Large-Scale Comparative Analyses of Tick Genomes Elucidate Their Genetic Diversity and Vector Capacities

Jia, Na; Wang, Jinfeng; Shi, Wenqiang; Du, Lifeng; Sun, Yuena; Zhan, Wei; Jiang, Jia-Fu; Wang, Qian; Zhang, Bing; Ji, Peifeng; Bell‐Sakyi, Lesley; Cui, Xiaoming; Yuan, Tingting; Jiang, Bao-Gui; Yang, Weifei; Lam, Tommy Tsan-Yuk; Chang, Qiao‐Cheng; Ding, Shujun; Wang, Xianjun; Zhu, Jin-Guo; Xue-yu, Ruan; Zhao, Lin; Jia, Chongqi; Ye, Run-Ze; Que, Teng Cheng; Du, Chunhong; Zhou, Yongdong; Cheng, Jing; Dai, Pei-Fang; Guo, Wenbin; Han, Xiaohu; Huang, En-Jiong; Li, Lian-Feng; Wei, Wei; Gao, Yuchi; Liu, Jingze; Shao, Hongxia; Wang, Xin; Wang, Chongcai; Yang, Tian‐Ci; Huo, Qiu-Bo; Li, Wei; Chen, Haiying; Chen, Shen-En; Zhou, Long; Ni, Xue-Bing; Tian, Jingkui; Sheng, Yue; Liu, Tao; Pan, Yu-Sheng; Xia, Luo‐Yuan; Li, Jie; Genome, Tick; Zhao, Fangqing; Cao, Wu‐Chun

doi:10.1016/j.cell.2020.07.023

Cited by 180 publications

(183 citation statements)

References 110 publications

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“…Indeed, the genome of the I. scapularis tick was published in 2016 but has still not been fully annotated [23]. More recently, Jia et al have published the genomes of six tick species [55], including Ixodes persulcatus, and some efforts are made to sequenced and annotated the genome of I. ricinus [56,57]. In this situation, the choice of strategies to establish a PPI network is limited.…”

Section: Choice Of Y2h Methodsmentioning

confidence: 99%

“…Immediate downstream consequences of TRAF signalling include activation of the transcription factor NFκB and mitogen-activated protein kinases (MAPK). By analogy to to cytosolic viral recognition in mammals, in which viral RNA is sensed by various RLR and leads to NF-κB activation, an antiviral response is triggered in insects upon recognition of cytosolic viral RNA by the RIG-I family member Dicer-2 (54,55). In Culex mosquitoes, aviviral infection has been shown to activate the NF-κB ortholog Rel2 in a signalling cascade requiring TRAF (56).…”

Section: Signal Transduction / Transcriptional Response / Protein Degmentioning

confidence: 99%

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Exploration of Binary Protein-Protein Interactions Between Tick-Borne Flaviviruses and Ixodes Ricinus

LEMASSON

CAIGNARD

UNTERFINGER

et al. 2020

Preprint

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BackgroundLouping ill virus (LIV) and tick-borne encephalitis virus (TBEV) are tick-borne flaviviruses that are both transmitted by the major European tick, Ixodes ricinus. Despite the importance of I. ricinus as an arthropod vector, its capacity to acquire and subsequently transmit viruses, known as vector competence, is poorly understood. At the molecular scale, vector competence is governed in part by binary interactions established between viral and cellular proteins within infected tick cells.MethodsTo investigate virus-vector protein-protein interactions (PPIs), the entire set of open reading frames for LIV and TBEV was screened against an I. ricinus cDNA library established from three embryonic tick cell lines using yeast two-hybrid methodology (Y2H). PPIs revealed for each viral bait were retested in yeast by applying a gap repair (GR) strategy and notably against the cognate protein of both viruses, to determine whether the PPIs were specific for a single virus or common to both. The interacting tick proteins were identified by automatic BLASTX and in silico analyses were performed to expose the biological processes targeted by LIV and TBEV.ResultsFor each virus, we identified 24 different PPIs involving six viral proteins and 22 unique tick proteins, with all PPIs being common to both viruses. According to our data, several viral proteins (pM, M, NS2A, NS4A, 2K and NS5) target multiple tick protein modules implicated in critical biological pathways. Of note, the NS5 and pM viral proteins establish PPI with several tumor necrosis factor (TNF) receptor-associated factor (TRAF) proteins, which are essential adaptor proteins at the nexus of multiple signal transduction pathways.ConclusionWe provide the first description of the TBEV/LIV-I. ricinus PPI network, and indeed of any PPI network involving a tick-borne virus and its tick vector. While further investigation will be needed to elucidate the role of each tick protein in the replication cycle of tick-borne flaviviruses, our study provides a foundation for understanding the vector competence of I. ricinus at the molecular level. Indeed, certain PPIs may represent molecular determinants of vector competence of I. ricinus for TBEV and LIV, and potentially for other tick-borne flaviviruses.

