cultivable members. A total of 30 different genera including 91 strains were obtained, the majority of which has previously been reported from Antarctica. However, for the genera Microterricola, Dyadobacter, Filibacter, Duganella, Ensifer, Antarcticirhabdus and Microvirga, this is the first report in Antarctica. In addition, seven strains represented novel taxa, two of which were psychropoilic and could be valuable resources for further research of cold-adaptability and their ecological significance in Antarctica.
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Affiliation(s)
- Siqi Cui
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, Beijing 100081, China; (S.C.); (J.D.); (L.Z.); (D.X.)
| | - Jie Du
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, Beijing 100081, China; (S.C.); (J.D.); (L.Z.); (D.X.)
| | - Lin Zhu
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, Beijing 100081, China; (S.C.); (J.D.); (L.Z.); (D.X.)
| | - Di Xin
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, Beijing 100081, China; (S.C.); (J.D.); (L.Z.); (D.X.)
| | - Yuhua Xin
- China General Microbiological Culture Collection Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China;
| | - Jianli Zhang
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, Beijing 100081, China; (S.C.); (J.D.); (L.Z.); (D.X.)
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Zhong R, Wang PR, Sun PJ, Lin W, Ren AX, Ren YK, Sun M, Gao ZQ. [Effects of Long-term Tillage on Soil Bacterial Community Structure and Physicochemical Properties of Dryland Wheat Fields in Northern China]. Huan Jing Ke Xue 2023; 44:5800-5812. [PMID: 37827795 DOI: 10.13227/j.hjkx.202210316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 10/14/2023]
Abstract
To explore the effects of long-term tillage on bacterial community structure in different soil layers of dryland wheat fields and its relationship with soil physicochemical properties, a long-term field experiment was conducted from 2016 to 2021 in Wenxi Experimental Demonstration Base of Shanxi Agricultural University, Shanxi Province. We studied the effects of no-tillage (NT), subsoiling-tillage (ST), and deep plowing (DP) on soil physicochemical properties; α and β diversity of the bacterial community; and dominant and different species of phyla and genera in different soil layers. Additionally, PICRUSt2 was used to predict the metabolic function of soil bacterial community. The results revealed that subsoiling-tillage and deep plowing significantly increased the soil water content in the 20-40 cm soil layer and significantly decreased the soil organic carbon content in the 0-20 cm soil layer compared with that under no-tillage for five consecutive years. Compared with that under deep plowing, subsoiling-tillage significantly increased soil water content, soil organic carbon content, dissolved organic carbon content, and dissolved organic nitrogen content in the 0-20 cm soil layer. Compared with that under no-tillage, subsoiling-tillage and deep plowing increased the α diversity of the soil bacterial community in the 0-40 cm soil layer, and subsoiling-tillage was higher than deep plowing. Compared with that under no-tillage, subsoiling-tillage and deep plowing significantly increased the relative abundances of Acidobacteria and Nitrospirae in the 0-20 cm soil layer and Acidobacteria, Chloroflexi, Gemmatimonadetes, Rokubacteria, GAL15, and Nitrospirae in the 20-40 cm soil layer. Compared with that under no-tillage, subsoiling-tillage and deep plowing significantly increased the relative abundance of Nitrospira in the 0-20 cm soil layer and Rubrobacter and Streptomyces in the 20-40 cm soil layer. Compared with that under deep plowing, subsoiling-tillage significantly increased the relative abundance of Acidobacteria and Gemmatimonadetes in the 0-40 cm soil layer. Redundancy analysis demonstrated that the contents of soil organic carbon, dissolved organic carbon, and dissolved organic nitrogen in the 0-20 cm soil layer exerted positive effects on Actinobacteria and Blastococcus, and the soil water content in the 0-40 cm soil layer exerted positive effects on Acidobacteria, Chloroflexi, and Gemmatimonadetes under subsoiling-tillage. The results of PICRUSt2 prediction showed that subsoiling-tillage and deep plowing significantly increased the relative abundance of amino acid metabolism and the metabolism of cofactors and vitamins but decreased the relative abundance of lipid metabolism of bacterial communities in the 20-40 cm soil layer compared with that under no-tillage. Compared with that under deep plowing, subsoiling-tillage significantly increased the relative abundances of amino acid metabolism in the 0-40 cm soil layer and other amino acid metabolism in the 0-20 cm soil layer. In conclusion, subsoiling-tillage or deep plowing could increase the soil water content, α diversity of the soil bacterial community, and their metabolic capacity in the dryland wheat fields during the summer fallow period. The relative abundance of Acidobacteria and Gemmatimonadetes and the ability of amino acid metabolism of the bacterial community were increased by subsoiling-tillage, and thus the contents of soil dissolved organic carbon and dissolved nitrogen can be increased.
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Affiliation(s)
- Rong Zhong
- College of Agriculture, Shanxi Agriculture University, Taigu 030801, China
- Collaborative Innovation Center for High-quality and Efficient Production of Characteristic Crops on the Loess Plateau Jointly Built by Provinces and Ministries, Taigu 030801, China
| | - Pei-Ru Wang
- College of Agriculture, Shanxi Agriculture University, Taigu 030801, China
- Collaborative Innovation Center for High-quality and Efficient Production of Characteristic Crops on the Loess Plateau Jointly Built by Provinces and Ministries, Taigu 030801, China
| | - Pei-Jie Sun
- College of Agriculture, Shanxi Agriculture University, Taigu 030801, China
- Collaborative Innovation Center for High-quality and Efficient Production of Characteristic Crops on the Loess Plateau Jointly Built by Provinces and Ministries, Taigu 030801, China
| | - Wen Lin
- College of Agriculture, Shanxi Agriculture University, Taigu 030801, China
- Collaborative Innovation Center for High-quality and Efficient Production of Characteristic Crops on the Loess Plateau Jointly Built by Provinces and Ministries, Taigu 030801, China
| | - Ai-Xia Ren
- College of Agriculture, Shanxi Agriculture University, Taigu 030801, China
- Collaborative Innovation Center for High-quality and Efficient Production of Characteristic Crops on the Loess Plateau Jointly Built by Provinces and Ministries, Taigu 030801, China
| | - Yong-Kang Ren
- College of Agriculture, Shanxi Agriculture University, Taigu 030801, China
- Collaborative Innovation Center for High-quality and Efficient Production of Characteristic Crops on the Loess Plateau Jointly Built by Provinces and Ministries, Taigu 030801, China
| | - Min Sun
- College of Agriculture, Shanxi Agriculture University, Taigu 030801, China
- Collaborative Innovation Center for High-quality and Efficient Production of Characteristic Crops on the Loess Plateau Jointly Built by Provinces and Ministries, Taigu 030801, China
| | - Zhi-Qiang Gao
- College of Agriculture, Shanxi Agriculture University, Taigu 030801, China
- Collaborative Innovation Center for High-quality and Efficient Production of Characteristic Crops on the Loess Plateau Jointly Built by Provinces and Ministries, Taigu 030801, China
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Hao J, Lu Y, Dang M, Xia R, Xu L, Zhu Z, Yu Y. The complete chloroplast genome sequence of Plectranthus hadiensis (Lamiaceae) and phylogenetic analysis. Mitochondrial DNA B Resour 2023; 8:1049-1053. [PMID: 37810612 PMCID: PMC10557565 DOI: 10.1080/23802359.2023.2262689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Accepted: 09/19/2023] [Indexed: 10/10/2023] Open
Abstract
Plants of the genus Plectranthus are used for the treatment of digestive problems, skin diseases, and allergies, with a wide variety of uses. Here, the complete chloroplast genome sequence of Plectranthus hadiensis (Benth. ex E.Mey) Codd. 1788 was assembled and characterized for the first time. The full length of the chloroplast genome is 152,484 bp, consisting of a small single-copy region of 17,686 bp, a large single-copy region of 83,380 bp, and a pair of inverted repeats of 51,418 bp. The overall GC content is 37.73%. The chloroplast genome contains 131 unique genes, including 87 protein-coding genes, 36 transfer RNA genes, and eight ribosomal RNA genes. Phylogenetic tree construction based on the complete chloroplast genome sequences of 25 species (23 Nepetoideae, two Ajugoideae) of the Lamiaceae family showed that P. hadiensis exhibited the closest relationship with Isodon.
