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4. Comparative genomic analysis and phylogenetic position of Theileria equi

Author

Kappmeyer Lowell S, Thiagarajan Mathangi, Herndon David R, Ramsay Joshua D, Caler Elisabet, Djikeng Appolinaire, Gillespie Joseph J, Lau Audrey OT, Roalson Eric H, Silva Joana C, Silva Marta G, Suarez Carlos E, Ueti Massaro W, Nene Vishvanath M, Mealey Robert H, Knowles Donald P, and Brayton Kelly A

Subjects
Apicomplexa, Parasite, Vaccine, Horse, Vector-borne disease, Biotechnology, TP248.13-248.65, Genetics, QH426-470
Abstract

Abstract Background Transmission of arthropod-borne apicomplexan parasites that cause disease and result in death or persistent infection represents a major challenge to global human and animal health. First described in 1901 as Piroplasma equi, this re-emergent apicomplexan parasite was renamed Babesia equi and subsequently Theileria equi, reflecting an uncertain taxonomy. Understanding mechanisms by which apicomplexan parasites evade immune or chemotherapeutic elimination is required for development of effective vaccines or chemotherapeutics. The continued risk of transmission of T. equi from clinically silent, persistently infected equids impedes the goal of returning the U. S. to non-endemic status. Therefore comparative genomic analysis of T. equi was undertaken to: 1) identify genes contributing to immune evasion and persistence in equid hosts, 2) identify genes involved in PBMC infection biology and 3) define the phylogenetic position of T. equi relative to sequenced apicomplexan parasites. Results The known immunodominant proteins, EMA1, 2 and 3 were discovered to belong to a ten member gene family with a mean amino acid identity, in pairwise comparisons, of 39%. Importantly, the amino acid diversity of EMAs is distributed throughout the length of the proteins. Eight of the EMA genes were simultaneously transcribed. As the agents that cause bovine theileriosis infect and transform host cell PBMCs, we confirmed that T. equi infects equine PBMCs, however, there is no evidence of host cell transformation. Indeed, a number of genes identified as potential manipulators of the host cell phenotype are absent from the T. equi genome. Comparative genomic analysis of T. equi revealed the phylogenetic positioning relative to seven apicomplexan parasites using deduced amino acid sequences from 150 genes placed it as a sister taxon to Theileria spp. Conclusions The EMA family does not fit the paradigm for classical antigenic variation, and we propose a novel model describing the role of the EMA family in persistence. T. equi has lost the putative genes for host cell transformation, or the genes were acquired by T. parva and T. annulata after divergence from T. equi. Our analysis identified 50 genes that will be useful for definitive phylogenetic classification of T. equi and closely related organisms.

Published
2012
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5. Re-annotation of the Theileria parva genome refines 53% of the proteome and uncovers essential components of N-glycosylation, a conserved pathway in many organisms

Author

Tretina, Kyle, primary, Pelle, Roger, additional, Orvis, Joshua, additional, Gotia, Hanzel T., additional, Ifeonu, Olukemi O., additional, Kumari, Priti, additional, Palmateer, Nicholas C., additional, Iqbal, Shaikh B.A., additional, Fry, Lindsay, additional, Nene, Vishvanath M., additional, Daubenberger, Claudia, additional, Bishop, Richard P., additional, and Silva, Joana C., additional

Published
2019
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6. Reassociation kinetics-based approach for partial genome sequencing of the cattle tick, Rhipicephalus (Boophilus) microplus

Author

Bellgard Matthew, Caler Elisabet, Bidwell Shelby, Peterson Daniel G, Moolhuijzen Paula, Guerrero Felix D, Nene Vishvanath M, and Djikeng Appolinaire

Subjects
Biotechnology, TP248.13-248.65, Genetics, QH426-470
Abstract

Abstract Background The size and repetitive nature of the Rhipicephalus microplus genome makes obtaining a full genome sequence fiscally and technically problematic. To selectively obtain gene-enriched regions of this tick's genome, Cot filtration was performed, and Cot-filtered DNA was sequenced via 454 FLX pyrosequencing. Results The sequenced Cot-filtered genomic DNA was assembled with an EST-based gene index of 14,586 unique entries where each EST served as a potential "seed" for scaffold formation. The new sequence assembly extended the lengths of 3,913 of the 14,586 gene index entries. Over half of the extensions corresponded to extensions of over 30 amino acids. To survey the repetitive elements in the tick genome, the complete sequences of five BAC clones were determined. Both Class I and II transposable elements were found. Comparison of the BAC and Cot filtration data indicates that Cot filtration was highly successful in filtering repetitive DNA out of the genomic DNA used in 454 sequencing. Conclusion Cot filtration is a very useful strategy to incorporate into genome sequencing projects on organisms with large genome sizes and which contain high percentages of repetitive, difficult to assemble, genomic DNA. Combining the Cot selection approach with 454 sequencing and assembly with a pre-existing EST database as seeds resulted in extensions of 27% of the members of the EST database.

