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Ochi A, Kidaka T, Hakimi H, Asada M, Yamagishi J. Chromosome-level genome assembly of Babesia caballi reveals diversity of multigene families among Babesia species. BMC Genomics 2023; 24:483. [PMID: 37620766 PMCID: PMC10463595 DOI: 10.1186/s12864-023-09540-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Accepted: 07/27/2023] [Indexed: 08/26/2023] Open
Abstract
BACKGROUND Babesia caballi is an intraerythrocytic parasite from the phylum Apicomplexa, capable of infecting equids and causing equine piroplasmosis. However, since there is limited genome information available on B. caballi, molecular mechanisms involved in host specificity and pathogenicity of this species have not been fully elucidated yet. RESULTS Genomic DNA from a B. caballi subclone was purified and sequenced using both Illumina and Nanopore technologies. The resulting assembled sequence consisted of nine contigs with a size of 12.9 Mbp, rendering a total of 5,910 protein-coding genes. The phylogenetic tree of Apicomplexan species was reconstructed using 263 orthologous genes. We identified 481 ves1-like genes and named "ves1c". In contrast, expansion of the major facilitator superfamily (mfs) observed in closely related B. bigemina and B. ovata species was not found in B. caballi. A set of repetitive units containing an open reading frame with a size of 297 bp was also identified. CONCLUSIONS We present a chromosome-level genome assembly of B. caballi. Our genomic data may contribute to estimating gene expansion events involving multigene families and exploring the evolution of species from this genus.
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Affiliation(s)
- Akihiro Ochi
- Equine Research Institute, Japan Racing Association, Shimotsuke, Tochigi, Japan
| | - Taishi Kidaka
- International Institute for Zoonosis Control, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Hassan Hakimi
- National Research Center for Protozoan Diseases, Obihiro University of Agriculture and Veterinary Medicine, Obihiro, Hokkaido, Japan
- Department of Veterinary Pathobiology, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas, USA
| | - Masahito Asada
- National Research Center for Protozoan Diseases, Obihiro University of Agriculture and Veterinary Medicine, Obihiro, Hokkaido, Japan
| | - Junya Yamagishi
- International Institute for Zoonosis Control, Hokkaido University, Sapporo, Hokkaido, Japan.
- Global Station for Zoonosis Control, GI-CoRE, Hokkaido University, Sapporo, Hokkaido, Japan.
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Yamagishi J, Ceylan O, Xuan X, Sevinc F. Whole genome sequence and diversity in multigene families of Babesia ovis. Front Cell Infect Microbiol 2023; 13:1194608. [PMID: 37662008 PMCID: PMC10471129 DOI: 10.3389/fcimb.2023.1194608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 07/04/2023] [Indexed: 09/05/2023] Open
Abstract
Ovine babesiosis, caused by Babesia ovis, is an acute, lethal, and endemic disease worldwide and causes a huge economic loss to animal industry. Pathogen genome sequences can be utilized for selecting diagnostic markers, drug targets, and antigens for vaccine development; however, those for B. ovis have not been available so far. In this study, we obtained a draft genome sequence for B. ovis isolated from an infected sheep in Turkey. The genome size was 7.81 Mbp with 3,419 protein-coding genes. It consisted of 41 contigs, and the N50 was 526 Kbp. There were 259 orthologs identified among eight Babesia spp., Plasmodium falciparum, and Toxoplasma gondii. A phylogeny was estimated on the basis of the orthologs, which showed B. ovis to be closest to B. bovis. There were 43 ves genes identified using hmm model as well. They formed a discriminating cluster to other ves multigene family of Babesia spp. but showed certain similarities to those of B. bovis, B. caballi, and Babesia sp. Xinjiang, which is consistent with the phylogeny. Comparative genomics among B. ovis and B. bovis elucidated uniquely evolved genes in these species, which may account for the adaptation.