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Affiliation(s)
- Jiaojiao Hao
- College of Horticulture Science, Ministry of Agriculture and Rural Affairs, Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, Zhejiang A&F University, Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable, Hangzhou, China
| | - Yanchi Lu
- College of Horticulture Science, Ministry of Agriculture and Rural Affairs, Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, Zhejiang A&F University, Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable, Hangzhou, China
| | - Menghuan Dang
- College of Horticulture Science, Ministry of Agriculture and Rural Affairs, Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, Zhejiang A&F University, Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable, Hangzhou, China
| | - Rui Xia
- College of Horticulture Science, Ministry of Agriculture and Rural Affairs, Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, Zhejiang A&F University, Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable, Hangzhou, China
| | - Liai Xu
- College of Horticulture Science, Ministry of Agriculture and Rural Affairs, Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, Zhejiang A&F University, Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable, Hangzhou, China
| | - Zhujun Zhu
- College of Horticulture Science, Ministry of Agriculture and Rural Affairs, Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, Zhejiang A&F University, Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable, Hangzhou, China
| | - Youjian Yu
- College of Horticulture Science, Ministry of Agriculture and Rural Affairs, Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, Zhejiang A&F University, Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable, Hangzhou, China
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Zhang P, Zhang F, Wu Z, Cahaeraduqin S, Liu W, Yan Y. Analysis on the salt tolerance of Nitraria sibirica Pall. based on Pacbio full-length transcriptome sequencing. Plant Cell Rep 2023; 42:1665-1686. [PMID: 37479883 DOI: 10.1007/s00299-023-03052-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 07/12/2023] [Indexed: 07/23/2023]
Abstract
KEY MESSAGE Nitraria sibirica Pall. regulates its tolerance to salt stress mainly by adjusting ion balance, modifying cell wall structure, and activating signal transduction pathways. N. sibirica, as a typical halophyte, can not only effectively restore saline-alkali land, but also has high economic value. However, studies on its salt tolerance at combining molecular and physiological levels were limited. In this study, the salt tolerance of N. sibirica was analyzed based on Pacbio full-length transcriptome sequencing, and the salt tolerance in the physiological level was verified by key genes. The results showed that 89,017 full-length transcripts were obtained, of which 84,632 sequences were annotated. A total of 86,482 coding sequences (CDS) were predicted and 6561 differentially expressed genes (DEGs) were identified. DEGs were significantly enriched in "sodium ion homeostasis", "response to osmotic stress", "reactive oxygen species metabolic process", "defense response by cell wall thickening", "signal transduction", etc. The expression levels for most of these DEGs increased under salt stress. A total of 69 key genes were screened based on weighted gene co-expression network analysis (WGCNA), of which 33 were first reported on salt tolerance. Moreover, NsRabE1c gene with the highest expression level was selected to verify its salt tolerance. Over-expression of NsRabE1c gene enhanced the germination potential and root length of transgenic Arabidopsis thaliana plants without salt treatment as compared to those of Col-0 and AtRabE1c mutant. The expression levels of NsRabE1c decreased in the growth stagnation phase, while significantly increased in the growth recovery phase under salt stress. We predicted that NsRabE1c gene help N. sibirica resist salt stress through the regulation of plant growth. The results of this study deepen the understanding of salinity resistance in N. sibirica.
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Affiliation(s)
- Panpan Zhang
- School of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, 150030, China
| | - Fengxiang Zhang
- School of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, 150030, China
| | - Zhiheng Wu
- School of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, 150030, China
| | - Sunaer Cahaeraduqin
- School of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, 150030, China
| | - Wei Liu
- School of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, 150030, China.
| | - Yongqing Yan
- School of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, 150030, China.
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Lim HGM, Fann YC, Lee YCG. COWID: an efficient cloud-based genomics workflow for scalable identification of SARS-COV-2. Brief Bioinform 2023; 24:bbad280. [PMID: 37738400 PMCID: PMC10516370 DOI: 10.1093/bib/bbad280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 07/15/2023] [Accepted: 07/19/2023] [Indexed: 09/24/2023] Open
Abstract
Implementing a specific cloud resource to analyze extensive genomic data on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) poses a challenge when resources are limited. To overcome this, we repurposed a cloud platform initially designed for use in research on cancer genomics (https://cgc.sbgenomics.com) to enable its use in research on SARS-CoV-2 to build Cloud Workflow for Viral and Variant Identification (COWID). COWID is a workflow based on the Common Workflow Language that realizes the full potential of sequencing technology for use in reliable SARS-CoV-2 identification and leverages cloud computing to achieve efficient parallelization. COWID outperformed other contemporary methods for identification by offering scalable identification and reliable variant findings with no false-positive results. COWID typically processed each sample of raw sequencing data within 5 min at a cost of only US$0.01. The COWID source code is publicly available (https://github.com/hendrick0403/COWID) and can be accessed on any computer with Internet access. COWID is designed to be user-friendly; it can be implemented without prior programming knowledge. Therefore, COWID is a time-efficient tool that can be used during a pandemic.
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Affiliation(s)
- Hendrick Gao-Min Lim
- Graduate Institute of Biomedical Informatics, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan 11031
- Department of Medical Research, Tzu Chi Hospital Indonesia, Pantai Indah Kapuk, Greater Jakarta, Indonesia 14470
| | - Yang C Fann
- IT and Bioinformatics Program, Division of Intramural, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, USA 20892
| | - Yuan-Chii Gladys Lee
- Graduate Institute of Biomedical Informatics, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan 11031
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Xiao Y, Bao F, Xu X, Yu K, Wu B, Gao Y, Zhang J. The influence of precipitation timing and amount on soil microbial community in a temperate desert ecosystem. Front Microbiol 2023; 14:1249036. [PMID: 37744930 PMCID: PMC10512721 DOI: 10.3389/fmicb.2023.1249036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 08/23/2023] [Indexed: 09/26/2023] Open
Abstract
Introduction Global climate change may lead to changes in precipitation patterns. This may have a significant impact on the microbial communities present in the soil. However, the way these communities respond to seasonal variations in precipitation, particularly in the context of increased precipitation amounts, is not yet well understood. Methods To explore this issue, a five-year (2012-2016) field study was conducted at the northeast boundary of the Ulan Buh Desert, examining the effects of increased precipitation during different periods of the growing season on both bacterial and fungal communities. The study included five precipitation pattern treatments: a control group (C), as well as groups receiving 50 and 100% of the local mean annual precipitation amount (145 mm) during either the early growing season (E50 and E100) or the late growing season (L50 and L100). The taxonomic composition of the soil bacterial and fungal communities was analyzed using Illumina sequencing. Results After 5 years, the bacterial community composition had significantly changed in all treatment groups, with soil bacteria proving to be more sensitive to changes in precipitation timing than to increased precipitation amounts within the desert ecosystem. Specifically, the alpha diversity of bacterial communities in the late growing season plots (L50 and L100) decreased significantly, while no significant changes were observed in the early growing season plots (E50 and E100). In contrast, fungal community composition remained relatively stable in response to changes in precipitation patterns. Predictions of bacterial community function suggested that the potential functional taxa in the bacterial community associated with the cycling of carbon and nitrogen were significantly altered in the late growing season (L50 and L100). Discussion These findings emphasize the importance of precipitation timing in regulating microbial communities and ecosystem functions in arid regions experiencing increased precipitation amounts.