Published
2010
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7. Global comparative analysis of ESTs from the southern cattle tick, Rhipicephalus (Boophilus) microplus

Author

Pertea Geo, Guerrero Felix D, Wang Minghua, and Nene Vishvanath M

Subjects
Biotechnology, TP248.13-248.65, Genetics, QH426-470
Abstract

Abstract Background The southern cattle tick, Rhipicephalus (Boophilus) microplus, is an economically important parasite of cattle and can transmit several pathogenic microorganisms to its cattle host during the feeding process. Understanding the biology and genomics of R. microplus is critical to developing novel methods for controlling these ticks. Results We present a global comparative genomic analysis of a gene index of R. microplus comprised of 13,643 unique transcripts assembled from 42,512 expressed sequence tags (ESTs), a significant fraction of the complement of R. microplus genes. The source material for these ESTs consisted of polyA RNA from various tissues, lifestages, and strains of R. microplus, including larvae exposed to heat, cold, host odor, and acaricide. Functional annotation using RPS-Blast analysis identified conserved protein domains in the conceptually translated gene index and assigned GO terms to those database transcripts which had informative BlastX hits. Blast Score Ratio and SimiTri analysis compared the conceptual transcriptome of the R. microplus database to other eukaryotic proteomes and EST databases, including those from 3 ticks. The most abundant protein domains in BmiGI were also analyzed by SimiTri methodology. Conclusion These results indicate that a large fraction of BmiGI entries have no homologs in other sequenced genomes. Analysis with the PartiGene annotation pipeline showed 64% of the members of BmiGI could not be assigned GO annotation, thus minimal information is available about a significant fraction of the tick genome. This highlights the important insights in tick biology which are likely to result from a tick genome sequencing project. Global comparative analysis identified some tick genes with unexpected phylogenetic relationships which detailed analysis attributed to gene losses in some members of the animal kingdom. Some tick genes were identified which had close orthologues to mammalian genes. Members of this group would likely be poor choices as targets for development of novel tick control technology.

Published
2007
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8. Genomic insights into the Ixodes scapularis tick vector of Lyme disease