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Affiliation(s)
- Junya Yamagishi
- International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
- Global Station for Zoonosis Control, GI-CoRE, Hokkaido University, Sapporo, Japan
| | - Onur Ceylan
- Department of Parasitology, Faculty of Veterinary Medicine, University of Selcuk, Konya, Türkiye
| | - Xuenan Xuan
- National Research Center for Protozoan Diseases, Obihiro University of Agriculture and Veterinary Medicine, Obihiro, Japan
| | - Ferda Sevinc
- Department of Parasitology, Faculty of Veterinary Medicine, University of Selcuk, Konya, Türkiye
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Ulucesme MC, Ozubek S, Karoglu A, Turk ZI, Olmus I, Irehan B, Aktas M. Small Ruminant Piroplasmosis: High Prevalence of Babesia aktasi n. sp. in Goats in Türkiye. Pathogens 2023; 12:pathogens12040514. [PMID: 37111400 PMCID: PMC10142182 DOI: 10.3390/pathogens12040514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 03/23/2023] [Accepted: 03/24/2023] [Indexed: 03/29/2023] Open
Abstract
Small ruminant piroplasmosis is the hemoparasitic infection of sheep and goats caused by Babesia and Theileria species responsible for clinical infections with high mortality outcomes. The disease is transmitted by ixodid ticks and prevalent in the tropical and subtropical regions of the world, including Türkiye. A prevalence survey, using molecular methods, is conducted in this study to determine the frequency of newly defined Babesia aktasi n. sp. and other tick-borne piroplasm species in small ruminants in Turkiye. A total of 640 blood samples from sheep (n = 137) and goats (n = 503) were analyzed by nested PCR-based reverse line blot (RLB) hybridization. The results show that 32.3% (207/640) of apparently healthy, small ruminants are infected with three Theileria and two Babesia species. Babesia aktasi n. sp. was the most prevalent species in goats, with 22.5% of samples being positive, followed by B. ovis (4%), T. ovis (2.8%), T. annulata (2.6%), and Theileria sp. (0.6%). None of the sheep samples were positive for Babesia aktasi n. sp.; however, 51.8% were infected with T. ovis. In conclusion, the findings reveal that B. aktasi n. sp. is highly prevalent in goats, but absent in sheep. In future studies, experimental infections will determine whether B. aktasi n. sp. is infectious to sheep, as well as its pathogenicity in small ruminants.
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Rezvani Y, Keroack CD, Elsworth B, Arriojas A, Gubbels MJ, Duraisingh MT, Zarringhalam K. Comparative single-cell transcriptional atlases of Babesia species reveal conserved and species-specific expression profiles. PLoS Biol 2022; 20:e3001816. [PMID: 36137068 PMCID: PMC9531838 DOI: 10.1371/journal.pbio.3001816] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 10/04/2022] [Accepted: 09/05/2022] [Indexed: 11/18/2022] Open
Abstract
Babesia is a genus of apicomplexan parasites that infect red blood cells in vertebrate hosts. Pathology occurs during rapid replication cycles in the asexual blood stage of infection. Current knowledge of Babesia replication cycle progression and regulation is limited and relies mostly on comparative studies with related parasites. Due to limitations in synchronizing Babesia parasites, fine-scale time-course transcriptomic resources are not readily available. Single-cell transcriptomics provides a powerful unbiased alternative for profiling asynchronous cell populations. Here, we applied single-cell RNA sequencing to 3 Babesia species (B. divergens, B. bovis, and B. bigemina). We used analytical approaches and algorithms to map the replication cycle and construct pseudo-synchronized time-course gene expression profiles. We identify clusters of co-expressed genes showing "just-in-time" expression profiles, with gradually cascading peaks throughout asexual development. Moreover, clustering analysis of reconstructed gene curves reveals coordinated timing of peak expression in epigenetic markers and transcription factors. Using a regularized Gaussian graphical model, we reconstructed co-expression networks and identified conserved and species-specific nodes. Motif analysis of a co-expression interactome of AP2 transcription factors identified specific motifs previously reported to play a role in DNA replication in Plasmodium species. Finally, we present an interactive web application to visualize and interactively explore the datasets.
