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Li J, Fan Y, Li N, Guo Y, Wang W, Feng K, He W, Li F, Huang J, Xu Y, Xiao L, Feng Y. Comparative genomics analysis reveals sequence characteristics potentially related to host preference in Cryptosporidium xiaoi. Int J Parasitol 2024; 54:379-390. [PMID: 38492779 DOI: 10.1016/j.ijpara.2024.03.004] [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: 10/25/2023] [Revised: 02/26/2024] [Accepted: 03/12/2024] [Indexed: 03/18/2024]
Abstract
Cryptosporidium spp. are important diarrhea-associated pathogens in humans and livestock. Among the known species, Cryptosporidium xiaoi, which causes cryptosporidiosis in sheep and goats, was previously recognized as a genotype of the bovine-specific Cryptosporidium bovis based on their high sequence identity in the ssrRNA gene. However, the lack of genomic data has limited characterization of the genetic differences between the two closely related species. In this study, we sequenced the genomes of two C. xiaoi isolates and performed comparative genomic analysis to identify the sequence uniqueness of this ovine-adapted species compared with other Cryptosporidium spp. Our results showed that C. xiaoi is genetically related to C. bovis as shown by their 95.8% genomic identity and similar gene content. Consistent with this, both C. xiaoi and C. bovis appear to have fewer genes encoding mitochondrial metabolic enzymes and invasion-related protein families. However, they appear to possess several species-specific genes. Further analysis indicates that the sequence differences between these two Cryptosporidium spp. are mainly in 24 highly polymorphic genes, half of which are located in the subtelomeric regions. Some of these subtelomeric genes encode secretory proteins that have undergone positive selection. In addition, the genomes of two C. xiaoi isolates, identified as subtypes XXIIIf and XXIIIh, share 99.9% nucleotide sequence identity, with six highly divergent genes encoding putative secretory proteins. Therefore, these species-specific genes and sequence polymorphism in subtelomeric genes probably contribute to the different host preference of C. xiaoi and C. bovis.
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Affiliation(s)
- Jiayu Li
- State Key Laboratory for Animal Disease Control and Prevention, South China Agricultural University, Guangzhou 510642, China
| | - Yingying Fan
- State Key Laboratory for Animal Disease Control and Prevention, South China Agricultural University, Guangzhou 510642, China
| | - Na Li
- State Key Laboratory for Animal Disease Control and Prevention, South China Agricultural University, Guangzhou 510642, China
| | - Yaqiong Guo
- State Key Laboratory for Animal Disease Control and Prevention, South China Agricultural University, Guangzhou 510642, China
| | - Weijian Wang
- State Key Laboratory for Animal Disease Control and Prevention, South China Agricultural University, Guangzhou 510642, China
| | - Kangli Feng
- State Key Laboratory for Animal Disease Control and Prevention, South China Agricultural University, Guangzhou 510642, China
| | - Wei He
- State Key Laboratory for Animal Disease Control and Prevention, South China Agricultural University, Guangzhou 510642, China
| | - Falei Li
- State Key Laboratory for Animal Disease Control and Prevention, South China Agricultural University, Guangzhou 510642, China
| | - Jianbo Huang
- State Key Laboratory for Animal Disease Control and Prevention, South China Agricultural University, Guangzhou 510642, China
| | - Yanhua Xu
- State Key Laboratory for Animal Disease Control and Prevention, South China Agricultural University, Guangzhou 510642, China
| | - Lihua Xiao
- State Key Laboratory for Animal Disease Control and Prevention, South China Agricultural University, Guangzhou 510642, China.
| | - Yaoyu Feng
- State Key Laboratory for Animal Disease Control and Prevention, South China Agricultural University, Guangzhou 510642, China.