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Affiliation(s)
- Yao Xiao
- Key Laboratory of Forest Disaster Warning and Control in Yunnan Province, Faculty of Biodiversity Conservation, Southwest Forestry University, Kunming, China
- Institute of Desertification Studies, Chinese Academy of Forestry, Beijing, China
- Institute of Ecological Conservation and Restoration, Chinese Academy of Forestry, Beijing, China
| | - Fang Bao
- Institute of Desertification Studies, Chinese Academy of Forestry, Beijing, China
- Institute of Ecological Conservation and Restoration, Chinese Academy of Forestry, Beijing, China
| | - Xiaotian Xu
- Beijing Academy of Forestry and Pomology Sciences, Beijing, China
| | - Ke Yu
- School of Environment and Energy, Shenzhen Graduate School, Peking University, Shenzhen, China
| | - Bo Wu
- Institute of Desertification Studies, Chinese Academy of Forestry, Beijing, China
- Institute of Ecological Conservation and Restoration, Chinese Academy of Forestry, Beijing, China
| | - Ying Gao
- Institute of Desertification Studies, Chinese Academy of Forestry, Beijing, China
- Institute of Ecological Conservation and Restoration, Chinese Academy of Forestry, Beijing, China
| | - Junzhong Zhang
- Key Laboratory of Forest Disaster Warning and Control in Yunnan Province, Faculty of Biodiversity Conservation, Southwest Forestry University, Kunming, China
- Key Laboratory of Forest Resources Conservation and Utilization in the Southwest Mountains of China Ministry of Education, Southwest Forestry University, Kunming, China
- Key Laboratory of State Forestry and Grassland Administration on Highly-Efficient Utilization of Forestry Biomass Resources in Southwest China, Southwest Forestry University, Kunming, China
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Chi Y, Song S, Xiong K. Effects of different grassland use patterns on soil bacterial communities in the karst desertification areas. Front Microbiol 2023; 14:1208971. [PMID: 37720153 PMCID: PMC10500843 DOI: 10.3389/fmicb.2023.1208971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 08/07/2023] [Indexed: 09/19/2023] Open
Abstract
Soil bacteria are closely related to soil environmental factors, and their community structure is an important indicator of ecosystem health and sustainability. A large number of artificial grasslands have been established to control rocky desertification in the karst areas of southern China, but the influence of different use patterns on the soil bacterial community in artificial grasslands is not clear. In this study, three grassland use patterns [i.e., grazing (GG), mowing (MG), and enclosure (EG)] were used to investigate the effects of different use patterns on the soil bacterial community in artificial grassland by using 16S rDNA Illumina sequencing and 12 soil environmental indicators. It was found that, compared with EG, GG significantly changed soil pH, increased alkaline hydrolyzable nitrogen (AN) content (P < 0.05), and decreased soil total phosphorus (TP) content (P < 0.05). However, MG significantly decreased the contents of soil organic carbon (SOC), total phosphorus (TP), available nitrogen (AN), ammonium nitrogen (NH4+-N), β-1,4-glucosidase (BG), and N-acetyl-β-D-glucamosonidase (NAG) (P < 0.05). The relative abundance of chemoheterotrophy was significantly decreased by GG and MG (P < 0.05). GG significantly increased the relative abundance of Acidobacteria and Gemmatimonadota (P < 0.05) and significantly decreased the relative abundance of Proteobacteria (P < 0.05), but the richness index (Chao 1) and diversity index (Shannon) of the bacterial community in GG, MG, and EG were not significantly different (P > 0.05). The pH (R2 = 0.79, P = 0.029) was the main factor affecting the bacterial community structure. This finding can provide a scientific reference for ecological restoration and sustainable utilization of grasslands in the karst desertification areas.
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Affiliation(s)
- Yongkuan Chi
- School of Karst Science, Guizhou Normal University, Guiyang, China
- Guizhou Engineering Laboratory for Karst Desertification Control and Eco-Industry, Guiyang, China
| | - Shuzhen Song
- School of Karst Science, Guizhou Normal University, Guiyang, China
| | - Kangning Xiong
- School of Karst Science, Guizhou Normal University, Guiyang, China
- Guizhou Engineering Laboratory for Karst Desertification Control and Eco-Industry, Guiyang, China
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Dong H, Tang X, Ye J, Xiao W. 16S rRNA gene sequencing reveals the effect of fluoxetine on gut microbiota in chronic unpredictable stress-induced depressive-like rats. Ann Gen Psychiatry 2023; 22:27. [PMID: 37537583 PMCID: PMC10398965 DOI: 10.1186/s12991-023-00458-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 07/24/2023] [Indexed: 08/05/2023] Open
Abstract
OBJECTIVES Gut microbiota is relevant to the pathogenesis of mental disorders including depression. This study aimed to investigate the influence of fluoxetine (FLX) on the gut microbiota in rats with Chronic Unpredictable Mild Stresses (CUMS)-induced depression. RESULTS We confirmed that the 28-day CUMS-induced depression rat model. Chronic FLX administration weakly improved depressive-like behaviors in rats. Illumina 16S rRNA gene sequencing on rat feces showed CUMS increased the relative abundance of Firmicutes (60.31% vs. 48.09% in Control, p < 0.05) and Lactobacillus genus (21.06% vs. 6.82% in control, p < 0.05); FLX and CUMS increased Bacilli class (20.00% ~ 24.08% vs. 10.31% in control, p < 0.05). CONCLUSION Collectively, our study showed that both CUMS and FLX changed the compositions of gut microbiota in rats. FLX and CUMS distinctly regulated the gut microbiota in depressed rats.
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Affiliation(s)
- Hui Dong
- Teaching hospital of Yangzhou University, Wutaishan Hospital, Yangzhou, Jiangsu Province, China.
| | - Xiaowei Tang
- Teaching hospital of Yangzhou University, Wutaishan Hospital, Yangzhou, Jiangsu Province, China
| | - Jie Ye
- Teaching hospital of Yangzhou University, Wutaishan Hospital, Yangzhou, Jiangsu Province, China
| | - Wenhuan Xiao
- Teaching hospital of Yangzhou University, Wutaishan Hospital, Yangzhou, Jiangsu Province, China
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Khan MH, Liu H, Zhu A, Khan MH, Hussain S, Cao H. Conservation tillage practices affect soil microbial diversity and composition in experimental fields. Front Microbiol 2023; 14:1227297. [PMID: 37601340 PMCID: PMC10433396 DOI: 10.3389/fmicb.2023.1227297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 07/06/2023] [Indexed: 08/22/2023] Open
Abstract
Introduction Conservation tillage is a widely used technique worldwide, but the effects of conservation tillage on bacterial community structure are poorly understood. We explored proportional alterations in the bacterial community under different tillage treatments. Methodology Hence, this study utilized high-throughput sequencing technique to investigate the structure and assembly processes of microbial communities in different tillage treatments. Results and discussion Tillage treatments included tillage no-straw retention (CntWt), no-tillage with straw retention (CntWntS), tillage with straw retention (CntWtS), no-tillage and no-straw retention (CntWnt). The influence of tillage practices on soil bacterial communities was investigated using Illumina MiSeq sequencing. Different tillage methods and straw retention systems significantly influenced soil parameters such as total potassium and pH were not affected by tillage practices, while straw retention significantly affected soil parameters including nitrogen content, available phosphorus and available potassium. Straw retention decreased bacterial diversity while increased bacterial richness. The effect of straw retention and tillage on bacterial communities was greater than with no tillage. Phylogenetic β-diversity analysis showed that deterministic homogeneous selection processes were dominated, while stochastic processes were more pronounced in tillage without straw retention. Ecological network analysis showed that microbial community correlation was increased in CntWntS and CntWnt. Straw retention treatment significantly increased the relative abundance of bacterial taxa Proteobacteria, Bacteroidetes, and OD1, while Nitrospirae, Actinobacteria, and Verrucomicrobia significantly decreased. Conclusion The conservation tillage practices significantly affect soil properties, bacterial composition, and assembly processes; however, further studies are required to investigate the impact of different crops, tillage practices and physiological characteristics on bacterial community structure and functions.