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Affiliation(s)
- Yasaman Rezvani
- Department of Mathematics, University of Massachusetts Boston, Boston, Massachusetts, United States of America
| | - Caroline D. Keroack
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, Massachusetts, United States of America
| | - Brendan Elsworth
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, Massachusetts, United States of America
| | - Argenis Arriojas
- Department of Mathematics, University of Massachusetts Boston, Boston, Massachusetts, United States of America
- Department of Physics, University of Massachusetts Boston, Boston, Massachusetts, United States of America
| | - Marc-Jan Gubbels
- Department of Biology, Boston College, Chestnut Hill, Massachusetts, United States of America
| | - Manoj T. Duraisingh
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, Massachusetts, United States of America
- * E-mail: (MTD); (KZ)
| | - Kourosh Zarringhalam
- Department of Mathematics, University of Massachusetts Boston, Boston, Massachusetts, United States of America
- Center for Personalized Cancer Therapy, University of Massachusetts Boston, Boston, Massachusetts, United States of America
- * E-mail: (MTD); (KZ)
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Sivakumar T, Tuvshintulga B, Otgonsuren D, Batmagnai E, Ahedor B, Kothalawala H, Vimalakumar SC, Silva SSP, Yamagishi J, Yokoyama N. Phylogenetic analyses of the mitochondrial, plastid, and nuclear genes of Babesia sp. Mymensingh and its naming as Babesia naoakii n. sp. Parasit Vectors 2022; 15:299. [PMID: 36002908 PMCID: PMC9404586 DOI: 10.1186/s13071-022-05374-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 06/26/2022] [Indexed: 12/05/2022] Open
Abstract
Background The recently discovered Babesia sp. Mymensingh, which causes clinical bovine babesiosis, has a wide geographical distribution. We investigated the phylogenetic position of Babesia sp. Mymensingh using its mitochondrial, plastid, and nuclear genes. Based on morphological and molecular data, Babesia sp. Mymensingh is a unique species and we named it as Babesia naoakii n. sp. Methods A blood DNA sample from a Babesia sp. Mymensingh-infected cow was subjected to genome sequencing to obtain the sequences of mitochondrial, plastid, and nuclear genes. Six phylogenetic trees were then constructed with (1) concatenated amino acid sequences of cytochrome oxidase subunit I, cytochrome oxidase subunit III, and cytochrome b genes of the mitochondrial genome; (2) 16S rRNA of the plastid genome; (3) nucleotide sequences of the elongation factor Tu gene of the plastid genome; (4) ITS1-5.8S rRNA-ITS2; (5) concatenated nucleotide sequences of 89 nuclear genes; and (6) concatenated amino acid sequences translated from the 89 nuclear genes. Results In all six phylogenetic trees, B. naoakii n. sp. formed a sister clade to the common ancestor of Babesia bigemina and B. ovata. The concatenated nuclear genes of B. naoakii n. sp. and their translated amino acid sequences shared lower identity scores with the sequences from B. bigemina (82.7% and 84.7%, respectively) and B. ovata (83.5% and 85.5%, respectively) compared with the identity scores shared between the B. bigemina and B. ovata sequences (86.3% and 87.9%, respectively). Conclusions Our study showed that B. naoakii n. sp. occupies a unique phylogenetic position distinct from existing Babesia species. Our findings, together with morphological differences, identify B. naoakii n. sp. as a distinct parasite species. Graphical Abstract ![]()
Supplementary Information The online version contains supplementary material available at 10.1186/s13071-022-05374-9.
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Affiliation(s)
- Thillaiampalam Sivakumar
- National Research Center for Protozoan Diseases, Obihiro University of Agriculture and Veterinary Medicine, Inada-cho, Obihiro, Hokkaido, 080-8555, Japan
| | - Bumduuren Tuvshintulga
- National Research Center for Protozoan Diseases, Obihiro University of Agriculture and Veterinary Medicine, Inada-cho, Obihiro, Hokkaido, 080-8555, Japan
| | - Davaajav Otgonsuren
- National Research Center for Protozoan Diseases, Obihiro University of Agriculture and Veterinary Medicine, Inada-cho, Obihiro, Hokkaido, 080-8555, Japan
| | - Enkhbaatar Batmagnai
- National Research Center for Protozoan Diseases, Obihiro University of Agriculture and Veterinary Medicine, Inada-cho, Obihiro, Hokkaido, 080-8555, Japan
| | - Believe Ahedor
- National Research Center for Protozoan Diseases, Obihiro University of Agriculture and Veterinary Medicine, Inada-cho, Obihiro, Hokkaido, 080-8555, Japan
| | | | | | | | - Junya Yamagishi
- Division of Collaboration and Education, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Naoaki Yokoyama
- National Research Center for Protozoan Diseases, Obihiro University of Agriculture and Veterinary Medicine, Inada-cho, Obihiro, Hokkaido, 080-8555, Japan. .,OIE Reference Laboratory for Bovine Babesiosis, National Research Center for Protozoan Diseases, Obihiro University of Agriculture and Veterinary Medicine, Obihiro, Hokkaido, Japan.