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Li J, Li N, Roellig DM, Zhao W, Guo Y, Feng Y, Xiao L. High subtelomeric GC content in the genome of a zoonotic Cryptosporidium species. Microb Genom 2023; 9:mgen001052. [PMID: 37399068 PMCID: PMC10438818 DOI: 10.1099/mgen.0.001052] [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: 01/06/2023] [Accepted: 05/24/2023] [Indexed: 07/04/2023] Open
Abstract
Cryptosporidium canis is a zoonotic species causing cryptosporidiosis in humans in addition to its natural hosts dogs and other fur animals. To understand the genetic basis for host adaptation, we sequenced the genomes of C. canis from dogs, minks, and foxes and conducted a comparative genomics analysis. While the genomes of C. canis have similar gene contents and organisations, they (~41.0 %) and C. felis (39.6 %) have GC content much higher than other Cryptosporidium spp. (24.3-32.9 %) sequenced to date. The high GC content is mostly restricted to subtelomeric regions of the eight chromosomes. Most of these GC-balanced genes encode Cryptosporidium-specific proteins that have intrinsically disordered regions and are involved in host-parasite interactions. Natural selection appears to play a more important role in the evolution of codon usage in GC-balanced C. canis, and most of the GC-balanced genes have undergone positive selection. While the identity in whole genome sequences between the mink- and dog-derived isolates is 99.9 % (9365 SNVs), it is only 96.0 % (362 894 SNVs) between them and the fox-derived isolate. In agreement with this, the fox-derived isolate possesses more subtelomeric genes encoding invasion-related protein families. Therefore, the change in subtelomeric GC content appears to be responsible for the more GC-balanced C. canis genomes, and the fox-derived isolate could represent a new Cryptosporidium species.
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Affiliation(s)
- Jiayu Li
- State Key Laboratory for Animal Disease Control and Prevention, South China Agricultural University, Guangzhou 510642, PR China
| | - Na Li
- State Key Laboratory for Animal Disease Control and Prevention, South China Agricultural University, Guangzhou 510642, PR China
| | - Dawn M. Roellig
- Division of Foodborne, Waterborne, and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - Wentao Zhao
- State Key Laboratory for Animal Disease Control and Prevention, South China Agricultural University, Guangzhou 510642, PR China
| | - Yaqiong Guo
- State Key Laboratory for Animal Disease Control and Prevention, South China Agricultural University, Guangzhou 510642, PR China
| | - Yaoyu Feng
- State Key Laboratory for Animal Disease Control and Prevention, South China Agricultural University, Guangzhou 510642, PR China
| | - Lihua Xiao
- State Key Laboratory for Animal Disease Control and Prevention, South China Agricultural University, Guangzhou 510642, PR China
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Complete Plastome of Physalis angulata var. villosa, Gene Organization, Comparative Genomics and Phylogenetic Relationships among Solanaceae. Genes (Basel) 2022; 13:genes13122291. [PMID: 36553558 PMCID: PMC9778145 DOI: 10.3390/genes13122291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 11/28/2022] [Accepted: 11/30/2022] [Indexed: 12/12/2022] Open
Abstract
Physalis angulata var. villosa, rich in withanolides, has been used as a traditional Chinese medicine for many years. To date, few extensive molecular studies of this plant have been conducted. In the present study, the plastome of P. angulata var. villosa was sequenced, characterized and compared with that of other Physalis species, and a phylogenetic analysis was conducted in the family Solanaceae. The plastome of P. angulata var. villosa was 156,898 bp in length with a GC content of 37.52%, and exhibited a quadripartite structure typical of land plants, consisting of a large single-copy (LSC, 87,108 bp) region, a small single-copy (SSC, 18,462 bp) region and a pair of inverted repeats (IR: IRA and IRB, 25,664 bp each). The plastome contained 131 genes, of which 114 were unique and 17 were duplicated in IR regions. The genome consisted of 85 protein-coding genes, eight rRNA genes and 38 tRNA genes. A total of 38 long, repeat sequences of three types were identified in the plastome, of which forward repeats had the highest frequency. Simple sequence repeats (SSRs) analysis revealed a total of 57 SSRs, of which the T mononucleotide constituted the majority, with most of SSRs being located in the intergenic spacer regions. Comparative genomic analysis among nine Physalis species revealed that the single-copy regions were less conserved than the pair of inverted repeats, with most of the variation being found in the intergenic spacer regions rather than in the coding regions. Phylogenetic analysis indicated a close relationship between Physalis and Withania. In addition, Iochroma, Dunalia, Saracha and Eriolarynx were paraphyletic, and clustered together in the phylogenetic tree. Our study published the first sequence and assembly of the plastome of P. angulata var. villosa, reported its basic resources for evolutionary studies and provided an important tool for evaluating the phylogenetic relationship within the family Solanaceae.