Author

Gulia-Nuss, Monika, Nuss, Andrew B., Meyer, Jason M., Sonenshine, Daniel E., Roe, R. Michael, Waterhouse, Robert M., Sattelle, David B., de la Fuente, Jose, Ribeiro, Jose M., Megy, Karine, Thimmapuram, Jyothi, Miller, Jason R., Walenz, Brian P., Koren, Sergey, Hostetler, Jessica B., Thiagarajan, Mathangi, Joardar, Vinita S., Hannick, Linda I., Bidwell, Shelby, Hammond, Martin P., Young, Sarah, Zeng, Qiandong, Abrudan, Jenica L., Almeida, Francisca C., Ayllon, Nieves, Bhide, Ketaki, Bissinger, Brooke W., Bonzon-Kulichenko, Elena, Buckingham, Steven D., Caffrey, Daniel R., Caimano, Melissa J., Croset, Vincent, Driscoll, Timothy, Gilbert, Don, Gillespie, Joseph J., Giraldo-Calderon, Gloria I., Grabowski, Jeffrey M., Jiang, David, Khalil, Sayed M. S., Kim, Donghun, Kocan, Katherine M., Koci, Juraj, Kuhn, Richard J., Kurtti, Timothy J., Lees, Kristin, Lang, Emma G., Kennedy, Ryan C., Kwon, Hyeogsun, Perera, Rushika, Qi, Yumin, Radolf, Justin D., Sakamoto, Joyce M., Sanchez-Gracia, Alejandro, Severo, Maiara S., Silverman, Neal, Simo, Ladislav, Tojo, Marta, Tornador, Cristian, Van Zee, Janice P., Vazquez, Jesus, Vieira, Filipe G., Villar, Margarita, Wespiser, Adam R., Yang, Yunlong, Zhu, Jiwei, Arensburger, Peter, Pietrantonio, Patricia V., Barker, Stephen C., Shao, Renfu, Zdobnov, Evgeny M., Hauser, Frank, Grimmelikhuijzen, Cornelis J. P., Park, Yoonseong, Rozas, Julio, Benton, Richard, Pedra, Joao H. F., Nelson, David R., Unger, Maria F., Tubio, Jose M. C., Tu, Zhijian Jake, Robertson, Hugh M., Shumway, Martin, Sutton, Granger, Wortman, Jennifer R., Lawson, Daniel, Wikel, Stephen K., Nene, Vishvanath M., Fraser, Claire M., Collins, Frank H., Birren, Bruce, Nelson, Karen E., Caler, Elisabet, Hill, Catherine A., Gulia-Nuss, Monika, Nuss, Andrew B., Meyer, Jason M., Sonenshine, Daniel E., Roe, R. Michael, Waterhouse, Robert M., Sattelle, David B., de la Fuente, Jose, Ribeiro, Jose M., Megy, Karine, Thimmapuram, Jyothi, Miller, Jason R., Walenz, Brian P., Koren, Sergey, Hostetler, Jessica B., Thiagarajan, Mathangi, Joardar, Vinita S., Hannick, Linda I., Bidwell, Shelby, Hammond, Martin P., Young, Sarah, Zeng, Qiandong, Abrudan, Jenica L., Almeida, Francisca C., Ayllon, Nieves, Bhide, Ketaki, Bissinger, Brooke W., Bonzon-Kulichenko, Elena, Buckingham, Steven D., Caffrey, Daniel R., Caimano, Melissa J., Croset, Vincent, Driscoll, Timothy, Gilbert, Don, Gillespie, Joseph J., Giraldo-Calderon, Gloria I., Grabowski, Jeffrey M., Jiang, David, Khalil, Sayed M. S., Kim, Donghun, Kocan, Katherine M., Koci, Juraj, Kuhn, Richard J., Kurtti, Timothy J., Lees, Kristin, Lang, Emma G., Kennedy, Ryan C., Kwon, Hyeogsun, Perera, Rushika, Qi, Yumin, Radolf, Justin D., Sakamoto, Joyce M., Sanchez-Gracia, Alejandro, Severo, Maiara S., Silverman, Neal, Simo, Ladislav, Tojo, Marta, Tornador, Cristian, Van Zee, Janice P., Vazquez, Jesus, Vieira, Filipe G., Villar, Margarita, Wespiser, Adam R., Yang, Yunlong, Zhu, Jiwei, Arensburger, Peter, Pietrantonio, Patricia V., Barker, Stephen C., Shao, Renfu, Zdobnov, Evgeny M., Hauser, Frank, Grimmelikhuijzen, Cornelis J. P., Park, Yoonseong, Rozas, Julio, Benton, Richard, Pedra, Joao H. F., Nelson, David R., Unger, Maria F., Tubio, Jose M. C., Tu, Zhijian Jake, Robertson, Hugh M., Shumway, Martin, Sutton, Granger, Wortman, Jennifer R., Lawson, Daniel, Wikel, Stephen K., Nene, Vishvanath M., Fraser, Claire M., Collins, Frank H., Birren, Bruce, Nelson, Karen E., Caler, Elisabet, and Hill, Catherine A.

Abstract

Ticks transmit more pathogens to humans and animals than any other arthropod. We describe the 2.1 Gbp nuclear genome of the tick, Ixodes scapularis (Say), which vectors pathogens that cause Lyme disease, human granulocytic anaplasmosis, babesiosis and other diseases. The large genome reflects accumulation of repetitive DNA, new lineages of retro-transposons, and gene architecture patterns resembling ancient metazoans rather than pancrustaceans. Annotation of scaffolds representing similar to 57% of the genome, reveals 20,486 protein-coding genes and expansions of gene families associated with tick-host interactions. We report insights from genome analyses into parasitic processes unique to ticks, including host 'questing', prolonged feeding, cuticle synthesis, blood meal concentration, novel methods of haemoglobin digestion, haem detoxification, vitellogenesis and prolonged off-host survival. We identify proteins associated with the agent of human granulocytic anaplasmosis, an emerging disease, and the encephalitis-causing Langat virus, and a population structure correlated to life-history traits and transmission of the Lyme disease agent.