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6
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Wang J, Chen K, Yang J, Zhang S, Li Y, Liu G, Luo J, Yin H, Wang G, Guan G. Comparative genomic analysis of Babesia duncani responsible for human babesiosis. BMC Biol 2022; 20:153. [PMID: 35790982 PMCID: PMC9258201 DOI: 10.1186/s12915-022-01361-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 06/23/2022] [Indexed: 11/29/2022] Open
Abstract
Background Human babesiosis, caused by parasites of the genus Babesia, is an emerging and re-emerging tick-borne disease that is mainly transmitted by tick bites and infected blood transfusion. Babesia duncani has caused majority of human babesiosis in Canada; however, limited data are available to correlate its genomic information and biological features. Results We generated a B. duncani reference genome using Oxford Nanopore Technology (ONT) and Illumina sequencing technology and uncovered its biological features and phylogenetic relationship with other Apicomplexa parasites. Phylogenetic analyses revealed that B. duncani form a clade distinct from B. microti, Babesia spp. infective to bovine and ovine species, and Theileria spp. infective to bovines. We identified the largest species-specific gene family that could be applied as diagnostic markers for this pathogen. In addition, two gene families show signals of significant expansion and several genes that present signatures of positive selection in B. duncani, suggesting their possible roles in the capability of this parasite to infect humans or tick vectors. Conclusions Using ONT sequencing and Illumina sequencing technologies, we provide the first B. duncani reference genome and confirm that B. duncani forms a phylogenetically distinct clade from other Piroplasm parasites. Comparative genomic analyses show that two gene families are significantly expanded in B. duncani and may play important roles in host cell invasion and virulence of B. duncani. Our study provides basic information for further exploring B. duncani features, such as host-parasite and tick-parasite interactions. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-022-01361-9.
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Affiliation(s)
- Jinming Wang
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Science, Lanzhou, 730046, Gansu, China.
| | - Kai Chen
- Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Jifei Yang
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Science, Lanzhou, 730046, Gansu, China
| | - Shangdi Zhang
- Department of Clinical Laboratory, The Second Hospital of Lanzhou University, Lanzhou, 730030, China
| | - Youquan Li
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Science, Lanzhou, 730046, Gansu, China
| | - Guangyuan Liu
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Science, Lanzhou, 730046, Gansu, China
| | - Jianxun Luo
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Science, Lanzhou, 730046, Gansu, China
| | - Hong Yin
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Science, Lanzhou, 730046, Gansu, China.,Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonoses, Yangzhou University, Yangzhou, 225009, China
| | - Guangying Wang
- Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.
| | - Guiquan Guan
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Science, Lanzhou, 730046, Gansu, China.
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Parodi P, Armúa-Fernández MT, Corbellini LG, Rivero R, Miraballes C, Riet-Correa F, Venzal JM. Description of bovine babesiosis and anaplasmosis outbreaks in northern Uruguay between 2016 and 2018. VETERINARY PARASITOLOGY: REGIONAL STUDIES AND REPORTS 2022; 29:100700. [DOI: 10.1016/j.vprsr.2022.100700] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 11/27/2021] [Accepted: 01/26/2022] [Indexed: 04/08/2023]
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The Piroplasmida Babesia, Cytauxzoon, and Theileria in farm and companion animals: species compilation, molecular phylogeny, and evolutionary insights. Parasitol Res 2022; 121:1207-1245. [DOI: 10.1007/s00436-022-07424-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 01/02/2022] [Indexed: 12/13/2022]
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Recent Advances in Molecular Genetic Tools for Babesia. Vet Sci 2021; 8:vetsci8100222. [PMID: 34679052 PMCID: PMC8541370 DOI: 10.3390/vetsci8100222] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 09/15/2021] [Accepted: 10/02/2021] [Indexed: 11/21/2022] Open
Abstract
Development of in vitro culture and completion of genome sequencing of several Babesia parasites promoted the efforts to establish transfection systems for these parasites to dissect the gene functions. It has been more than a decade since the establishment of first transfection for Babesia bovis, the causative agent of bovine babesiosis. However, the number of genes that were targeted by genetic tools in Babesia parasites is limited. This is partially due to the low efficiencies of these methods. The recent adaptation of CRISPR/Cas9 for genome editing of Babesia bovis can accelerate the efforts for dissecting this parasite’s genome and extend the knowledge on biological aspects of erythrocytic and tick stages of Babesia. Additionally, glmS ribozyme as a conditional knockdown system is available that could be used for the characterization of essential genes. The development of high throughput genetic tools is needed to dissect the function of multigene families, targeting several genes in a specific pathway, and finally genome-wide identification of essential genes to find novel drug targets. In this review, we summarized the current tools that are available for Babesia and the genes that are being targeted by these tools. This may draw a perspective for the future development of genetic tools and pave the way for the identification of novel drugs or vaccine targets.