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Wang X, Xing Y, Ji Y, Xi H, Liu X, Yang L, Lei L, Han W, Gu J. The Combination of Phages and Faecal Microbiota Transplantation Can Effectively Treat Mouse Colitis Caused by Salmonella enterica Serovar Typhimurium. Front Microbiol 2022; 13:944495. [PMID: 35875536 PMCID: PMC9301289 DOI: 10.3389/fmicb.2022.944495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Accepted: 06/03/2022] [Indexed: 11/17/2022] Open
Abstract
Salmonella enterica serovar Typhimurium (S. Typhimurium) is one of the common causes of human colitis. In the present study, two lytic phages vB_SenS-EnJE1 and vB_SenS-EnJE6 were isolated and the therapeutic effect of the combination of phages and faecal microbiota transplantation (FMT) on S. Typhimurium-induced mouse colitis was investigated. The characteristics and genome analysis indicated that they are suitable phages for phage therapy. Results showed that vB_SenS-EnJE1 lysis 41/54 Salmonella strains of serotype O4, and vB_SenS-EnJE6 lysis 46/54 Salmonella strains of serotypes O4 and O9. Severe inflammatory symptoms and disruption of the intestinal barrier were observed in S. Typhimurium -induced colitis. Interestingly, compared with a single phage cocktail (Pc) or single FMT, the combination of Pc and FMT (PcFMT) completely removed S. Typhimurium after 72 h of treatment, and significantly improved pathological damage and restored the intestinal barrier. Furthermore, PcFMT effectively restored the intestinal microbial diversity, especially for Firmicutes/Bacteroidetes [predominantly bacterial phyla responsible for the production of short-chain fatty acids (SCFA)]. Additionally, we found that PcFMT treatment significantly increased the levels of SCFA. All these data indicated that the combination of phages and FMT possesses excellent therapeutic effects on S. Typhimurium -induced intestinal microbiota disorder diseases. Pc and FMT played roles in “eliminating pathogens” and “strengthening vital qi,” respectively. This study provides a new idea for the treatment of intestinal microbiota disorder diseases caused by specific bacterial infections.
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Affiliation(s)
- Xinwu Wang
- State Key Laboratory for Zoonotic Diseases, Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Jilin, China
| | - Yating Xing
- The Second Hospital of Jilin University, Changchun, China
| | - Yalu Ji
- State Key Laboratory for Zoonotic Diseases, Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Jilin, China
| | - Hengyu Xi
- State Key Laboratory for Zoonotic Diseases, Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Jilin, China
| | - Xiaohe Liu
- The Second Hospital of Jilin University, Changchun, China
| | - Li Yang
- State Key Laboratory for Zoonotic Diseases, Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Jilin, China
| | - Liancheng Lei
- State Key Laboratory for Zoonotic Diseases, Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Jilin, China
| | - Wenyu Han
- State Key Laboratory for Zoonotic Diseases, Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Jilin, China
- Jiangsu Co-innovation Center for the Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
| | - Jingmin Gu
- State Key Laboratory for Zoonotic Diseases, Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Jilin, China
- Jiangsu Co-innovation Center for the Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
- *Correspondence: Jingmin Gu,
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Zheng WB, Zou Y, Zhu XQ, Liu GH. Toxocara "omics" and the promises it holds for medicine and veterinary medicine. ADVANCES IN PARASITOLOGY 2020; 109:89-108. [PMID: 32381233 DOI: 10.1016/bs.apar.2020.01.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Toxocariasis is one of the most neglected worldwide zoonoses that is caused by larval nematode parasites of the genus Toxocara, Toxocara canis, and to a lesser extent, Toxocara cati, whose migration mechanism is still largely unknown. Fortunately, some advanced tools have been employed, such as genomics, transcriptomics, and proteomics, to better understand the molecular biology and regulatory mechanisms of Toxocara. Using genomics and transcriptomics, we can identify a large number of genes that participate in the development of Toxocara and the interaction of parasites and their hosts and can predict the functions of unknown genes by comparing them with other relevant species. Using proteomics, we can identify somatic proteins and excretory and secretory (ES) proteins that perform specific biological functions in tissue degradation, pathogen invasion, immune evasion or modulation. These "omics" techniques also can contribute enormously to the development of new drugs, vaccines and diagnostic tools for toxocariasis. In a word, by utilizing "omics", we can better understand the Toxocara and toxocariasis. In this review, we summarized the representative achievements in Toxocara and the interaction between Toxocara spp. and their hosts based on expressed sequence tags (ESTs), microarray gene expression, next-generation sequencing (NGS) technologies and liquid chromatography-tandem mass spectrometry (LC-MS/MS), hoping to better understand the molecular biology of Toxocara, and contribute to new progress in the application areas of new drugs, vaccines and diagnostic tool for toxocariasis in the future.
