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Check the list of papers from NScTI Citrus
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2020
Castillo, Andreina I.; Chacón-Díaz, Carlos; Rodríguez-Murillo, Neysa; Coletta-Filho, Helvecio D.; Almeida, Rodrigo P. P.
Impacts of local population history and ecology on the evolution of a globally dispersed pathogen Journal Article
In: BMC Genomics, vol. 21, iss. 1, pp. 1-20, 2020, ISSN: 14712164.
Abstract | Links | BibTeX | Tags: genetic diversity, Inter-subspecific recombination, Pan genome, WGS, Xylella fastidiosa
@article{Castillo2020,
title = {Impacts of local population history and ecology on the evolution of a globally dispersed pathogen},
author = {Andreina I. Castillo and Carlos Chacón-Díaz and Neysa Rodríguez-Murillo and Helvecio D. Coletta-Filho and Rodrigo P. P. Almeida},
url = {https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-020-06778-6},
doi = {10.1186/S12864-020-06778-6/FIGURES/4},
issn = {14712164},
year = {2020},
date = {2020-01-01},
journal = {BMC Genomics},
volume = {21},
issue = {1},
pages = {1-20},
publisher = {BioMed Central Ltd.},
abstract = {Background: Pathogens with a global distribution face diverse biotic and abiotic conditions across populations. Moreover, the ecological and evolutionary history of each population is unique. Xylella fastidiosa is a xylem-dwelling bacterium infecting multiple plant hosts, often with detrimental effects. As a group, X. fastidiosa is divided into distinct subspecies with allopatric historical distributions and patterns of multiple introductions from numerous source populations. The capacity of X. fastidiosa to successfully colonize and cause disease in naïve plant hosts varies among subspecies, and potentially, among populations. Within Central America (i.e. Costa Rica) two X. fastidiosa subspecies coexist: the native subsp. fastidiosa and the introduced subsp. pauca. Using whole genome sequences, the patterns of gene gain/loss, genomic introgression, and genetic diversity were characterized within Costa Rica and contrasted to other X. fastidiosa populations. Results: Within Costa Rica, accessory and core genome analyses showed a highly malleable genome with numerous intra- and inter-subspecific gain/loss events. Likewise, variable levels of inter-subspecific introgression were found within and between both coexisting subspecies; nonetheless, the direction of donor/recipient subspecies to the recombinant segments varied. Some strains appeared to recombine more frequently than others; however, no group of genes or gene functions were overrepresented within recombinant segments. Finally, the patterns of genetic diversity of subsp. fastidiosa in Costa Rica were consistent with those of other native populations (i.e. subsp. pauca in Brazil). Conclusions: Overall, this study shows the importance of characterizing local evolutionary and ecological history in the context of world-wide pathogen distribution.},
keywords = {genetic diversity, Inter-subspecific recombination, Pan genome, WGS, Xylella fastidiosa},
pubstate = {published},
tppubtype = {article}
}
Background: Pathogens with a global distribution face diverse biotic and abiotic conditions across populations. Moreover, the ecological and evolutionary history of each population is unique. Xylella fastidiosa is a xylem-dwelling bacterium infecting multiple plant hosts, often with detrimental effects. As a group, X. fastidiosa is divided into distinct subspecies with allopatric historical distributions and patterns of multiple introductions from numerous source populations. The capacity of X. fastidiosa to successfully colonize and cause disease in naïve plant hosts varies among subspecies, and potentially, among populations. Within Central America (i.e. Costa Rica) two X. fastidiosa subspecies coexist: the native subsp. fastidiosa and the introduced subsp. pauca. Using whole genome sequences, the patterns of gene gain/loss, genomic introgression, and genetic diversity were characterized within Costa Rica and contrasted to other X. fastidiosa populations. Results: Within Costa Rica, accessory and core genome analyses showed a highly malleable genome with numerous intra- and inter-subspecific gain/loss events. Likewise, variable levels of inter-subspecific introgression were found within and between both coexisting subspecies; nonetheless, the direction of donor/recipient subspecies to the recombinant segments varied. Some strains appeared to recombine more frequently than others; however, no group of genes or gene functions were overrepresented within recombinant segments. Finally, the patterns of genetic diversity of subsp. fastidiosa in Costa Rica were consistent with those of other native populations (i.e. subsp. pauca in Brazil). Conclusions: Overall, this study shows the importance of characterizing local evolutionary and ecological history in the context of world-wide pathogen distribution.
2019
Paula, Larissa Bonevaes; Lin, Hong; Stuchi, Eduardo Sanches; Francisco, Carolina Sardinha; Safady, Nágela Gomes; Coletta-Filho, Helvécio Della
Genetic diversity of ‘Candidatus Liberibacter asiaticus’ in Brazil analyzed in different geographic regions and citrus varieties Journal Article
In: European Journal of Plant Pathology, vol. 154, iss. 4, pp. 863-872, 2019, ISSN: 15738469.