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Wang J, Wang X, Guan G, Yang J, Liu J, Liu A, Li Y, Luo J, Yin H. Stable transfection system for Babesia sp. Xinjiang. Parasit Vectors 2021; 14:463. [PMID: 34503543 PMCID: PMC8428105 DOI: 10.1186/s13071-021-04940-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 08/10/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Stable transfection systems have been described in many protozoan parasites, including Plasmodium falciparum, Cryptosporidium parvum, Babesia bovis, Babesia ovata, and Babesia gibsoni. For Babesia sp. Xinjiang (Bxj), which is the causative pathogen of ovine babesiosis and mainly prevails across China, the platform of those techniques remains absent. Genetic manipulation techniques are powerful tools to enhance our knowledge on parasite biology, which may provide potential drug targets and diagnostic markers. METHODS We evaluated the inhibition efficiency of blasticidin (BSD) and WR99210 to Bxj. Then, a plasmid was constructed bearing selectable marker BSD, green fluorescent protein (GFP) gene, and rhoptry-associated protein-1 3' terminator region (rap 3' TR). The plasmid was integrated into the elongation factor-1 alpha (ef-1α) site of Bxj genome by cross-over homologous recombination technique. Twenty μg of plasmid was transfected into Bxj merozoites. Subsequently, drug selection was performed 24 h after transfection to generate transfected parasites. RESULTS Transfected parasite lines, Bxj-c1, Bxj-c2, and Bxj-c3, were successfully obtained after transfection, drug selection, and colonization. Exogenous genes were integrated into the Bxj genome, which were confirmed by PCR amplification and sequencing. In addition, results of western blot (WB) and indirect immunofluorescence assay (IFA) revealed that GFP-BSD had expressed for 11 months. CONCLUSIONS In our present study, stable transfection system for Bxj was successfully developed. We anticipate that this platform will greatly facilitate basic research of Bxj.
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Affiliation(s)
- Jinming Wang
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Science, Xujiaping 1, Lanzhou, 730046, Gansu, China
| | - Xiaoxing Wang
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Science, Xujiaping 1, Lanzhou, 730046, Gansu, China
| | - Guiquan Guan
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Science, Xujiaping 1, Lanzhou, 730046, Gansu, China.
| | - Jifei Yang
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Science, Xujiaping 1, Lanzhou, 730046, Gansu, China
| | - Junlong Liu
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Science, Xujiaping 1, Lanzhou, 730046, Gansu, China
| | - Aihong Liu
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Science, Xujiaping 1, Lanzhou, 730046, Gansu, China
| | - Youquan Li
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Science, Xujiaping 1, Lanzhou, 730046, Gansu, China
| | - Jianxun Luo
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Science, Xujiaping 1, Lanzhou, 730046, Gansu, China
| | - Hong Yin
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Science, Xujiaping 1, Lanzhou, 730046, Gansu, China. .,Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonose, Yangzhou University, Yangzhou, 225009, China.
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11
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Wang J, Chen K, Ren Q, Zhang Y, Liu J, Wang G, Liu A, Li Y, Liu G, Luo J, Miao W, Xiong J, Yin H, Guan G. Systematic Comparison of the Performances of De Novo Genome Assemblers for Oxford Nanopore Technology Reads From Piroplasm. Front Cell Infect Microbiol 2021; 11:696669. [PMID: 34485177 PMCID: PMC8415751 DOI: 10.3389/fcimb.2021.696669] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Accepted: 06/29/2021] [Indexed: 01/06/2023] Open
Abstract
Background Emerging long reads sequencing technology has greatly changed the landscape of whole-genome sequencing, enabling scientists to contribute to decoding the genetic information of non-model species. The sequences generated by PacBio or Oxford Nanopore Technology (ONT) be assembled de novo before further analyses. Some genome de novo assemblers have been developed to assemble long reads generated by ONT. The performance of these assemblers has not been completely investigated. However, genome assembly is still a challenging task. Methods and Results We systematically evaluated the performance of nine de novo assemblers for ONT on different coverage depth datasets. Several metrics were measured to determine the performance of these tools, including N50 length, sequence coverage, runtime, easy operation, accuracy of genome and genomic completeness in varying depths of coverage. Based on the results of our assessments, the performances of these tools are summarized as follows: 1) Coverage depth has a significant effect on genome quality; 2) The level of contiguity of the assembled genome varies dramatically among different de novo tools; 3) The correctness of an assembled genome is closely related to the completeness of the genome. More than 30× nanopore data can be assembled into a relatively complete genome, the quality of which is highly dependent on the polishing using next generation sequencing data. Conclusion Considering the results of our investigation, the advantage and disadvantage of each tool are summarized and guidelines of selecting assembly tools are provided under specific conditions.