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Affiliation(s)
- Wen-Bin Zheng
- Hunan Provincial Key Laboratory of Protein Engineering in Animal Vaccines, College of Veterinary Medicine, Hunan Agricultural University, Changsha, China; State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Yang Zou
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Xing-Quan Zhu
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China; Jiangsu Co-innovation Center for the Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University College of Veterinary Medicine, Yangzhou, China.
| | - Guo-Hua Liu
- Hunan Provincial Key Laboratory of Protein Engineering in Animal Vaccines, College of Veterinary Medicine, Hunan Agricultural University, Changsha, China.
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Ding YR, Yan ZT, Si FL, Li XD, Mao QM, Asghar S, Chen B. Mitochondrial genes associated with pyrethroid resistance revealed by mitochondrial genome and transcriptome analyses in the malaria vector Anopheles sinensis (Diptera: Culicidae). PEST MANAGEMENT SCIENCE 2020; 76:769-778. [PMID: 31392850 DOI: 10.1002/ps.5579] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 08/03/2019] [Accepted: 08/08/2019] [Indexed: 06/10/2023]
Abstract
BACKGROUND Insecticides are still the main method of mosquito control, but mosquito resistance presents a large obstacle. The function of mitochondrial genes in the evolution of insecticide resistance is still poorly understood. Pyrethroid is the most commonly used insecticide, and Anopheles sinensis is an important malaria vector in China and Southeast Asia. In this study, we investigated the mitochondrial genes associated with pyrethroid resistance through their genetic and expression variation based on analyses of transcriptomes and 36 individuals with resequencing in three geographical populations in China. RESULTS The nucleotide diversity (Pi) in 18 resistant individuals was much lower than that in 18 susceptible individuals, which suggests that some sites experienced purifying selection subject to pyrethroid stress. Ka/Ks and amino acid analyses showed that ND4 experienced positive selection and had 23 amino acid mutations due to pyrethroid stress. These mutations might change the ND4 structure and function and thus alter the efficiency of the respiratory chain. ND5 was significantly upregulated, and ATP8 was significantly downregulated in these three pyrethroid resistant populations, which suggests that these two genes function in the production and maintenance of pyrethroid resistance. There are differences in mitochondrial genes involved in pyrethroid resistance among these three populations. CONCLUSION This is the first study to reveal the association of mitochondrial genes in the evolution of insecticide resistance through amino acid mutation and expression patterns and can help us further understand insecticide resistance mechanisms. © 2019 Society of Chemical Industry.
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Affiliation(s)
- Yi-Ran Ding
- Chongqing Key Laboratory of Vector Insects; Institute of Entomology and Molecular Biology, Chongqing Normal University, Chongqing, China
| | - Zhen-Tian Yan
- Chongqing Key Laboratory of Vector Insects; Institute of Entomology and Molecular Biology, Chongqing Normal University, Chongqing, China
| | - Feng-Ling Si
- Chongqing Key Laboratory of Vector Insects; Institute of Entomology and Molecular Biology, Chongqing Normal University, Chongqing, China
| | - Xu-Dong Li
- Chongqing Key Laboratory of Vector Insects; Institute of Entomology and Molecular Biology, Chongqing Normal University, Chongqing, China
| | - Qi-Meng Mao
- Chongqing Key Laboratory of Vector Insects; Institute of Entomology and Molecular Biology, Chongqing Normal University, Chongqing, China
| | - Sana Asghar
- Chongqing Key Laboratory of Vector Insects; Institute of Entomology and Molecular Biology, Chongqing Normal University, Chongqing, China
| | - Bin Chen
- Chongqing Key Laboratory of Vector Insects; Institute of Entomology and Molecular Biology, Chongqing Normal University, Chongqing, China
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Environmental microbiology: Perspectives for legal and occupational medicine. Leg Med (Tokyo) 2018; 35:34-43. [DOI: 10.1016/j.legalmed.2018.09.014] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Revised: 08/09/2018] [Accepted: 09/23/2018] [Indexed: 11/18/2022]
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