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Affiliation(s)
- Muzammil Hassan Khan
- College of Life Sciences/Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, Nanjing Agricultural University, Nanjing, China
| | - Hao Liu
- College of Life Sciences/Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, Nanjing Agricultural University, Nanjing, China
| | - Anning Zhu
- Fengqiu Agro-Ecological Experimental Station, State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Mudassir Hassan Khan
- Department of Biological Sciences, Karakoram International University, Gilgit, Pakistan
| | - Sarfraz Hussain
- College of Life Sciences/Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, Nanjing Agricultural University, Nanjing, China
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes of Ministry of Education, College of Environment, Hohai University, Nanjing, China
| | - Hui Cao
- College of Life Sciences/Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, Nanjing Agricultural University, Nanjing, China
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Abstract
Background Kawasaki disease (KD) is a multi-systemic vasculitis that primarily affects children and has an unknown cause. Although an increasing number of studies linking the gut microbiota with KD, the unchallengeable etiology of KD is not available. Methods Here, we obtained fecal and oral samples from KD patients and healthy controls, and then we use high-throughput sequencing to examine the diversity and composition of microbiota. Results Results showed that both in the gut and oral microbiota, the diversity of KD patients was significantly lower than that of the healthy controls. In the gut microbiota, a higher abundance of Enterococcus (40.12% vs less than 0.1%), Bifidobacterium (20.71% vs 3.06%), Escherichia-Shigella (17.56% vs 0.61%), Streptococcus (5.97% vs 0.11%) and Blautia (4.69% vs 0.1%) was observed in the KD patients, and enrichment of Enterococcus in the patients was observed. In terms of oral microbiota, the prevalence of Streptococcus (21.99% vs 0.1%), Rothia (3.02% vs 0.1%), and Escherichia-Shigella (0.68% vs 0.0%) were significantly higher in the KD patients, with the enrichment of Streptococcus and Escherichia-Shigella. Additionally, significant differences in microbial community function between KD patients and healthy controls in the fecal samples were also observed, which will affect the colonization and reproduction of gut microbiota. Conclusions These results suggested that the dysbiosis of gut and oral microbiota are both related to KD pathogenesis, of which, the prevalence of Enterococcus in the gut and higher abundance of Streptococcus and Escherichia-Shigella in the oral cavity will be a potential biomarker of the KD. Overall, this study not only confirms that the disturbance of gut microbiota is a causative trigger of KD but also provides new insight into the oral microbiota involved in KD pathogenesis.
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Affiliation(s)
- Qinghuang Zeng
- School of Clinical Medicine, Fujian Medical University, Fuzhou, China
- Affiliated Hospital of Putian University, Putian, Fujian, China
| | - Renhe Zeng
- School of Clinical Medicine, Fujian Medical University, Fuzhou, China
- Affiliated Hospital of Putian University, Putian, Fujian, China
| | - Jianbin Ye
- School of Basic Medicine Science, Putian University, Putian, China
- School of Pharmarcy, Fujian Medical University, Fuzhou, China
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Tombácz D, Torma G, Gulyás G, Fülöp Á, Dörmő Á, Prazsák I, Csabai Z, Mizik M, Hornyák Á, Zádori Z, Kakuk B, Boldogkői Z. Hybrid sequencing discloses unique aspects of the transcriptomic architecture in equid alphaherpesvirus 1. Heliyon 2023; 9:e17716. [PMID: 37449092 PMCID: PMC10336594 DOI: 10.1016/j.heliyon.2023.e17716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 06/05/2023] [Accepted: 06/26/2023] [Indexed: 07/18/2023] Open
Abstract
This study employed both short-read sequencing (SRS, Illumina) and long-read sequencing (LRS Oxford Nanopore Technologies) platforms to conduct a comprehensive analysis of the equid alphaherpesvirus 1 (EHV-1) transcriptome. The study involved the annotation of canonical mRNAs and their transcript variants, encompassing transcription start site (TSS) and transcription end site (TES) isoforms, in addition to alternative splicing forms. Furthermore, the study revealed the presence of numerous non-coding RNA (ncRNA) molecules, including intergenic and antisense transcripts, produced by EHV-1. An intriguing finding was the abundant production of chimeric transcripts, some of which potentially encode fusion polypeptides. Moreover, EHV-1 exhibited a greater incidence of transcriptional overlaps and splicing compared to related viruses. It is noteworthy that many genes have their unique TESs along with the co-terminal transcription ends, a characteristic scarcely seen in other alphaherpesviruses. The study also identified transcripts that overlap the replication origins of the virus. Moreover, a novel ncRNA, referred to as NOIR, was found to intersect with the 5'-ends of longer transcript isoform specified by the major transactivator genes ORF64 and ORF65, surrounding the OriL. These findings together imply the existence of a key regulatory mechanism that governs both transcription and replication through, among others, a process that involves interference between the DNA and RNA synthesis machineries.
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Affiliation(s)
- Dóra Tombácz
- Department of Medical Biology, Faculty of Medicine, University of Szeged, Szeged, Hungary
| | - Gábor Torma
- Department of Medical Biology, Faculty of Medicine, University of Szeged, Szeged, Hungary
| | - Gábor Gulyás
- Department of Medical Biology, Faculty of Medicine, University of Szeged, Szeged, Hungary
| | - Ádám Fülöp
- Department of Medical Biology, Faculty of Medicine, University of Szeged, Szeged, Hungary
| | - Ákos Dörmő
- Department of Medical Biology, Faculty of Medicine, University of Szeged, Szeged, Hungary
| | - István Prazsák
- Department of Medical Biology, Faculty of Medicine, University of Szeged, Szeged, Hungary
| | - Zsolt Csabai
- Department of Medical Biology, Faculty of Medicine, University of Szeged, Szeged, Hungary
| | - Máté Mizik
- Department of Medical Biology, Faculty of Medicine, University of Szeged, Szeged, Hungary
| | - Ákos Hornyák
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Budapest, Hungary
| | - Zoltán Zádori
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Budapest, Hungary
| | - Balázs Kakuk
- Department of Medical Biology, Faculty of Medicine, University of Szeged, Szeged, Hungary
| | - Zsolt Boldogkői
- Department of Medical Biology, Faculty of Medicine, University of Szeged, Szeged, Hungary
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Schröder L, Rupp O, Senkler M, Rugen N, Hohnjec N, Goesmann A, Küster H, Braun HP. The Viscum album Gene Space database. Front Plant Sci 2023; 14:1193122. [PMID: 37484460 PMCID: PMC10359728 DOI: 10.3389/fpls.2023.1193122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 06/02/2023] [Indexed: 07/25/2023]
Abstract
The hemiparasitic flowering plant Viscum album (European mistletoe) is known for its very special life cycle, extraordinary biochemical properties, and extremely large genome. The size of its genome is estimated to be 30 times larger than the human genome and 600 times larger than the genome of the model plant Arabidopsis thaliana. To achieve insights into the Gene Space of the genome, which is defined as the space including and surrounding protein-coding regions, a transcriptome project based on PacBio sequencing has recently been conducted. A database resulting from this project contains sequences of 39,092 different open reading frames encoding 32,064 distinct proteins. Based on 'Benchmarking Universal Single-Copy Orthologs' (BUSCO) analysis, the completeness of the database was estimated to be in the range of 78%. To further develop this database, we performed a transcriptome project of V. album organs harvested in summer and winter based on Illumina sequencing. Data from both sequencing strategies were combined. The new V. album Gene Space database II (VaGs II) contains 90,039 sequences and has a completeness of 93% as revealed by BUSCO analysis. Sequences from other organisms, particularly fungi, which are known to colonize mistletoe leaves, have been removed. To evaluate the quality of the new database, proteome data of a mitochondrial fraction of V. album were re-analyzed. Compared to the original evaluation published five years ago, nearly 1000 additional proteins could be identified in the mitochondrial fraction, providing new insights into the Oxidative Phosphorylation System of V. album. The VaGs II database is available at https://viscumalbum.pflanzenproteomik.de/. Furthermore, all V. album sequences have been uploaded at the European Nucleotide Archive (ENA).