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Affiliation(s)
- Jinming Wang
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Science, Lanzhou, China
| | - Kai Chen
- Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Qiaoyun Ren
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Science, Lanzhou, China
| | - Ying Zhang
- Key Laboratory of Functional Genomics and Molecular Diagnosis, Lanzhou Baiyuan Gene Technology Co., Ltd, Lanzhou, China
| | - Junlong Liu
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Science, Lanzhou, China
| | - Guangying Wang
- Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Aihong Liu
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Science, Lanzhou, China
| | - Youquan Li
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Science, Lanzhou, China
| | - Guangyuan Liu
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Science, Lanzhou, China
| | - Jianxun Luo
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Science, Lanzhou, China
| | - Wei Miao
- Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Jie Xiong
- Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Hong Yin
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Science, Lanzhou, China.,Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonoses, Yangzhou University, Yangzhou, China
| | - Guiquan Guan
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Science, Lanzhou, China
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12
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Florin-Christensen M, Rodriguez AE, Suárez CE, Ueti MW, Delgado FO, Echaide I, Schnittger L. N-Glycosylation in Piroplasmids: Diversity within Simplicity. Pathogens 2021; 10:50. [PMID: 33429911 PMCID: PMC7826898 DOI: 10.3390/pathogens10010050] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Revised: 01/04/2021] [Accepted: 01/05/2021] [Indexed: 02/03/2023] Open
Abstract
N-glycosylation has remained mostly unexplored in Piroplasmida, an order of tick-transmitted pathogens of veterinary and medical relevance. Analysis of 11 piroplasmid genomes revealed three distinct scenarios regarding N-glycosylation: Babesia sensu stricto (s.s.) species add one or two N-acetylglucosamine (NAcGlc) molecules to proteins; Theileria equi and Cytauxzoon felis add (NAcGlc)2-mannose, while B. microti and Theileria s.s. synthesize dolichol-P-P-NAcGlc and dolichol-P-P-(NAcGlc)2 without subsequent transfer to proteins. All piroplasmids possess the gene complement needed for the synthesis of the N-glycosylation substrates, dolichol-P and sugar nucleotides. The oligosaccharyl transferase of Babesia species, T. equi and C. felis, is predicted to be composed of only two subunits, STT3 and Ost1. Occurrence of short N-glycans in B. bovis merozoites was experimentally demonstrated by fluorescence microscopy using a NAcGlc-specific lectin. In vitro growth of B. bovis was significantly impaired by tunicamycin, an inhibitor of N-glycosylation, indicating a relevant role for N-glycosylation in this pathogen. Finally, genes coding for N-glycosylation enzymes and substrate biosynthesis are transcribed in B. bovis blood and tick stages, suggesting that this pathway is biologically relevant throughout the parasite life cycle. Elucidation of the role/s exerted by N-glycans will increase our understanding of these successful parasites, for which improved control measures are needed.
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Affiliation(s)
- Monica Florin-Christensen
- Instituto de Patobiología Veterinaria (INTA-CONICET), CICVyA, Instituto Nacional de Tecnología Agropecuaria (INTA), Hurlingham 1686, Argentina; (A.E.R.); (F.O.D.); (L.S.)
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ciudad Autónoma de Buenos Aires C1033AAJ, Argentina
| | - Anabel E. Rodriguez
- Instituto de Patobiología Veterinaria (INTA-CONICET), CICVyA, Instituto Nacional de Tecnología Agropecuaria (INTA), Hurlingham 1686, Argentina; (A.E.R.); (F.O.D.); (L.S.)
| | - Carlos E. Suárez
- Department of Veterinary Microbiology and Pathology, College of Veterinary Medicine, Washington State University, Pullman, WA 99163, USA; (C.E.S.); (M.W.U.)
- Animal Disease Research Unit, United States Department of Agricultural-Agricultural Research Service, Pullman, WA 99163, USA
| | - Massaro W. Ueti
- Department of Veterinary Microbiology and Pathology, College of Veterinary Medicine, Washington State University, Pullman, WA 99163, USA; (C.E.S.); (M.W.U.)
