DSpace Repository
Chromosomal copy number variation reveals differential levels of genomic plasticity in distinct Trypanosoma cruzi strains
- DSpace Home
- →
- Artículos
- →
- Editados por otras instituciones
- →
- Artículos en revistas indizadas
- →
- View Item
JavaScript is disabled for your browser. Some features of this site may not work without it.
Chromosomal copy number variation reveals differential levels of genomic plasticity in distinct Trypanosoma cruzi strains
Reis-Cunha, J.L.; Rodrigues-Luiz, G.F.; Valdivia, H.O.; Baptista, R.P.; Mendes, T.A.O.; Loss de Morais, G.; Guedes, R.; Macedo, A.M.; Bern, C.; Gilman, Robert Hugh; Talavera Lopez, C.; Andersson, B.; Vasconcelos, A.T.; Bartholomeu, D.C.
Date:
2015
Abstract:
Background: Trypanosoma cruzi, the etiologic agent of Chagas disease, is currently divided into six discrete typing units (DTUs), named TcI-TcVI. CL Brener, the reference strain of the T. cruzi genome project, is a hybrid with a genome assembled into 41 putative chromosomes. Gene copy number variation (CNV) is well documented as an important mechanism to enhance gene expression and variability in T. cruzi. Chromosomal CNV (CCNV) is another level of gene CNV in which whole blocks of genes are expanded simultaneously. Although the T. cruzi karyotype is not well defined, several studies have demonstrated a significant variation in the size and content of chromosomes between different T. cruzi strains. Despite these studies, the extent of diversity in CCNV among T. cruzi strains based on a read depth coverage analysis has not been determined. Results: We identify the CCNV in T. cruzi strains from the TcI, TcII and TcIII DTUs, by analyzing the depth coverage of short reads from these strains using the 41 CL Brener chromosomes as reference. This study led to the identification of a broader extent of CCNV in T. cruzi than was previously speculated. The TcI DTU strains have very few aneuploidies, while the strains from TcII and TcIII DTUs present a high degree of chromosomal expansions. Chromosome 31, which is the only chromosome that is supernumerary in all six T. cruzi samples evaluated in this study, is enriched with genes related to glycosylation pathways, highlighting the importance of glycosylation to parasite survival. Conclusions: Increased gene copy number due to chromosome amplification may contribute to alterations in gene expression, which represents a strategy that may be crucial for parasites that mainly depend on post-transcriptional mechanisms to control gene expression.
Files in this item
| Files | Size | Format | View |
|---|---|---|---|
|
There are no files associated with this item. |
|||
This item appears in the following Collection(s)
-
Artículos en revistas indizadas [4988]
Recuperados de bases de datos bibliográficas
Except where otherwise noted, this item's license is described as info:eu-repo/semantics/restrictedAccess
Related items
Showing items related by title, author, creator and subject.
-
1000 Genomes Project; Auton, A.; Abecasis, G.R.; Altshuler, D.M.; Durbin, R.M.; Bentley, D.R.; Chakravarti, A.; Clark, A.G.; Donnelly, P.; Eichler, E.E.; Flicek, P.; Gabriel, S.B.; Gibbs, R.A.; Green, E.D.; Hurles, M.E.; Knoppers, B.M.; Korbel, J.O.; Lander, E.S.; Lee, C.; Lehrach, H.; Mardis, E.R.; Marth, G.T.; McVean, G.A.; Nickerson, D.A.; Schmidt, J.P.; Sherry, S.T.; Wang, J.; Wilson, R.K.; Boerwinkle, E.; Doddapaneni, H.; Han, Y.; Korchina, V.; Kovar, C.; Lee, S.; Muzny, D.; Reid, J.G.; Zhu, Y.; Chang, Y.; Feng, Q.; Fang, X.; Guo, X.; Jian, M.; Jiang, H.; Jin