Abstract | Links | BibTeX | Tags: Citrus pathogen, genetic diversity, Greening, SSR
@article{nokey,
title = {Genetic diversity of ‘Candidatus Liberibacter asiaticus’ in Brazil analyzed in different geographic regions and citrus varieties},
author = {Larissa Bonevaes Paula and Hong Lin and Eduardo Sanches Stuchi and Carolina Sardinha Francisco and Nágela Gomes Safady and Helvécio Della Coletta-Filho},
url = {https://link.springer.com/article/10.1007/s10658-019-01695-1},
doi = {10.1007/S10658-019-01695-1/METRICS},
issn = {15738469},
year = {2019},
date = {2019-01-01},
journal = {European Journal of Plant Pathology},
volume = {154},
issue = {4},
pages = {863-872},
publisher = {Springer Netherlands},
abstract = {The bacterium ‘Candidatus Liberibacter asiaticus’ - CLas, the agent associated with citrus huanglongbing disease was first reported in Sao Paulo State in 2004 and has spread throughout the citrus-growing regions of Sao Paulo and further to the states of Minas Gerais and Parana. However, little information is available regarding the genetic diversity of CLas since its introduction. Understanding the genetic diversity of this bacterium is important for tracing migration routes and for identifying evolutionary selection forces that may affect the genetic diversity of this pathogen. Total DNA from 199 HLB-diseased citrus species trees was sampled from geographic regions in Sao Paulo, Parana and Minas Gerais states and the CLas isolates were genotyped by simple sequence DNA repeats (SSR). Nei’s genetic diversity index was observed to be low in all populations (HNei = 0.11–0.26). Wright’s fixation index (FST), which measures population genetic differentiation, did not differ significantly between CLas populations from Sao Paulo State and from Minas Gerais, but significant values (FST = 0.118–0.191) of the Parana CLas population distinguish it from the others. Interestingly, higher values (FST = 0.275–0.445) were observed for the CLas populations obtained from different citrus species compared to sweet orange, suggesting that the citrus genotypes could be driven the genetic diversity of CLas. Clustering analysis supports the FST results that split the CLas samples into three genetically distinct populations. These results indicate that genetically homogeneous populations of CLas infect sweet orange plants in various regions of Sao Paulo State and Minas Gerais, but not Parana, suggesting that different introduction events may have occurred for the Sao Paulo and Parana states.},
keywords = {Citrus pathogen, genetic diversity, Greening, SSR},
pubstate = {published},
tppubtype = {article}
}
The bacterium ‘Candidatus Liberibacter asiaticus’ - CLas, the agent associated with citrus huanglongbing disease was first reported in Sao Paulo State in 2004 and has spread throughout the citrus-growing regions of Sao Paulo and further to the states of Minas Gerais and Parana. However, little information is available regarding the genetic diversity of CLas since its introduction. Understanding the genetic diversity of this bacterium is important for tracing migration routes and for identifying evolutionary selection forces that may affect the genetic diversity of this pathogen. Total DNA from 199 HLB-diseased citrus species trees was sampled from geographic regions in Sao Paulo, Parana and Minas Gerais states and the CLas isolates were genotyped by simple sequence DNA repeats (SSR). Nei’s genetic diversity index was observed to be low in all populations (HNei = 0.11–0.26). Wright’s fixation index (FST), which measures population genetic differentiation, did not differ significantly between CLas populations from Sao Paulo State and from Minas Gerais, but significant values (FST = 0.118–0.191) of the Parana CLas population distinguish it from the others. Interestingly, higher values (FST = 0.275–0.445) were observed for the CLas populations obtained from different citrus species compared to sweet orange, suggesting that the citrus genotypes could be driven the genetic diversity of CLas. Clustering analysis supports the FST results that split the CLas samples into three genetically distinct populations. These results indicate that genetically homogeneous populations of CLas infect sweet orange plants in various regions of Sao Paulo State and Minas Gerais, but not Parana, suggesting that different introduction events may have occurred for the Sao Paulo and Parana states.
Paula, Larissa Bonevaes; Lin, Hong; Stuchi, Eduardo Sanches; Francisco, Carolina Sardinha; Safady, Nágela Gomes; Coletta-Filho, Helvécio Della
Genetic diversity of ‘Candidatus Liberibacter asiaticus’ in Brazil analyzed in different geographic regions and citrus varieties Journal Article
In: European Journal of Plant Pathology, vol. 154, iss. 4, pp. 863-872, 2019, ISSN: 15738469.