- Animal Disease Research Unit, United States Department of Agricultural-Agricultural Research Service, Pullman, WA 99163, USA
| | - Fernando O. Delgado
- Instituto de Patobiología Veterinaria (INTA-CONICET), CICVyA, Instituto Nacional de Tecnología Agropecuaria (INTA), Hurlingham 1686, Argentina; (A.E.R.); (F.O.D.); (L.S.)
| | - Ignacio Echaide
- Estación Experimental Agrícola INTA-Rafaela, Santa Fe, Provincia de Buenos Aires S2300, Argentina;
| | - Leonhard Schnittger
- Instituto de Patobiología Veterinaria (INTA-CONICET), CICVyA, Instituto Nacional de Tecnología Agropecuaria (INTA), Hurlingham 1686, Argentina; (A.E.R.); (F.O.D.); (L.S.)
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ciudad Autónoma de Buenos Aires C1033AAJ, Argentina
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13
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Maboko BB, Featherston J, Sibeko-Matjila KP, Mans BJ. Whole genome sequencing of Theileria parva using target capture. Genomics 2020; 113:429-438. [PMID: 33370583 DOI: 10.1016/j.ygeno.2020.12.033] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 12/02/2020] [Accepted: 12/22/2020] [Indexed: 10/22/2022]
Abstract
Protozoan parasite isolation and purification are laborious and time-consuming processes required for high quality genomic DNA used in whole genome sequencing. The objective of this study was to capture whole Theileria parva genomes directly from cell cultures and blood samples using RNA baits. Cell culture material was bait captured or sequenced directly, while blood samples were all captured. Baits had variable success in capturing T. parva genomes from blood samples but were successful in cell cultures. Genome mapping uncovered extensive host contamination in blood samples compared to cell cultures. Captured cell cultures had over 81 fold coverage for the reference genome compared to 0-33 fold for blood samples. Results indicate that baits are specific to T. parva, are a good alternative to conventional methods and thus ideal for genomic studies. This study also reports the first whole genome sequencing of South African T. parva.
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Affiliation(s)
- Boitumelo B Maboko
- Agricultural Research Council, Onderstepoort Veterinary Research, Private Bag X05, Onderstepoort, 0110 Pretoria, South Africa; Department of Veterinary Tropical Diseases, Vector and Vector-borne Disease Research Programme, University of Pretoria, Private Bag X04, Onderstepoort, 0110 Pretoria, South Africa
| | - Jonathan Featherston
- Agricultural Research Council, Biotechnology Platform, Private Bag X05, Onderstepoort, 0110 Pretoria, South Africa
| | - Kgomotso P Sibeko-Matjila
- Department of Veterinary Tropical Diseases, Vector and Vector-borne Disease Research Programme, University of Pretoria, Private Bag X04, Onderstepoort, 0110 Pretoria, South Africa
| | - Ben J Mans
- Agricultural Research Council, Onderstepoort Veterinary Research, Private Bag X05, Onderstepoort, 0110 Pretoria, South Africa; Department of Veterinary Tropical Diseases, Vector and Vector-borne Disease Research Programme, University of Pretoria, Private Bag X04, Onderstepoort, 0110 Pretoria, South Africa; School of Life Sciences, University of KwaZulu-Natal, Private Bag X54001, Durban 4000, South Africa; Department of Life and Consumer Sciences, University of South Africa, Florida 1709, South Africa.
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14
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Hakimi H, Templeton TJ, Sakaguchi M, Yamagishi J, Miyazaki S, Yahata K, Uchihashi T, Kawazu SI, Kaneko O, Asada M. Novel Babesia bovis exported proteins that modify properties of infected red blood cells. PLoS Pathog 2020; 16:e1008917. [PMID: 33017449 PMCID: PMC7561165 DOI: 10.1371/journal.ppat.1008917] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 10/15/2020] [Accepted: 08/20/2020] [Indexed: 11/19/2022] Open
Abstract
Babesia bovis causes a pathogenic form of babesiosis in cattle. Following invasion of red blood cells (RBCs) the parasite extensively modifies host cell structural and mechanical properties via the export of numerous proteins. Despite their crucial role in virulence and pathogenesis, such proteins have not been comprehensively characterized in B. bovis. Here we describe the surface biotinylation of infected RBCs (iRBCs), followed by proteomic analysis. We describe a multigene family (mtm) that encodes predicted multi-transmembrane integral membrane proteins which are exported and expressed on the surface of iRBCs. One mtm gene was downregulated in blasticidin-S (BS) resistant parasites, suggesting an association with BS uptake. Induced knockdown of a novel exported protein encoded by BBOV_III004280, named VESA export-associated protein (BbVEAP), resulted in a decreased growth rate, reduced RBC surface ridge numbers, mis-localized VESA1, and abrogated cytoadhesion to endothelial cells, suggesting that BbVEAP is a novel virulence factor for B. bovis.