, X.; Lan, T.; Li, G.; Li, J.; Li, Y.; Liu, S.; Liu, X.; Lu, Y.; Ma, X.; Tang, M.; Wang, B.; Wang, G.; Wu, H.; Wu, R.; Xu, X.; Yin, Y.; Zhang, D.; Zhang, W.; Zhao, J.; Zhao, M.; Zheng, X.; Gupta, N.; Gharani, N.; Toji, L.H.; Gerry, N.P.; Resch, A.M.; Barker, J.; Clarke, L.; Gil, L.; Hunt, S.E.; Kelman, G.; Kulesha, E.; Leinonen, R.; McLaren, W.M.; Radhakrishnan, R.; Roa, A.; Smirnov, D.; Smith, R.E.; Streeter, I.; Thormann, A.; Toneva, I.; Vaughan, B.; Zheng-Bradley, X.; Grocock, R.; Humphray, S.; James, T.; Kingsbury, Z.; Sudbrak, R.; Albrecht, M.W.; Amstislavskiy, V.S.; Borodina, T.A.; Lienhard, M.; Mertes, F.; Sultan, M.; Timmermann, B.; Yaspo, M.-L.; Fulton, L.; Ananiev, V.; Belaia, Z.; Beloslyudtsev, D.; Bouk, N.; Chen, C.; Church, D.; Cohen, R.; Cook, C.; Garner, J.; Hefferon, T.; Kimelman, M.; Liu, C.; Lopez, J.; Meric, P.; O'Sullivan, C.; Ostapchuk, Y.; Phan, L.; Ponomarov, S.; Schneider, V.; Shekhtman, E.; Sirotkin, K.; Slotta, D.; Zhang, H.; Balasubramaniam, S.; Burton, J.; Danecek, P.; Keane, T.M.; Kolb-Kokocinski, A.; McCarthy, S.; Stalker, J.; Quail, M.; Davies, C.J.; Gollub, J.; Webster, T.; Wong, B.; Zhan, Y.; Campbell, C.L.; Kong, Y.; Marcketta, A.; Yu, F.; Antunes, L.; Bainbridge, M.; Sabo, A.; Huang, Z.; Coin, L.J.M.; Fang, L.; Li, Q.; Li, Z.; Lin, H.; Liu, B.; Luo, R.; Shao, H.; Xie, Y.; Ye, C.; Yu, C.; Zhang, F.; Zheng, H.; Zhu, H.; Alkan, C.; Dal, E.; Kahveci, F.; Garrison, E.P.; Kural, D.; Lee, W.-P.; Leong, W.F.; Stromberg, M.; Ward, A.N.; Wu, J.; Zhang, M.; Daly, M.J.; DePristo, M.A.; Handsaker, R.E.; Banks, E.; Bhatia, G.; Del Angel, G.; Genovese, G.; Li, H.; Kashin, S.; McCarroll, S.A.; Nemesh, J.C.; Poplin, R.E.; Yoon, S.C.; Lihm, J.; Makarov, V.; Gottipati, S.; Keinan, A.; Rodriguez-Flores, J.L.; Rausch, T.; Fritz, M.H.; Stütz, A.M.; Beal, K.; Datta, A.; Herrero, J.; Ritchie, G.R.S.; Zerbino, D.; Sabeti, P.C.; Shlyakhter, I.; Schaffner, S.F.; Vitti, J.; Cooper, D.N.; Ball, E.V.; Stenson, P.D.; Barnes, B.; Bauer, M.; Cheetham, R.K.; Cox, A.; Eberle, M.; Kahn, S.; Murray, L.; Peden, J.; Shaw, R.; Kenny, E.E.; Batzer, M.A.; Konkel, M.K.; Walker, J.A.; MacArthur, D.G.; Lek, M.; Herwig, R.; Ding, L.; Koboldt, D.C.; Larson, D.; Ye, K.; Gravel, S.; Swaroop, A.; Chew, E.; Lappalainen, T.; Erlich, Y.; Gymrek, M.; Willems, T.F.; Simpson, J.T.; Shriver, M.D.; Rosenfeld, J.A.; Bustamante, C.D.; Montgomery, S.B.; De La Vega, F.M.; Byrnes, J.K.; Carroll, A.W.; DeGorter, M.K.; Lacroute, P.; Maples, B.K.; Martin, A.R.; Moreno-Estrada, A.; Shringarpure, S.S.; Zakharia, F.; Halperin, E.; Baran, Y.; Cerveira, E.; Hwang, J.; Malhotra, A.; Plewczynski, D.; Radew, K.; Romanovitch, M.; Zhang, C.; Hyland, F.C.L.; Craig, D.W.; Christoforides, A.; Homer, N.; Izatt, T.; Kurdoglu, A.A.; Sinari, S.A.; Squire, K.; Xiao, C.; Sebat, J.; Antaki, D.; Gujral, M.; Noor, A.; Ye, K.; Burchard, E.G.; Hernandez, R.D.; Gignoux, C.R.; Haussler, D.; Katzman, S.J.; Kent, W.J.; Howie, B.; Ruiz-Linares, A.; Dermitzakis, E.T.; Devine, S.E.; Kang, H.M.; Kidd, J.M.; Blackwell, T.; Caron, S.; Chen, W.; Emery, S.; Fritsche, L.; Fuchsberger, C.; Jun, G.; Li, B.; Lyons, R.; Scheller, C.; Sidore, C.; Song, S.; Sliwerska, E.; Taliun, D.; Tan, A.; Welch, R.; Wing, M.K.; Zhan, X.; Awadalla, P.; Hodgkinson, A.; Li, Y.; Shi, X.; Quitadamo, A.; Lunter, G.; Marchini, J.L.; Myers, S.; Churchhouse, C.; Delaneau, O.; Gupta-Hinch, A.; Kretzschmar, W.; Iqbal, Z.; Mathieson, I.; Menelaou, A.; Rimmer, A.; Xifara, D.K.; Oleksyk, T.K.; Fu, Y.; Liu, X.; Xiong, M.; Jorde, L.; Witherspoon, D.; Xing, J.; Browning, B.L.; Browning, S.R.; Hormozdiari, F.; Sudmant, P.H.; Khurana, E.; Tyler-Smith, C.; Albers, C.A.; Ayub, Q.; Chen, Y.; Colonna, V.; Jostins, L.; Walter, K.; Xue, Y.; Gerstein, M.B.; Abyzov, A.; Balasubramanian, S.; Chen, J.; Clarke, D.; Fu, Y.; Harmanci, A.O.; Jin, M.; Lee, D.; Liu, J.; Mu, X.J.; Zhang, J.; Zhang, Y.; Hartl, C.; Shakir, K.; Degenhardt, J.; Meiers, S.; Raeder, B.; Casale, F.P.; Stegle, O.; Lameijer, E.