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Affiliation(s)
- Lucie Schröder
- Plant Proteomics, Institute of Plant Genetics, Leibniz Universität Hannover, Hannover, Germany
| | - Oliver Rupp
- Bioinformatics and Systems Biology, Justus-Liebig-Universität Gießen, Gießen, Germany
| | - Michael Senkler
- Plant Proteomics, Institute of Plant Genetics, Leibniz Universität Hannover, Hannover, Germany
| | - Nils Rugen
- Plant Proteomics, Institute of Plant Genetics, Leibniz Universität Hannover, Hannover, Germany
| | - Natalija Hohnjec
- Plant Genomics, Institute of Plant Genetics, Leibniz Universität Hannover, Hannover, Germany
| | - Alexander Goesmann
- Bioinformatics and Systems Biology, Justus-Liebig-Universität Gießen, Gießen, Germany
| | - Helge Küster
- Plant Genomics, Institute of Plant Genetics, Leibniz Universität Hannover, Hannover, Germany
| | - Hans-Peter Braun
- Plant Proteomics, Institute of Plant Genetics, Leibniz Universität Hannover, Hannover, Germany
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Lamb CE, Watts JEM. Microbiome species diversity and seasonal stability of two temperate marine sponges Hymeniacidon perlevis and Suberites massa. Environ Microbiome 2023; 18:52. [PMID: 37291644 DOI: 10.1186/s40793-023-00508-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 05/26/2023] [Indexed: 06/10/2023]
Abstract
BACKGROUND Marine sponges are diverse and functionally important members of marine benthic systems, well known to harbour complex and abundant symbiotic microorganisms as part of their species-specific microbiome. Changes in the sponge microbiome have previously been observed in relation to natural environmental changes, including nutrient availability, temperature and light. With global climate change altering seasonal temperatures, this study aims to better understand the potential effects of natural seasonal fluctuations on the composition and functions of the sponge microbiome. RESULTS Metataxonomic sequencing of two marine sponge species native to the U.K. (Hymeniacidon perlevis and Suberites massa) was performed at two different seasonal temperatures from the same estuary. A host-specific microbiome was observed in each species between both seasons. Detected diversity within S. massa was dominated by one family, Terasakiellaceae, with remaining dominant families also being detected in the associated seawater. H. perlevis demonstrated sponge specific bacterial families including aforementioned Terasakiellaceae as well as Sphingomonadaceae and Leptospiraceae with further sponge enriched families present. CONCLUSIONS To our knowledge, these results describe for the first time the microbial diversity of the temperate marine sponge species H. perlevis and S. massa using next generation sequencing. This analysis detected the presence of core sponge taxa identified in each sponge species was not changed by seasonal temperature alterations, however, there were shifts observed in overall community composition due to fluctuations in less abundant taxa, demonstrating that microbiome stability across seasons is likely to be host species specific.
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Affiliation(s)
| | - Joy E M Watts
- Centre for Enzyme Innovation, Portsmouth, UK.
- School of Biological Sciences, University of Portsmouth, Portsmouth, UK.
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44
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Bendele KG, Guerrero FD, Lohmeyer KH, Foil LD, Metz RP, Johnson CD. Horn fly transcriptome data of ten populations from the southern United States with varying degrees and molecular mechanisms of pesticide resistance. Data Brief 2023; 48:109272. [PMID: 37363058 PMCID: PMC10285531 DOI: 10.1016/j.dib.2023.109272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 05/13/2023] [Accepted: 05/22/2023] [Indexed: 06/28/2023] Open
Abstract
Haematobia irritans irritans (Linnaeus, 1758: Diptera: Muscidae), the horn fly, is an external parasite of penned and pastured livestock that causes a major economic impact on cattle production worldwide. Pesticides such as synthetic pyrethroids and organophosphates are routinely used to control horn flies; however, resistance to these chemicals has become a concern in several countries. To further elucidate the molecular mechanisms of resistance in horn fly populations, we sequenced the transcriptomes of ten populations of horn flies from the southern US possessing varying degrees of pesticide resistance levels to pyrethroids, organophosphates, and endosulfans. We employed an Illumina paired end HiSeq approach, followed by de novo assembly of the transcriptomes using CLC Genomics Workbench 8.0.1 De Novo Assembler using multiple kmers, and annotation using Blast2GO PRO version 5.2.5. The Gene Ontology biological process term Response to Insecticide was found in all the populations, but at an increased frequency in the populations with higher levels of insecticide resistance. The raw sequence reads are archived in the Sequence Read Archive (SRA) and assembled population transcriptomes in the Transcriptome Shotgun Assembly (TSA) at the National Center for Biotechnology Information (NCBI).
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Affiliation(s)
- Kylie G. Bendele
- USDA-ARS Knipling-Bushland US Livestock Insects Research Laboratory, 2700 Fredericksburg Rd., Kerrville, TX 78028, USA
| | - Felix D. Guerrero
- USDA-ARS Knipling-Bushland US Livestock Insects Research Laboratory, 2700 Fredericksburg Rd., Kerrville, TX 78028, USA
- Massey University, School of Veterinary Science, Genetics and Molecular Biology, Private Bag 11 222, Palmerston North, Manawatu-Wanganui 4442, New Zealand
| | - Kimberly H. Lohmeyer
- USDA-ARS Knipling-Bushland US Livestock Insects Research Laboratory, 2700 Fredericksburg Rd., Kerrville, TX 78028, USA
| | - Lane D. Foil
- Department of Entomology, Louisiana State University Agriculture Center, Baton Rouge, LA 70803, USA
| | - Richard P. Metz
- Genomics and Bioinformatics Service, Texas A&M AgriLife Research, 1500 Research Parkway, Room 250, Centeq Building A, College Station, TX 77845, USA
| | - Charles D. Johnson
- Genomics and Bioinformatics Service, Texas A&M AgriLife Research, 1500 Research Parkway, Room 250, Centeq Building A, College Station, TX 77845, USA
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Brinkmann A, Kohl C, Pape K, Bourquain D, Thürmer A, Michel J, Schaade L, Nitsche A. Extensive ITR expansion of the 2022 Mpox virus genome through gene duplication and gene loss. Virus Genes 2023:10.1007/s11262-023-02002-1. [PMID: 37256469 DOI: 10.1007/s11262-023-02002-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 04/29/2023] [Indexed: 06/01/2023]
Abstract
Poxviruses are known to evolve slower than RNA viruses with only 1-2 mutations/genome/year. Rather than single mutations, rearrangements such as gene gain and loss, which have been discussed as a possible driver for host adaption, were described in poxviruses. In 2022 and 2023 the world is being challenged by the largest global outbreak so far of Mpox virus, and the virus seems to have established itself in the human community for an extended period of time. Here, we report five Mpox virus genomes from Germany with extensive gene duplication and loss, leading to the expansion of the ITR regions from 6400 to up to 24,600 bp. We describe duplications of up to 18,200 bp to the opposed genome end, and deletions at the site of insertion of up to 16,900 bp. Deletions and duplications of genes with functions of supposed immune modulation, virulence and host adaption as B19R, B21R, B22R and D10L are described. In summary, we highlight the need for monitoring rearrangements of the Mpox virus genome rather than for monitoring single mutations only.