Published
2016
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9. Genomic insights into the Ixodes scapularis tick vector of Lyme disease

Author

Biochemistry, Fralin Life Sciences Institute, Gulia-Nuss, Monika, Nuss, Andrew B., Meyer, Jason M., Sonenshine, Daniel E., Roe, R. Michael, Waterhouse, Robert M., Sattelle, David B., de la Fuente, Jose, Ribeiro, Jose M., Megy, Karine, Thimmapuram, Jyothi, Miller, Jason R., Walenz, Brian P., Koren, Sergey, Hostetler, Jessica B., Thiagarajan, Mathangi, Joardar, Vinita S., Hannick, Linda I., Bidwell, Shelby, Hammond, Martin P., Young, Sarah, Zeng, Qiandong, Abrudan, Jenica L., Almeida, Francisca C., Ayllon, Nieves, Bhide, Ketaki, Bissinger, Brooke W., Bonzon-Kulichenko, Elena, Buckingham, Steven D., Caffrey, Daniel R., Caimano, Melissa J., Croset, Vincent, Driscoll, Timothy, Gilbert, Don, Gillespie, Joseph J., Giraldo-Calderon, Gloria I., Grabowski, Jeffrey M., Jiang, David, Khalil, Sayed M. S., Kim, Donghun, Kocan, Katherine M., Koci, Juraj, Kuhn, Richard J., Kurtti, Timothy J., Lees, Kristin, Lang, Emma G., Kennedy, Ryan C., Kwon, Hyeogsun, Perera, Rushika, Qi, Yumin, Radolf, Justin D., Sakamoto, Joyce M., Sanchez-Gracia, Alejandro, Severo, Maiara S., Silverman, Neal, Simo, Ladislav, Tojo, Marta, Tornador, Cristian, Van Zee, Janice P., Vazquez, Jesus, Vieira, Filipe G., Villar, Margarita, Wespiser, Adam R., Yang, Yunlong, Zhu, Jiwei, Arensburger, Peter, Pietrantonio, Patricia V., Barker, Stephen C., Shao, Renfu, Zdobnov, Evgeny M., Hauser, Frank, Grimmelikhuijzen, Cornelis J. P., Park, Yoonseong, Rozas, Julio, Benton, Richard, Pedra, Joao H. F., Nelson, David R., Unger, Maria F., Tubio, Jose M. C., Tu, Zhijian Jake, Robertson, Hugh M., Shumway, Martin, Sutton, Granger, Wortman, Jennifer R., Lawson, Daniel, Wikel, Stephen K., Nene, Vishvanath M., Fraser, Claire M., Collins, Frank H., Birren, Bruce, Nelson, Karen E., Caler, Elisabet, Hill, Catherine A., Biochemistry, Fralin Life Sciences Institute, Gulia-Nuss, Monika, Nuss, Andrew B., Meyer, Jason M., Sonenshine, Daniel E., Roe, R. Michael, Waterhouse, Robert M., Sattelle, David B., de la Fuente, Jose, Ribeiro, Jose M., Megy, Karine, Thimmapuram, Jyothi, Miller, Jason R., Walenz, Brian P., Koren, Sergey, Hostetler, Jessica B., Thiagarajan, Mathangi, Joardar, Vinita S., Hannick, Linda I., Bidwell, Shelby, Hammond, Martin P., Young, Sarah, Zeng, Qiandong, Abrudan, Jenica L., Almeida, Francisca C., Ayllon, Nieves, Bhide, Ketaki, Bissinger, Brooke W., Bonzon-Kulichenko, Elena, Buckingham, Steven D., Caffrey, Daniel R., Caimano, Melissa J., Croset, Vincent, Driscoll, Timothy, Gilbert, Don, Gillespie, Joseph J., Giraldo-Calderon, Gloria I., Grabowski, Jeffrey M., Jiang, David, Khalil, Sayed M. S., Kim, Donghun, Kocan, Katherine M., Koci, Juraj, Kuhn, Richard J., Kurtti, Timothy J., Lees, Kristin, Lang, Emma G., Kennedy, Ryan C., Kwon, Hyeogsun, Perera, Rushika, Qi, Yumin, Radolf, Justin D., Sakamoto, Joyce M., Sanchez-Gracia, Alejandro, Severo, Maiara S., Silverman, Neal, Simo, Ladislav, Tojo, Marta, Tornador, Cristian, Van Zee, Janice P., Vazquez, Jesus, Vieira, Filipe G., Villar, Margarita, Wespiser, Adam R., Yang, Yunlong, Zhu, Jiwei, Arensburger, Peter, Pietrantonio, Patricia V., Barker, Stephen C., Shao, Renfu, Zdobnov, Evgeny M., Hauser, Frank, Grimmelikhuijzen, Cornelis J. P., Park, Yoonseong, Rozas, Julio, Benton, Richard, Pedra, Joao H. F., Nelson, David R., Unger, Maria F., Tubio, Jose M. C., Tu, Zhijian Jake, Robertson, Hugh M., Shumway, Martin, Sutton, Granger, Wortman, Jennifer R., Lawson, Daniel, Wikel, Stephen K., Nene, Vishvanath M., Fraser, Claire M., Collins, Frank H., Birren, Bruce, Nelson, Karen E., Caler, Elisabet, and Hill, Catherine A.