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Section: Choice Of Y2h Methodsmentioning

confidence: 99%

Section: Signal Transduction / Transcriptional Response / Protein Degmentioning

confidence: 99%

Exploration of Binary Protein-Protein Interactions Between Tick-Borne Flaviviruses and Ixodes Ricinus

LEMASSON

CAIGNARD

UNTERFINGER

et al. 2020

Preprint

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“…Genome data is very important to tick transcriptome studies. Recently published tick genome study described 6 tick species that is common in the Old Continent [16]. These genome data are valuable in studying tick gene function, system evolution, and symbiotic relationship of the pathogen in different tick species.…”

Section: Annotationmentioning

confidence: 99%

“…The genome data of Ixodes scapularis Say is the rst genomic functional study that provided abundant references to gene annotations of tick species [15]. A very recent study on six tick genomes expounded the comparative genome analyses of ixodid tick species [16]. Together with the I. scapularis genome data, these tick genome data could be of crucial values for reference templates for omics studies such as transcriptome and proteome analyses on ixodid ticks and other tick species [16].…”

Section: Introductionmentioning

confidence: 99%

“…A very recent study on six tick genomes expounded the comparative genome analyses of ixodid tick species [16]. Together with the I. scapularis genome data, these tick genome data could be of crucial values for reference templates for omics studies such as transcriptome and proteome analyses on ixodid ticks and other tick species [16]. Currently RNA-seq is an effective approach to obtain transcripts on a speci c time point.…”

Section: Introductionmentioning

confidence: 99%

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De novo assembly and analysis of the transcriptome of the Dermacentor marginatus genes differentially expressed after blood feeding and long-term starvation

Yuan

et al. 2020

Preprint

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Background: The ixodid tick Dermacentor marginatus is a vector of many pathogens wide spread in Eurasia. Studies of gene sequence on many tick species have greatly increased the information on tick protective antigen which might have the potential to function as effective vaccine candidates or drug targets for eco-friendly acaricide development. In the current study, RNA-seq was applied to identify D. marginatus sequences and analyze differentially expressed unigenes.Methods: To obtain a broader picture of gene sequences and changes in expression level, RNA-seq was performed to obtain the whole-body transcriptome data of D. marginatus adult female ticks after engorgement and long-term starvation. Subsequently, the real-time quantitative PCR (RT-qPCR) was applied to validate the RNA-seq data.Results: RNA-seq produced 30,251 unigenes, of which 32% were annotated. Gene expression was compared among groups that differed by status as newly molted, starved and engorged female adult ticks. Nearly 1/3 of the unigenes in each group were differentially expressed compared to the other two groups, and the most numerous were genes encoding proteins involved in catalytic and binding activities and apoptosis. Selected up-regulated differentially expressed genes in each group were associated to protein, lipids, carbohydrate and chitin metabolism. Blood-feeding and long-term starvation also caused genes differentially expressed in the defense response and antioxidant response. RT-qPCR results indicated 6 differentially expressed transcripts showed similar trends in expression changes with RNA-seq results confirming that the gene expression profiles in transcriptome data is in consistent with RT-qPCR validation.Conclusions: Obtaining the sequence information of D. marginatus and characterizing the expression pattern of the genes involved in blood feeding and during starvation would be helpful in understanding molecular physiology of D. marginatus and provides data for anti-tick vaccine and drug development for controlling the tick.

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Characterisation of putative novel tick viruses and zoonotic risk prediction

Lin,

Pascall

2024

Ecology and Evolution

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Tick‐associated viruses remain a substantial zoonotic risk worldwide, so knowledge of the diversity of tick viruses has potential health consequences. Despite their importance, large amounts of sequences in public data sets from tick meta‐genomic and ‐transcriptomic projects remain unannotated, sequence data that could contain undocumented viruses. Through data mining and bioinformatic analysis of more than 37,800 public meta‐genomic and ‐transcriptomic data sets, we found 83 unannotated contigs exhibiting high identity with known tick viruses. These putative viral contigs were classified into three RNA viral families (Alphatetraviridae, Orthomyxoviridae and Chuviridae) and one DNA viral family (Asfarviridae). After manual checking of quality and dissimilarity towards other sequences in the data set, these 83 contigs were reduced to five contigs in the Alphatetraviridae from four putative viruses, four in the Orthomyxoviridae from two putative viruses and one in the Chuviridae which clustered with known tick‐associated viruses, forming a separate clade within the viral families. We further attempted to assess which previously known tick viruses likely represent zoonotic risks and thus deserve further investigation. We ranked the human infection potential of 133 known tick‐associated viruses using a genome composition‐based machine learning model. We found five high‐risk tick‐associated viruses (Langat virus, Lonestar tick chuvirus 1, Grotenhout virus, Taggert virus and Johnston Atoll virus) that have not been known to infect human and two viral families (Nairoviridae and Phenuiviridae) that contain a large proportion of potential zoonotic tick‐associated viruses. This adds to the knowledge of tick virus diversity and highlights the importance of surveillance of newly emerging tick‐associated diseases.

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Large-Scale Comparative Analyses of Tick Genomes Elucidate Their Genetic Diversity and Vector Capacities

Cited by 180 publications

References 110 publications

Exploration of Binary Protein-Protein Interactions Between Tick-Borne Flaviviruses and Ixodes Ricinus

Exploration of Binary Protein-Protein Interactions Between Tick-Borne Flaviviruses and Ixodes Ricinus

De novo assembly and analysis of the transcriptome of the Dermacentor marginatus genes differentially expressed after blood feeding and long-term starvation

Characterisation of putative novel tick viruses and zoonotic risk prediction

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