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Affiliation(s)
- Annika Brinkmann
- Centre for Biological Threats and Special Pathogens, WHO Collaborating Centre for Emerging Infections and Biological Threats, Highly Pathogenic Viruses, German Consultant Laboratory for Poxviruses, Robert Koch Institute, Seestraße 10, 13353, Berlin, Germany.
| | - Claudia Kohl
- Centre for Biological Threats and Special Pathogens, WHO Collaborating Centre for Emerging Infections and Biological Threats, Highly Pathogenic Viruses, German Consultant Laboratory for Poxviruses, Robert Koch Institute, Seestraße 10, 13353, Berlin, Germany
| | - Katharina Pape
- Centre for Biological Threats and Special Pathogens, WHO Collaborating Centre for Emerging Infections and Biological Threats, Highly Pathogenic Viruses, German Consultant Laboratory for Poxviruses, Robert Koch Institute, Seestraße 10, 13353, Berlin, Germany
| | - Daniel Bourquain
- Centre for Biological Threats and Special Pathogens, WHO Collaborating Centre for Emerging Infections and Biological Threats, Highly Pathogenic Viruses, German Consultant Laboratory for Poxviruses, Robert Koch Institute, Seestraße 10, 13353, Berlin, Germany
| | - Andrea Thürmer
- Genome Sequencing and Genomic Epidemiology, Methodology and Research Infrastructure, Robert Koch Institute, Seestraße 10, 13353, Berlin, Germany
| | - Janine Michel
- Centre for Biological Threats and Special Pathogens, WHO Collaborating Centre for Emerging Infections and Biological Threats, Highly Pathogenic Viruses, German Consultant Laboratory for Poxviruses, Robert Koch Institute, Seestraße 10, 13353, Berlin, Germany
| | - Lars Schaade
- Centre for Biological Threats and Special Pathogens, WHO Collaborating Centre for Emerging Infections and Biological Threats, Highly Pathogenic Viruses, German Consultant Laboratory for Poxviruses, Robert Koch Institute, Seestraße 10, 13353, Berlin, Germany
| | - Andreas Nitsche
- Centre for Biological Threats and Special Pathogens, WHO Collaborating Centre for Emerging Infections and Biological Threats, Highly Pathogenic Viruses, German Consultant Laboratory for Poxviruses, Robert Koch Institute, Seestraße 10, 13353, Berlin, Germany
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Li KK, Lau B, Suárez NM, Camiolo S, Gunson R, Davison AJ, Orton RJ. Direct Nanopore Sequencing of Human Cytomegalovirus Genomes from High-Viral-Load Clinical Samples. Viruses 2023; 15:1248. [PMID: 37376548 DOI: 10.3390/v15061248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 05/18/2023] [Accepted: 05/22/2023] [Indexed: 06/29/2023] Open
Abstract
Nanopore sequencing is becoming increasingly commonplace in clinical settings, particularly for diagnostic assessments and outbreak investigations, due to its portability, low cost, and ability to operate in near real-time. Although high sequencing error rates initially hampered the wider implementation of this technology, improvements have been made continually with each iteration of the sequencing hardware and base-calling software. Here, we assess the feasibility of using nanopore sequencing to determine the complete genomes of human cytomegalovirus (HCMV) in high-viral-load clinical samples without viral DNA enrichment, PCR amplification, or prior knowledge of the sequences. We utilised a hybrid bioinformatic approach that involved assembling the reads de novo, improving the consensus sequence by aligning reads to the best-matching genome from a collated set of published sequences, and polishing the improved consensus sequence. The final genomes from a urine sample and a lung sample, the former with an HCMV to human DNA load approximately 50 times greater than the latter, achieved 99.97 and 99.93% identity, respectively, to the benchmark genomes obtained independently by Illumina sequencing. Thus, we demonstrated that nanopore sequencing is capable of determining HCMV genomes directly from high-viral-load clinical samples with a high accuracy.
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Affiliation(s)
- Kathy K Li
- Medical Research Council, University of Glasgow Centre for Virus Research, Glasgow G61 1QH, UK
- Regional Virus Laboratory, Belfast Health and Social Care Trust, Belfast BT12 6BA, UK
| | - Betty Lau
- Medical Research Council, University of Glasgow Centre for Virus Research, Glasgow G61 1QH, UK
| | - Nicolás M Suárez
- Medical Research Council, University of Glasgow Centre for Virus Research, Glasgow G61 1QH, UK
| | - Salvatore Camiolo
- Medical Research Council, University of Glasgow Centre for Virus Research, Glasgow G61 1QH, UK
| | - Rory Gunson
- West of Scotland Specialist Virology Centre, NHS Greater Glasgow & Clyde, Glasgow G31 2ER, UK
| | - Andrew J Davison
- Medical Research Council, University of Glasgow Centre for Virus Research, Glasgow G61 1QH, UK
| | - Richard J Orton
- Medical Research Council, University of Glasgow Centre for Virus Research, Glasgow G61 1QH, UK
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Azziz G, Frade C, Igual JM, Del Pino A, Lezama F, Valverde Á. Legume Overseeding and P Fertilization Increases Microbial Activity and Decreases the Relative Abundance of AM Fungi in Pampas Natural Pastures. Microorganisms 2023; 11:1383. [PMID: 37374885 DOI: 10.3390/microorganisms11061383] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 05/19/2023] [Accepted: 05/23/2023] [Indexed: 06/29/2023] Open
Abstract
Natural grasslands provide a valuable resource for livestock grazing. In many parts of South America, legume overseeding and P fertilization are commonly used to enhance primary productivity. The effect of this practice on the plant community is well established. However, how this management regime affects the soil microbiome is less known. Here, to contribute to filling this knowledge gap, we analyzed the effect of Lotus subbiflorus overseeding, together with P fertilization, on soil microbial community diversity and activity in the Uruguayan Pampa region. The results showed that plant communities in the natural grassland paddocks significantly differed from those of the managed paddocks. In contrast, neither microbial biomass and respiration nor microbial diversity was significantly affected by management, although the structure of the bacterial and fungal communities were correlated with those of the plant communities. AM Fungi relative abundance, as well as several enzyme activities, were significantly affected by management. This could have consequences for the C, N, and P content of SOM in these soils, which in turn might affect SOM degradation.