-W.; Hall, I.; Bafna, V.; Michaelson, J.; Gardner, E.J.; Mills, R.E.; Dayama, G.; Chen, K.; Fan, X.; Chong, Z.; Chen, T.; Chaisson, M.J.; Huddleston, J.; Malig, M.; Nelson, B.J.; Parrish, N.F.; Blackburne, B.; Lindsay, S.J.; Ning, Z.; Zhang, Y.; Lam, H.; Sisu, C.; Challis, D.; Evani, U.S.; Lu, J.; Nagaswamy, U.; Yu, J.; Li, W.; Habegger, L.; Yu, H.; Cunningham, F.; Dunham, I.; Lage, K.; Jespersen, J.B.; Horn, H.; Kim, D.; Desalle, R.; Narechania, A.; Sayres, M.A.W.; Mendez, F.L.; Poznik, G.D.; Underhill, P.A.; Mittelman, D.; Banerjee, R.; Cerezo, M.; Fitzgerald, T.W.; Louzada, S.; Massaia, A.; Yang, F.; Kalra, D.; Hale, W.; Dan, X.; Barnes, K.C.; Beiswanger, C.; Cai, H.; Cao, H.; Henn, B.; Jones, D.; Kaye, J.S.; Kent, A.; Kerasidou, A.; Mathias, R.; Ossorio, P.N.; Parker, M.; Rotimi, C.N.; Royal, C.D.; Sandoval, K.; Su, Y.; Tian, Z.; Tishkoff, S.; Via, M.; Wang, Y.; Yang, H.; Yang, L.; Zhu, J.; Bodmer, W.; Bedoya, G.; Cai, Z.; Gao, Y.; Chu, J.; Peltonen, L.; Garcia-Montero, A.; Orfao, A.; Dutil, J.; Martinez-Cruzado, J.C.; Mathias, R.A.; Hennis, A.; Watson, H.; McKenzie, C.; Qadri, F.; LaRocque, R.; Deng, X.; Asogun, D.; Folarin, O.; Happi, C.; Omoniwa, O.; Stremlau, M.; Tariyal, R.; Jallow, M.; Joof, F.S.; Corrah, T.; Rockett, K.; Kwiatkowski, D.; Kooner, J.; Hien, T.T.; Dunstan, S.J.; ThuyHang, N.; Fonnie, R.; Garry, R.; Kanneh, L.; Moses, L.; Schieffelin, J.; Grant, D.S.; Gallo López-Aliaga, Carla Maria; Poletti, Giovanni; Saleheen, D.; Rasheed, A.; Brooks, L.D.; Felsenfeld, A.L.; McEwen, J.E.; Vaydylevich, Y.; Duncanson, A.; Dunn, M.; Schloss, J.A. (Springer Nature, 2015)The 1000 Genomes Project set out to provide a comprehensive description of common human genetic variation by applying whole-genome sequencing to a diverse set of individuals from multiple populations. Here we report ...
-
Berry, Alexander S. F.; Salazar Sánchez, Renzo Sadath; Castillo Neyra, Ricardo; Borrini-Mayori, Katty; Chipana-Ramos, Claudia; Vargas-Maquera, Melina; Ancca-Juarez, Jenny; Naquira Velarde, Cesar Gabriel; Levy, Michael Z.; Brisson, Dustin (Public Library of Science, 2019)Background: Sexual reproduction provides an evolutionary advantageous mechanism that combines favorable mutations that have arisen in separate lineages into the same individual. This advantage is especially pronounced in ...
-
Adhikari, K.; Mendoza-Revilla, J.; Sohail, A.; Fuentes-Guajardo, M.; Lampert, J.; Chacón-Duque, J.C.; Hurtado, M.; Villegas, V.; Granja, V.; Acuña-Alonzo, V.; Jaramillo, C.; Arias, W.; Lozano, R.B.; Everardo, P.; Gómez-Valdés, J.; Villamil-Ramírez, H.; Silva de Cerqueira, C.C.; Hunemeier, T.; Ramallo, V.; Schuler-Faccini, L.; Salzano, F.M.; Gonzalez-José, R.; Bortolini, M.-C.; Canizales-Quinteros, S.; Gallo López-Aliaga, Carla Maria; Poletti, G.; Bedoya, G.; Rothhammer, F.; Tobin, D.J.; Fumagalli, M.; Balding, D.; Ruiz-Linares, A. (Springer Nature, 2019)We report a genome-wide association scan in >6,000 Latin Americans for pigmentation of skin and eyes. We found eighteen signals of association at twelve genomic regions. These include one novel locus for skin pigmentation ...
Search DSpace
Browse
-
All of DSpace
-
This Collection