Abstract

Ticks transmit more pathogens to humans and animals than any other arthropod. We describe the 2.1 Gbp nuclear genome of the tick, Ixodes scapularis (Say), which vectors pathogens that cause Lyme disease, human granulocytic anaplasmosis, babesiosis and other diseases. The large genome reflects accumulation of repetitive DNA, new lineages of retro-transposons, and gene architecture patterns resembling ancient metazoans rather than pancrustaceans. Annotation of scaffolds representing similar to 57% of the genome, reveals 20,486 protein-coding genes and expansions of gene families associated with tick-host interactions. We report insights from genome analyses into parasitic processes unique to ticks, including host 'questing', prolonged feeding, cuticle synthesis, blood meal concentration, novel methods of haemoglobin digestion, haem detoxification, vitellogenesis and prolonged off-host survival. We identify proteins associated with the agent of human granulocytic anaplasmosis, an emerging disease, and the encephalitis-causing Langat virus, and a population structure correlated to life-history traits and transmission of the Lyme disease agent.

Published
2016

10. Genomic insights into the Ixodes scapularis tick vector of Lyme disease

Author

National Institute of Allergy and Infectious Diseases (US), National Institutes of Health (US), Department of Health and Human Services (US), Australian Research Council, Ministerio de Ciencia e Innovación (España), National Science Foundation (US), Xunta de Galicia, European Commission, Department of Agriculture (US), Texas AgriLife Research, European Research Council, Swiss National Science Foundation, Boehringer Ingelheim Fonds, Fundação para a Ciência e a Tecnologia (Portugal), Lundbeck Foundation, Gulia-Nuss, Monika, Nuss, Andrew B., Meyer, Jason M., Sonenshine, Daniel E., Roe, R. Michael, Waterhouse, Robert M., Sattelle, David B., Fuente, José de la, Ribeiro, Jose M., Megy, Karine, Thimmapuram, Jyothi, Miller, Jason R., Walenz, Brian P., Koren, Sergey, Hostetler, Jessica B., Thiagarajan, Mathangi, Joardar, Vinita S., Hannick, Linda I., Bidwell, Shelby, Hammond, Martin P., Young, Sarah, Zeng, Qiandong, Abrudan, Jenica L., Almeida, Francisca C., Ayllón, Nieves, Bhide, Ketaki, Bissinger, Brooke W., Bonzón-Kulichenko, Elena, Buckingham, Steven D., Caffrey, Daniel R., Caimano, Melissa J., Croset, Vincent, Driscoll, Timothy, Gilbert, Don, Gillespie, Joseph J., Giraldo-Calderón, Gloria I., Grabowski, Jeffrey M., Jiang, David, Khalil, Sayed M .S., Kim, Donghun, Kocan, Katherine M., Koči, Juraj, Kuhn, Richard J., Kurtti, Timothy J., Lees, Kristin, Lang, Emma G., Kennedy, Ryan C., Kwon, Hyeogsun, Perera, Rushika, Qi, Yumin, Radolf, Justin D., Sakamoto, Joyce M., Sánchez-Gracia, Alejandro, Severo, Maiara S., Silverman, Neal, Šimo, Ladislav, Tojo, Marta, Tornador, Cristian, Van