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Affiliation(s)
- Gastón Azziz
- Laboratorio de Microbiología, Departamento de Biología Vegetal, Facultad de Agronomía, Universidad de la República, Montevideo 12900, Uruguay
| | - Cristina Frade
- Grupo de Interacción Planta-Microorganismo, Instituto de Recursos Naturales y Agrobiología de Salamanca, CSIC, 37008 Salamanca, Spain
| | - José M Igual
- Grupo de Interacción Planta-Microorganismo, Instituto de Recursos Naturales y Agrobiología de Salamanca, CSIC, 37008 Salamanca, Spain
| | - Amabelia Del Pino
- Departamento de Suelos y Aguas, Facultad de Agronomía, Universidad de la República, Montevideo 12900, Uruguay
| | - Felipe Lezama
- Departamento de Sistemas Ambientales, Facultad de Agronomía, Universidad de la República, Montevideo 12900, Uruguay
| | - Ángel Valverde
- Grupo de Interacción Planta-Microorganismo, Instituto de Recursos Naturales y Agrobiología de Salamanca, CSIC, 37008 Salamanca, Spain
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Sun YQ, Ge Y. Relic DNA effects on the estimates of bacterial community composition and taxa dynamics in soil. Appl Microbiol Biotechnol 2023:10.1007/s00253-023-12576-3. [PMID: 37191685 DOI: 10.1007/s00253-023-12576-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 04/07/2023] [Accepted: 05/09/2023] [Indexed: 05/17/2023]
Abstract
DNA-based analyses have become routine methods in soil microbial research, for their high throughput and resolution in characterizing microbial communities. Yet, concerns arise regarding the interference of relic DNA in estimates of viable bacterial community composition and individual taxa dynamics in soils that recovered from post-gamma irradiation. In this study, different soil samples with varying bacterial diversity but similar soil properties were randomly selected. We split each sample into two parts: one part was treated with propidium monoazide (PMA) before DNA extraction, PMA can bind to relic DNA and inhibit PCR amplification by chemical modification; DNA of the other part was extracted following the same process but without PMA pretreatment. Then, soil bacterial abundance was quantified by quantitative polymerase chain reaction, and bacterial community structure was examined by Illumina metabarcoding sequencing of 16S rRNA gene. The results showed that the higher bacterial richness and evenness were estimated when relic DNA was present. The variation trends of bacterial abundance, alpha diversity, and beta diversity remained the same, as reflected by the significant correlations between PMA-treated and -untreated samples (P < 0.05). Moreover, as the mean abundance increased, the reproducibility of detecting individual taxa dynamics between relic DNA present and absent treatments increased. These findings provide empirical evidence that a more even distribution of species abundance derived from relic DNA would result in the overestimation of richness in the total DNA pools and also have crucial implications for guiding proper application of high-throughput sequencing to estimate bacterial community diversity and taxonomic population dynamic. KEY POINTS: • Relic DNA effects on the bacterial community in sterilized soils were assessed. • More even species abundance distribution in relic DNA overestimates true richness. • The reproducibility of individual taxa dynamics increased with their abundance.
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Affiliation(s)
- Yao-Qin Sun
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yuan Ge
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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Prajapati MR, Singh J, Kumar P, Dixit R. De novo transcriptome analysis and identification of defensive genes in garlic (Allium sativum L.) using high-throughput sequencing. J Genet Eng Biotechnol 2023; 21:56. [PMID: 37162611 PMCID: PMC10172436 DOI: 10.1186/s43141-023-00499-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 04/20/2023] [Indexed: 05/11/2023]
Abstract
BACKGROUND Garlic (Allium sativum L.) is the second most widely cultivated Allium which is mainly grown in temperate regions and used as a flavoring agent in a wide variety of foods. Garlic contains various bioactive compounds whose metabolic pathways, plant-pathogen interactions, defensive genes, identify interaction networks, and functional genomics were not previously predicted in the garlic at the genomic level. To address this issue, we constructed two garlic Illumina 2000 libraries from tissues of garlic clove and leaf. RESULTS Approximately 43 million 125 bp paired-end reads were obtained in the two libraries. A total of 239,973 contigs were generated by de novo assembly of both samples and were compared with the sequences in the NCBI non-redundant protein database (Nr). In total, 42% of contigs were matched to known proteins in public databases including Nr, Gene Ontology (GO), and Cluster Orthologous Gene Database (COG), and then, contigs were mapped to 138 via functional annotation against the Kyoto Encyclopedia of Genes and Genomes pathway database (KEGG). In addition, a number of regulatory genes including the CCHC (Zn) family, followed by WD40, bromodomain, bZIP, AP2-EREBP, BED-type (Zn) proteins, and defense response proteins related to different conserved domains, such as RGA3, NBS-LRR, TIR-NBS-LRR, LRR, NBS-ARC, and CC-NBS-LRR were discovered based on the transcriptome dataset. We compared the ortholog gene family of the A. sativum transcriptome to A. thaliana, O. sativa, and Z. mays and found that 12,077 orthologous gene families are specific to A. sativum L. Furthermore, we identified genes involved in plant defense mechanisms, their protein-protein interaction network, and plant-pathogen interaction pathways. CONCLUSIONS Our study contains an extensive sequencing and functional gene-annotation analysis of A. sativum L. The findings provide insights into the molecular basis of TFs, defensive genes, and a reference for future studies on the genetics and breeding of A. sativum L.
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Affiliation(s)
- Malyaj R Prajapati
- Division of Microbial and Environmental Biotechnology, College of Biotechnology, Sardar Vallabhbhai Patel University of Agriculture and Technology, Meerut, Uttar Pradesh, 250110, India
| | - Jitender Singh
- Department of Microbiology, Chaudhary Charan Singh University, Meerut, Uttar Pradesh, 250004, India.
| | - Pankaj Kumar
- Division of Microbial and Environmental Biotechnology, College of Biotechnology, Sardar Vallabhbhai Patel University of Agriculture and Technology, Meerut, Uttar Pradesh, 250110, India.