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Affiliation(s)
- Hassan Hakimi
- Department of Protozoology, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki, Japan
- National Research Center for Protozoan Diseases, Obihiro University of Agriculture and Veterinary Medicine, Obihiro, Hokkaido, Japan
- * E-mail: (HH); (MA)
| | - Thomas J. Templeton
- Department of Protozoology, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki, Japan
| | - Miako Sakaguchi
- Central Laboratory, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki, Japan
| | - Junya Yamagishi
- Division of Collaboration and Education, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan
- International Collaboration Unit, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Shinya Miyazaki
- Department of Protozoology, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki, Japan
| | - Kazuhide Yahata
- Department of Protozoology, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki, Japan
| | | | - Shin-ichiro Kawazu
- National Research Center for Protozoan Diseases, Obihiro University of Agriculture and Veterinary Medicine, Obihiro, Hokkaido, Japan
| | - Osamu Kaneko
- Department of Protozoology, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki, Japan
| | - Masahito Asada
- Department of Protozoology, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki, Japan
- National Research Center for Protozoan Diseases, Obihiro University of Agriculture and Veterinary Medicine, Obihiro, Hokkaido, Japan
- * E-mail: (HH); (MA)
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15
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He L, Liu Q, Yao B, Zhou Y, Hu M, Fang R, Zhao J. A Historical Overview of Research on Babesia orientalis, a Protozoan Parasite Infecting Water Buffalo. Front Microbiol 2017; 8:1323. [PMID: 28769894 PMCID: PMC5509917 DOI: 10.3389/fmicb.2017.01323] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Accepted: 06/29/2017] [Indexed: 11/22/2022] Open
Abstract
Babesiosis is a globally important zoonotic disease caused by tick-borne intraerythrocytic protozoan of the genus Babesia (phylum apicomplexa). In China, there are five species that infect cattle buffalo and cause great economic loss, which include Babesia bigemina, B. bovis, B. major, B. ovata, and B. orientalis. Among them, B. orientalis is the most recently identified new Babesia species epidemic in China. This review summarized the work done in the past 33 years to give an overview of what learned about this parasite. This parasitic protozoan was found in 1984 in Central and South China and then named as B. orientalis in 1997 based on its differences in transmitting host, morphology, pathogenicity and characteristics of in vitro cultivation when compared with B. bigemina and B. bovis. It was found that Rhipicephalus haemaphysaloides is the transmitting vector and water buffalo is the only reported host. Phylogenetic analysis based on the 18S rRNA gene also confirmed that B. orientalis is a new species. After species verification, four diagnostic methods including semi-nest PCR, loop-mediated isothermal amplification assay, reverse line blot hybridization assay, and real-time PCR were established for lab and field use purposes. Genomic sequencing was conducted and the complete genomes of mitochondria and apicoplast were annotated. Future work will be focused on developing effective vaccines, identifying drug targets and screening useful drugs for controlling B. orientalis in water buffalo.
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Affiliation(s)
- Lan He
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural UniversityWuhan, China.,Key Laboratory of Development of Veterinary Diagnostic Products, Ministry of Agriculture, Huazhong Agricultural UniversityWuhan, China
| | - Qin Liu
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, Key Laboratory of Parasite and Vector Biology, Ministry of Health, WHO Collaborating Center for Tropical DiseasesShanghai, China
| | - Baoan Yao
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural UniversityWuhan, China.,Key Laboratory of Development of Veterinary Diagnostic Products, Ministry of Agriculture, Huazhong Agricultural UniversityWuhan, China
| | - Yanqin Zhou
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural UniversityWuhan, China.,Key Laboratory of Development of Veterinary Diagnostic Products, Ministry of Agriculture, Huazhong Agricultural UniversityWuhan, China
| | - Min Hu
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural UniversityWuhan, China.,Key Laboratory of Development of Veterinary Diagnostic Products, Ministry of Agriculture, Huazhong Agricultural UniversityWuhan, China
| | - Rui Fang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural UniversityWuhan, China.,Key Laboratory of Development of Veterinary Diagnostic Products, Ministry of Agriculture, Huazhong Agricultural UniversityWuhan, China
| | - Junlong Zhao
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural UniversityWuhan, China.,Key Laboratory of Development of Veterinary Diagnostic Products, Ministry of Agriculture, Huazhong Agricultural UniversityWuhan, China
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