Zee, Janice P., Vázquez, Jesús, Vieira, Filipe G., Villar, Margarita, Wespiser, Adam R., Yang, Yunlong, Zhu, Jiwei, Arensburger, Peter, Pietrantonio, Patricia V., Barker, Stephen C., Shao, Renfu, Zdobnov, Evgeny M., Hauser, Frank, Grimmelikhuijzen, Cornelis J. P., Park, Yoonseong, Rozas, Julio, Benton, Richard, Pedra, Joao H. F., Nelson, David R., Unger, Maria F., Tubio, Jose M. C., Tu, Zhijian, Robertson, Hugh M., Shumway, Martin, Sutton, Granger, Wortman, Jennifer R., Lawson, Daniel, Wikel, Stephen K., Nene, Vishvanath M., Fraser, Claire M., Collins, Frank H., Birren, Bruce, Nelson, Karen E., Caler, Elisabet, Hill, Catherine A., National Institute of Allergy and Infectious Diseases (US), National Institutes of Health (US), Department of Health and Human Services (US), Australian Research Council, Ministerio de Ciencia e Innovación (España), National Science Foundation (US), Xunta de Galicia, European Commission, Department of Agriculture (US), Texas AgriLife Research, European Research Council, Swiss National Science Foundation, Boehringer Ingelheim Fonds, Fundação para a Ciência e a Tecnologia (Portugal), Lundbeck Foundation, Gulia-Nuss, Monika, Nuss, Andrew B., Meyer, Jason M., Sonenshine, Daniel E., Roe, R. Michael, Waterhouse, Robert M., Sattelle, David B., Fuente, José de la, Ribeiro, Jose M., Megy, Karine, Thimmapuram, Jyothi, Miller, Jason R., Walenz, Brian P., Koren, Sergey, Hostetler, Jessica B., Thiagarajan, Mathangi, Joardar, Vinita S., Hannick, Linda I., Bidwell, Shelby, Hammond, Martin P., Young, Sarah, Zeng, Qiandong, Abrudan, Jenica L., Almeida, Francisca C., Ayllón, Nieves, Bhide, Ketaki, Bissinger, Brooke W., Bonzón-Kulichenko, Elena, Buckingham, Steven D., Caffrey, Daniel R., Caimano, Melissa J., Croset, Vincent, Driscoll, Timothy, Gilbert, Don, Gillespie, Joseph J., Giraldo-Calderón, Gloria I., Grabowski, Jeffrey M., Jiang, David, Khalil, Sayed M .S., Kim, Donghun, Kocan, Katherine M., Koči, Juraj, Kuhn, Richard J., Kurtti, Timothy J., Lees, Kristin, Lang, Emma G., Kennedy, Ryan C., Kwon, Hyeogsun, Perera, Rushika, Qi, Yumin, Radolf, Justin D., Sakamoto, Joyce M., Sánchez-Gracia, Alejandro, Severo, Maiara S., Silverman, Neal, Šimo, Ladislav, Tojo, Marta, Tornador, Cristian, Van Zee, Janice P., Vázquez, Jesús, Vieira, Filipe G., Villar, Margarita, Wespiser, Adam R., Yang, Yunlong, Zhu, Jiwei, Arensburger, Peter, Pietrantonio, Patricia V., Barker, Stephen C., Shao, Renfu, Zdobnov, Evgeny M., Hauser, Frank, Grimmelikhuijzen, Cornelis J. P., Park, Yoonseong, Rozas, Julio, Benton, Richard, Pedra, Joao H. F., Nelson, David R., Unger, Maria F., Tubio, Jose M. C., Tu, Zhijian, Robertson, Hugh M., Shumway, Martin, Sutton, Granger, Wortman, Jennifer R., Lawson, Daniel, Wikel, Stephen K., Nene, Vishvanath M., Fraser, Claire M., Collins, Frank H., Birren, Bruce, Nelson, Karen E., Caler, Elisabet, and Hill, Catherine A.