| | - Rekha Dixit
- Division of Microbial and Environmental Biotechnology, College of Biotechnology, Sardar Vallabhbhai Patel University of Agriculture and Technology, Meerut, Uttar Pradesh, 250110, India
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Schoen R, de Koning PPM, de Krom C, Oplaat C, Westenberg M, Massart S, Temple C, De Jonghe K, Blouin AG, Botermans M. First report of lettuce ring necrosis virus in chili pepper and tomato in Belgium and The Netherlands. Plant Dis 2023. [PMID: 37093167 DOI: 10.1094/pdis-01-23-0036-pdn] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Lettuce ring necrosis virus (LRNV), genus Ophiovirus, was detected by the Netherlands Institute for Vectors, Invasive plants and Plant health (NIVIP) in June and November of 2021 in two samples of chili pepper fruits (Capsicum spp.), both in mixed infection with other viruses. The first sample originated from a production site in Belgium (Sample ID: 40009704) and the second from a production site in the Netherlands (Sample ID: 41115269). One of the fruits of 40009704 showed a light purple circular pattern, while fruits from 41115269 showed colored (ring)spots. The samples were analyzed using Illumina sequencing on a NovaSeq 6000 platform (PE 150) as described previously (Hammond et al., 2021), obtaining 39.9M and 22.8M total reads for 40009704 and 41115269. The corresponding sequence read archives (SRA) were deposited in the NCBI SRA database under BioProject accession number PRJNA917231. From both samples, the nearly complete genome of LRNV (RNA1-4) was obtained and deposited in GenBank (40009704, OQ160823- OQ160826 (7616, 1799, 1502, 1382 nt, mapped reads: 40K, 12K, 114K, 12K , average read coverage (ARC): 0.8K, 0.9K, 11.3K and 1.1K); 41115269, OQ160827- OQ160830 (7616, 1801, 1518, 1389 nt, mapped reads: 112K, 7K, 357K, 55K reads, ARC: 2.2K, 0.6K, 34K and 5.8K)). The shared sequence identities with the Genbank reference sequence of LRNV (NC_006051-NC_006051) were 99.2 and 99.2% (RNA1), 99.1 and 99.1% (RNA2), 98.3 and 98.8% (RNA3), 99.0 and 98.9% (RNA4) for 40009704 and 41115269 respectively. The shared sequence identities between 40009704 and 41115269 were 99.9 (RNA1), 99.0 (RNA2), 99.1 (RNA3) and 99.5% (RNA4). In addition to LRNV, the ophiovirus ranunculus white mottle virus (RWMV) was detected in both samples (OQ160831-OQ160834; OQ160835-OQ160838), while the tobamovirus pepper mild mottle virus (PMMoV) was present in the fruits of 41115269 (OQ160839). Since RWMV has been associated with leaf symptoms in pepper (Gambley et al., 2019; Rivarez et al., 2022) and the colored (ring)spots of 41115269 were very similar to reported symptoms of PMMoV-infected pepper fruits (Martínez-Ochoa et al., 2003), it remains unclear whether LRNV contributed to the observed symptoms. Additionally, LRNV was detected in tomato (Solanum lycopersicum) in Belgium in 2020. In the frame of a metagenomic survey using Virion-Associated Nucleic Acids (VANA)-based protocol (Maclot et al., 2021) on a Nextseq 500 platform (PE 150), partial genome sequences of LRNV were detected in two pools of tomato plants. One pool was made of 44 asymptomatic cultivars from a non-commercial grower (one sample per cultivar) yielding 118K total reads of which 84, 59, 335, and 18 reads mapped on RNA1, 2, 3, and 4, covering 35%, 69%, 100% and 55% of the genome, respectively. The other pool consisted of 15 plants from one cultivar from a production site yielding 3.1M total reads of which 6 and 5 reads mapped on RNA3 and 4, respectively. The detection of LRNV was confirmed for both pooled samples using the real-time RT-PCR method, targeting the CP gene, as described by Maachi et al. (2021). To our knowledge this is the first report of LRNV in pepper anywhere in the world. Additionally, although the disease lettuce ring necrosis in lettuce (Lactuca sativa) has been described in Belgium and the Netherlands before the causal agent was identified (Bos & Huijberts, 1996), this is the first official report of this virus in Belgium and the Netherlands. This publication resulted from pre-publication data sharing of sequences and biological data among plant virologists to provide more context to two independent findings (Hammond et al., 2021). Bos, L., & Huijberts, N. (1996). Lettuce ring necrosis, caused by a chytrid-borne agent distinct from lettuce big-vein 'virus'. European Journal of Plant Pathology, 102(9), 867-873. https://doi.org/10.1007/bf01877057 Gambley, C., Persley, D., & Thomas, J. E. (2019). First record of Ranunculus white mottle virus from Australia. New Disease Reports, 40(1), 13-13. https://doi.org/10.5197/j.2044-0588.2019.040.013 Hammond, J., Adams, I. P., Fowkes, A. R., McGreig, S., Botermans, M., Oorspronk, J. J. A., Westenberg, M., Verbeek, M., Dullemans, A. M., Stijger, C. C. M. M., Blouin, A. G., Massart, S., De Jonghe, K., Heyneman, M., Walsh, J. A., & Fox, A. (2021). Sequence analysis of 43-year old samples of Plantago lanceolata show that Plantain virus X is synonymous with Actinidia virus X and is widely distributed. Plant Pathology, 70, 249-258. https://doi.org/10.1111/ppa.13310 Maachi, A., Torre, C., Sempere, R. N., Hernando, Y., Aranda, M. A., & Donaire, L. (2021). Use of High-Throughput Sequencing and Two RNA Input Methods to Identify Viruses Infecting Tomato Crops. Microorganisms, 9(5). https://doi.org/10.3390/microorganisms9051043 Maclot, F. J., Debue, V., Blouin, A. G., Fontdevila Pareta, N., Tamisier, L., Filloux, D., & Massart, S. (2021). Identification, molecular and biological characterization of two novel secovirids in wild grass species in Belgium. Virus Res, 298, 198397. https://doi.org/10.1016/j.virusres.2021.198397 Martínez-Ochoa, N., Langston, D. B., Mullis, S. W., & Flanders, J. T. (2003). First Report of Pepper mild mottle virus in Jalapeno Pepper in Georgia. Plant Health Progress, 4(1). https://doi.org/10.1094/php-2003-1223-01-hn Rivarez, M. P. S., Kogej, Z., Jakos, N., Pecman, A., Seljak, G., Vucurovic, A., Ravnikar, M., Mehle, N., & Kutnjak, D. (2022). First Report of Ranunculus White Mottle Ophiovirus in Slovenia in Pepper with Yellow Leaf Curling Symptom and in Tomato. Plant Dis, PDIS08211624PDN. https://doi.org/10.1094/PDIS-08-21-1624-PDN.
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Affiliation(s)
- Ruben Schoen
- Dutch National Plant Protection Organization, Netherlands Institute for Vectors, Invasive plants and Plant health (NIVIP), Wageningen, Gelderland, Netherlands;
| | - Pier P M de Koning
- Dutch National Plant Protection Organization, Netherlands Institute for Vectors, Invasive plants and Plant health (NIVIP), Wageningen, Gelderland, Netherlands;
| | - Christel de Krom
- Dutch National Plant Protection Organization, Netherlands Institute for Vectors, Invasive plants and Plant health (NIVIP), Wageningen, Gelderland, Netherlands;
| | - Carla Oplaat
- Dutch National Plant Protection Organization, Netherlands Institute for Vectors, Invasive plants and Plant health (NIVIP), Wageningen, NL-GE, Netherlands;
| | - Marcel Westenberg
- Dutch National Plant Protection Organization, Netherlands Institute for Vectors, Invasive plants and Plant health (NIVIP), Wageningen, Netherlands;
| | - Sebastien Massart
- University of Liege Faculty of Gembloux Agro-Bio Tech, Integrated and Urban Plant Pathology Laboratory Av. Maréchal Juin 13, Bât 47, porte 4 Gembloux, BE 5030, Gembloux, Belgium;
| | - Coline Temple
- University of Liege Faculty of Gembloux Agro-Bio Tech, 82209, Integrated and Urban Plant Pathology Laboratory, Av. Maréchal Juin 13, Bât 47, porte 4, Gembloux, Belgium, 5030
- University of Liege Faculty of Gembloux Agro-Bio Tech, 82209, Integrated and Urban Plant Pathology Laboratory, Av. Maréchal Juin 13, Bât 47, porte 4, Gembloux, Belgium, 5030;
| | - Kris De Jonghe
- ILVO, 74875, Plant Sciences, Burgemeester Van Gansberghelaan 96, Merelbeke, Merelbeke, Belgium, 9820
- Burgemeester Van Gansberghelaan 96Burgemeester Van Gansberghelaan 96Belgium;
| | - Arnaud G Blouin
- Agroscope Location Changins, 54161, Virology-Phytoplasmology Laboratory, Nyon, Switzerland;
| | - Marleen Botermans
- Dutch National Plant Protection Organization, Netherlands Institute for Vectors, Invasive plants and Plant health (NIVIP), Geertjesweg 15, Wageningen, Gelderland, Netherlands, 6706EA;
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