Abstract | Links | BibTeX | Tags: Citrus pathogen, genetic diversity, Greening, SSR
@article{nokey,
title = {Genetic diversity of ‘Candidatus Liberibacter asiaticus’ in Brazil analyzed in different geographic regions and citrus varieties},
author = {Larissa Bonevaes Paula and Hong Lin and Eduardo Sanches Stuchi and Carolina Sardinha Francisco and Nágela Gomes Safady and Helvécio Della Coletta-Filho},
url = {https://link.springer.com/article/10.1007/s10658-019-01695-1},
doi = {10.1007/S10658-019-01695-1/METRICS},
issn = {15738469},
year = {2019},
date = {2019-01-01},
journal = {European Journal of Plant Pathology},
volume = {154},
issue = {4},
pages = {863-872},
publisher = {Springer Netherlands},
abstract = {The bacterium ‘Candidatus Liberibacter asiaticus’ - CLas, the agent associated with citrus huanglongbing disease was first reported in Sao Paulo State in 2004 and has spread throughout the citrus-growing regions of Sao Paulo and further to the states of Minas Gerais and Parana. However, little information is available regarding the genetic diversity of CLas since its introduction. Understanding the genetic diversity of this bacterium is important for tracing migration routes and for identifying evolutionary selection forces that may affect the genetic diversity of this pathogen. Total DNA from 199 HLB-diseased citrus species trees was sampled from geographic regions in Sao Paulo, Parana and Minas Gerais states and the CLas isolates were genotyped by simple sequence DNA repeats (SSR). Nei’s genetic diversity index was observed to be low in all populations (HNei = 0.11–0.26). Wright’s fixation index (FST), which measures population genetic differentiation, did not differ significantly between CLas populations from Sao Paulo State and from Minas Gerais, but significant values (FST = 0.118–0.191) of the Parana CLas population distinguish it from the others. Interestingly, higher values (FST = 0.275–0.445) were observed for the CLas populations obtained from different citrus species compared to sweet orange, suggesting that the citrus genotypes could be driven the genetic diversity of CLas. Clustering analysis supports the FST results that split the CLas samples into three genetically distinct populations. These results indicate that genetically homogeneous populations of CLas infect sweet orange plants in various regions of Sao Paulo State and Minas Gerais, but not Parana, suggesting that different introduction events may have occurred for the Sao Paulo and Parana states.},
keywords = {Citrus pathogen, genetic diversity, Greening, SSR},
pubstate = {published},
tppubtype = {article}
}
The bacterium ‘Candidatus Liberibacter asiaticus’ - CLas, the agent associated with citrus huanglongbing disease was first reported in Sao Paulo State in 2004 and has spread throughout the citrus-growing regions of Sao Paulo and further to the states of Minas Gerais and Parana. However, little information is available regarding the genetic diversity of CLas since its introduction. Understanding the genetic diversity of this bacterium is important for tracing migration routes and for identifying evolutionary selection forces that may affect the genetic diversity of this pathogen. Total DNA from 199 HLB-diseased citrus species trees was sampled from geographic regions in Sao Paulo, Parana and Minas Gerais states and the CLas isolates were genotyped by simple sequence DNA repeats (SSR). Nei’s genetic diversity index was observed to be low in all populations (HNei = 0.11–0.26). Wright’s fixation index (FST), which measures population genetic differentiation, did not differ significantly between CLas populations from Sao Paulo State and from Minas Gerais, but significant values (FST = 0.118–0.191) of the Parana CLas population distinguish it from the others. Interestingly, higher values (FST = 0.275–0.445) were observed for the CLas populations obtained from different citrus species compared to sweet orange, suggesting that the citrus genotypes could be driven the genetic diversity of CLas. Clustering analysis supports the FST results that split the CLas samples into three genetically distinct populations. These results indicate that genetically homogeneous populations of CLas infect sweet orange plants in various regions of Sao Paulo State and Minas Gerais, but not Parana, suggesting that different introduction events may have occurred for the Sao Paulo and Parana states.
2017
Sagawa, C. H. D.; Cristofani-Yaly, M.; Novelli, V. M.; Bastianel, M.; Machado, M. A.
Assessing genetic diversity of Citrus by DArT_seq™ genotyping Journal Article
In: https://doi.org/10.1080/11263504.2017.1341438, vol. 152, iss. 4, pp. 593-598, 2017, ISSN: 17245575.
Abstract | Links | BibTeX | Tags: citrus fingerprint, genetic diversity, Molecular markers, Poncirus, sweet orange
@article{Sagawa2017,
title = {Assessing genetic diversity of Citrus by DArT_seq™ genotyping},
author = {C. H. D. Sagawa and M. Cristofani-Yaly and V. M. Novelli and M. Bastianel and M. A. Machado},
url = {https://www.tandfonline.com/doi/abs/10.1080/11263504.2017.1341438},
doi = {10.1080/11263504.2017.1341438},
issn = {17245575},
year = {2017},
date = {2017-01-01},
journal = {https://doi.org/10.1080/11263504.2017.1341438},
volume = {152},
issue = {4},
pages = {593-598},
publisher = {Taylor & Francis},
abstract = {In citrus despite the diversity among cultivated genotypes related to morphological, physiological, and agronomic traits, low polymorphism is detected at the molecular marker level, and the number ...},
keywords = {citrus fingerprint, genetic diversity, Molecular markers, Poncirus, sweet orange},
pubstate = {published},
tppubtype = {article}
}
In citrus despite the diversity among cultivated genotypes related to morphological, physiological, and agronomic traits, low polymorphism is detected at the molecular marker level, and the number ...