Abstract

Ticks transmit more pathogens to humans and animals than any other arthropod. We describe the 2.1 Gbp nuclear genome of the tick, Ixodes scapularis (Say), which vectors pathogens that cause Lyme disease, human granulocytic anaplasmosis, babesiosis and other diseases. The large genome reflects accumulation of repetitive DNA, new lineages of retro-transposons, and gene architecture patterns resembling ancient metazoans rather than pancrustaceans. Annotation of scaffolds representing ∼57% of the genome, reveals 20,486 protein-coding genes and expansions of gene families associated with tick–host interactions. We report insights from genome analyses into parasitic processes unique to ticks, including host ‘questing’, prolonged feeding, cuticle synthesis, blood meal concentration, novel methods of haemoglobin digestion, haem detoxification, vitellogenesis and prolonged off-host survival. We identify proteins associated with the agent of human granulocytic anaplasmosis, an emerging disease, and the encephalitis-causing Langat virus, and a population structure correlated to life-history traits and transmission of the Lyme disease agent.

Published
2016

11. Genomic insights into the Ixodes scapularis tick vector of Lyme disease

Author

Gulia-Nuss, Monika, primary, Nuss, Andrew B., additional, Meyer, Jason M., additional, Sonenshine, Daniel E., additional, Roe, R. Michael, additional, Waterhouse, Robert M., additional, Sattelle, David B., additional, de la Fuente, José, additional, Ribeiro, Jose M., additional, Megy, Karine, additional, Thimmapuram, Jyothi, additional, Miller, Jason R., additional, Walenz, Brian P., additional, Koren, Sergey, additional, Hostetler, Jessica B., additional, Thiagarajan, Mathangi, additional, Joardar, Vinita S., additional, Hannick, Linda I., additional, Bidwell, Shelby, additional, Hammond, Martin P., additional, Young, Sarah, additional, Zeng, Qiandong, additional, Abrudan, Jenica L., additional, Almeida, Francisca C., additional, Ayllón, Nieves, additional, Bhide, Ketaki, additional, Bissinger, Brooke W., additional, Bonzon-Kulichenko, Elena, additional, Buckingham, Steven D., additional, Caffrey, Daniel R., additional, Caimano, Melissa J., additional, Croset, Vincent, additional, Driscoll, Timothy, additional, Gilbert, Don, additional, Gillespie, Joseph J., additional, Giraldo-Calderón, Gloria I., additional, Grabowski, Jeffrey M., additional, Jiang, David, additional, Khalil, Sayed M. S., additional, Kim, Donghun, additional, Kocan, Katherine M., additional, Koči, Juraj, additional, Kuhn, Richard J., additional, Kurtti, Timothy J., additional, Lees, Kristin, additional, Lang, Emma G., additional, Kennedy, Ryan C., additional, Kwon, Hyeogsun, additional, Perera, Rushika, additional, Qi, Yumin, additional, Radolf, Justin D., additional, Sakamoto, Joyce M., additional, Sánchez-Gracia, Alejandro, additional, Severo, Maiara S., additional, Silverman, Neal, additional, Šimo, Ladislav, additional, Tojo, Marta, additional, Tornador, Cristian, additional, Van Zee, Janice P., additional, Vázquez, Jesús, additional, Vieira, Filipe G., additional, Villar, Margarita, additional, Wespiser, Adam R., additional, Yang, Yunlong, additional, Zhu, Jiwei, additional, Arensburger, Peter, additional, Pietrantonio, Patricia V., additional, Barker, Stephen C., additional, Shao, Renfu, additional, Zdobnov, Evgeny M., additional, Hauser, Frank, additional, Grimmelikhuijzen, Cornelis J. P., additional, Park, Yoonseong, additional, Rozas, Julio, additional, Benton, Richard, additional, Pedra, Joao H. F., additional, Nelson, David R., additional, Unger, Maria F., additional, Tubio, Jose M. C., additional, Tu, Zhijian, additional, Robertson, Hugh M., additional, Shumway, Martin, additional, Sutton, Granger, additional, Wortman, Jennifer R., additional, Lawson, Daniel, additional, Wikel, Stephen K., additional, Nene, Vishvanath M., additional, Fraser, Claire M., additional, Collins, Frank H., additional, Birren, Bruce, additional, Nelson, Karen E., additional, Caler, Elisabet, additional, and Hill, Catherine A., additional

Published
2016
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12. Comparative genomic analysis and phylogenetic position of Theileria equi

Author

Kappmeyer, Lowell S., Thiagarajan, Mathangi, Herndon, David R., Ramsay, Joshua D., Caler, Elisabet, Djikeng, Appolinaire, Gillespie, Joseph J., Lau, Audrey O. T., Roalson, Eric H., Silva, Joana C., Silva, Marta G., Suarez, Carlos E., Ueti, Massaro W., Nene, Vishvanath M., Mealey, Robert H., Knowles, Donald P., and Brayton, Kelly A.

Subjects
animal diseases, parasitic diseases
Abstract

Background Transmission of arthropod-borne apicomplexan parasites that cause disease and result in death or persistent infection represents a major challenge to global human and animal health. First described in 1901 as Piroplasma equi, this re-emergent apicomplexan parasite was renamed Babesia equi and subsequently Theileria equi, reflecting an uncertain taxonomy. Understanding mechanisms by which apicomplexan parasites evade immune or chemotherapeutic elimination is required for development of effective vaccines or chemotherapeutics. The continued risk of transmission of T. equi from clinically silent, persistently infected equids impedes the goal of returning the U. S. to non-endemic status. Therefore comparative genomic analysis of T. equi was undertaken to: 1) identify genes contributing to immune evasion and persistence in equid hosts, 2) identify genes involved in PBMC infection biology and 3) define the phylogenetic position of T. equi relative to sequenced apicomplexan parasites. Results The known immunodominant proteins, EMA1, 2 and 3 were discovered to belong to a ten member gene family with a mean amino acid identity, in pairwise comparisons, of 39%. Importantly, the amino acid diversity of EMAs is distributed throughout the length of the proteins. Eight of the EMA genes were simultaneously transcribed. As the agents that cause bovine theileriosis infect and transform host cell PBMCs, we confirmed that T. equi infects equine PBMCs, however, there is no evidence of host cell transformation. Indeed, a number of genes identified as potential manipulators of the host cell phenotype are absent from the T. equi genome. Comparative genomic analysis of T. equi revealed the phylogenetic positioning relative to seven apicomplexan parasites using deduced amino acid sequences from 150 genes placed it as a sister taxon to Theileria spp. Conclusions The EMA family does not fit the paradigm for classical antigenic variation, and we propose a novel model describing the role of the EMA family in persistence. T. equi has lost the putative genes for host cell transformation, or the genes were acquired by T. parva and T. annulata after divergence from T. equi. Our analysis identified 50 genes that will be useful for definitive phylogenetic classification of T. equi and closely related organisms. Published version

Published
2012

13. Advances in the genomics of ticks and tick-borne pathogens

Author

European Commission, Jongejan, Frans, Nene, Vishvanath M., Fuente, José de la, Pain, Arnab, Willadsen, Peter, European Commission, Jongejan, Frans, Nene, Vishvanath M., Fuente, José de la, Pain, Arnab, and Willadsen, Peter

Abstract

Ticks and the diseases for which they are vectors engage in complex interactions with their mammalian hosts. These interactions involve the developmental processes of tick and pathogen, and interplay between the defensive responses and counter responses of host, tick and pathogen. Understanding these interactions has long been an intractable problem, but progress is now being made thanks to the flood of genomic information on host, tick and pathogen, and the attendant, novel experimental tools that have been generated. Each advance reveals new levels of complexity, but there are encouraging signs that genomics is leading to novel means of parasite control.

Published
2007

14. A Rickettsia Genome Overrun by Mobile Genetic Elements Provides Insight into the Acquisition of Genes Characteristic of an Obligate Intracellular Lifestyle

Author

Gillespie, Joseph J., primary, Joardar, Vinita, additional, Williams, Kelly P., additional, Driscoll, Timothy, additional, Hostetler, Jessica B., additional, Nordberg, Eric, additional, Shukla, Maulik, additional, Walenz, Brian, additional, Hill, Catherine A., additional, Nene, Vishvanath M., additional, Azad, Abdu F., additional, Sobral, Bruno W., additional, and Caler, Elisabet, additional

Published
2012
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18. Genome Sequence of Babesia bovis and Comparative Analysis of Apicomplexan Hemoprotozoa

Author

Brayton, Kelly A, primary, Lau, Audrey O. T, additional, Herndon, David R, additional, Hannick, Linda, additional, Kappmeyer, Lowell S, additional, Berens, Shawn J, additional, Bidwell, Shelby L, additional, Brown, Wendy C, additional, Crabtree, Jonathan, additional, Fadrosh, Doug, additional, Feldblum, Tamara, additional, Forberger, Heather A, additional, Haas, Brian J, additional, Howell, Jeanne M, additional, Khouri, Hoda, additional, Koo, Hean, additional, Mann, David J, additional, Norimine, Junzo, additional, Paulsen, Ian T, additional, Radune, Diana, additional, Ren, Qinghu, additional, Smith, Roger K, additional, Suarez, Carlos E, additional, White, Owen, additional, Wortman, Jennifer R, additional, Knowles, Donald P, additional, McElwain, Terry F, additional, and Nene, Vishvanath M, additional

Published
2007
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21. Gene Structure and Expression of a Pyrethroid-Metabolizing Esterase, CzEst9, from a Pyrethroid Resistant Mexican Populationof Rhipicephalus (Boophilus) microplus (Acari: Ixodidae)

Author

Guerrero, Felix D. and Nene, Vishvanath M.

Abstract

A population of Rhipicephalus (Boophilus) microplus (Canestrini) (Acari: Ixodidae), designated Coatzacoalcos, sampled from a ranch near Veracruz, Mexico, was found to possess a high level of resistance to pyrethroid-based acaricides. Bioassay and biochemical and molecular analysis had previously shown that resistance in this population could primarily be attributed to expression of a highly active metabolic esterase designated CzEST9. We cloned and sequenced the entire CzEST9 coding region, including introns and >1.0 kb upstream from the transcription start site, and we compared the upstream region sequence between individual resistant and susceptible ticks from several populations with different pyrethroid resistance characteristics. In the 1.0-kb upstream region sequence, four variant nucleotides were found, and a TGA trinucleotide occurred as either four, five, or nine tandem repeats. However, none of these promoter region sequence differences could be clearly associated with a pyrethroid-resistant phenotype; thus, we concluded that differences in gene promoter sequence were not responsible for the pyrethroid resistance mechanism in the Cz strain. CzEST9 was expressed in recombinant Escherichia coli and Pichia pastoris systems and esterase activity was obtained in recombinant CzEST9 from the P. pastoris system.

Published
2008
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