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Viana MC, Alves-Pereira A, Oliveira MAP, Valença-Barbosa C, Folly-Ramos E, Souza AP, Takiya DM, Almeida CE. Population genetics and genomics of Triatoma brasiliensis (Hemiptera, Reduviidae) in an area of high pressure of domiciliary infestation in Northeastern Brazil. Acta Trop 2024; 252:107144. [PMID: 38336343 DOI: 10.1016/j.actatropica.2024.107144] [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: 11/28/2023] [Revised: 02/05/2024] [Accepted: 02/06/2024] [Indexed: 02/12/2024]
Abstract
Understanding the population dynamics of vectors is crucial for effective control of vector-borne diseases. In the Northeastern Brazilian semi-arid region, Triatoma brasiliensis persists as the most significant Chagas disease vector, frequently displaying recurrent domiciliary infestations. This situation raises relevant public health concerns in the municipality of Currais Novos in the state of Rio Grande do Norte. This area has experienced a high prevalence of peridomiciliary re-infestations by T. brasiliensis, coupled with elevated rates of Trypanosoma cruzi infection. Therefore, we assessed the distribution of genetic variation via mitochondrial Cytochrome b gene (MT-CYB) sequencing (n = 109) and single nucleotide polymorphisms (SNPs, n = 86) to assess the gene flow among distinct populations distributed in varied geographic spots and environments, mainly sylvatic and peridomiciliary. Insects were collected from rural communities at Currais Novos, enclosed within a 16 km radius. Sampling included 13 populations: one intradomiciliary, eight peridomiciliary, and four sylvatic. Furthermore, an external population located 220 km from Currais Novos was also included in the study. The method employed to obtain SNP information relied on ddRAD-seq genotyping-by-sequencing (GBS), enabling a genome-wide analysis to infer genetic variation. Through AMOVA analysis of MT-CYB gene variation, we identified four distinct population groups with statistical significance (FCT= 0.42; p<0.05). We identified a total of 3,013 SNPs through GBS, with 11 loci showing putative signs of being under selection. The variation based on 3,002 neutral loci evidenced low genetic structuration based on low FST values (p>0.05), indicating local panmixia. However, resampling algorithms pointed out that three samples from the external population were assigned (>98 %) in a cluster contrasting from the ones putatively under local panmixia - validating the newly applied genome-wide marker for studies on the population genetics at finer-scale resolution for T. brasiliensis. The presence of population structuring in some of the sampled points, as suggested by the mitochondrial marker, leads us to assume that infestations were probably initiated by small populations of females - demographic event poses a risk for rapid re-infestations. The local panmictic pattern revealed by the GBS marker poses a challenge for vector control measures, as re-infestation foci may be distributed over a wide geographical and ecological range. In such instances, vectors exhibit reduced susceptibility to conventional insecticide spraying operations since sylvatic populations are beyond the reach of these interventions. The pattern of infestation exhibited by T. brasiliensis necessitates integrating innovative strategies into the existing control framework, holding the potential to create a more resilient and adaptive vector control program. In our dataset, the results demonstrated that the genetic signals from both markers were complementary. Therefore, it is essential to consider the nature and inheritance pattern of each marker when inferring the pattern of re-infestations.
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Affiliation(s)
- Maria Carolina Viana
- Instituto de Biologia (IB), Universidade de Campinas - UNICAMP, Campinas, Brazil; Programa de Pós-Graduação em Genética e Biologia Molecular, IB, UNICAMP; Coordenação de Prevenção e Vigilância do Câncer (CONPREV), Instituto Nacional de Câncer, Rio de Janeiro, Brazil
| | | | - Marcelo A P Oliveira
- Programa de Pós-Graduação em Genética- IB, Universidade Federal do Rio de Janeiro - UFRJ, Rio de Janeiro, Brazil
| | - Carolina Valença-Barbosa
- Instituto de Biologia (IB), Universidade de Campinas - UNICAMP, Campinas, Brazil; Grupo Triatomíneos, Instituto René Rachou, Fundação Oswaldo Cruz, Belo Horizonte, Fiocruz, Brazil
| | | | | | | | - Carlos E Almeida
- Instituto de Biologia (IB), Universidade de Campinas - UNICAMP, Campinas, Brazil; Programa de Pós-Graduação em Genética e Biologia Molecular, IB, UNICAMP; Laboratorio de Entomologia, Instituto de Biologia, UFRJ.
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2
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Grijalva MJ, Villacís AG, Ocaña-Mayorga S, Yumiseva CA, Nieto-Sanchez C, Baus EG, Moncayo AL. Evaluation of the Effectiveness of Chemical Control for Chagas Disease Vectors in Loja Province, Ecuador. Vector Borne Zoonotic Dis 2022; 22:449-458. [PMID: 36044033 PMCID: PMC9508444 DOI: 10.1089/vbz.2021.0089] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
The objective of this study was to evaluate the effectiveness of selective and community-wide house insecticide spraying in controlling triatomines in the subtropical areas of Loja Province, Ecuador. We designed a quasi-experimental pre–post-test without a control group to compare entomological levels before and after spraying. The baseline study was conducted in 2008. Second, third, and fourth visits were conducted in 2010, 2011, and 2012 in three rural communities. Out of the 130 domestic units (DU) visited, 41 domestic units were examined in each of the four visits. Selective and community-wide insecticide interventions included spraying with 5% deltamethrin at 25 mg/m2 active ingredient. At each visit, a questionnaire was administered to identify the characteristics of households, and DUs were searched for triatomine bugs. In addition, parasitological analysis was carried out in life triatomines. One and two rounds of selective insecticide spraying decreased the probability of infestation by 62% (pairwise odds ratios [POR] 0.38, 95% confidence interval [CI] 0.17–0.89, p = 0.024) and 51% (POR 0.49, 95% CI 0.23–1.01, p = 0.054), respectively. A similar effect was observed after one round of community-wide insecticide application in Chaquizhca and Guara (POR 0.55, CI 0.24–1.25, p = 0.155) and Bellamaria (POR 0.62, CI 0.22–1.79, p = 0.379); however, it was not statistically significant. Trypanosoma cruzi infection in triatomines (n = 483) increased overtime, from 2008 (42.9% and 8.5% for Rhodnius ecuadoriensis and Panstrongylus chinai, respectively) to 2012 (79.5% and 100%). Neither of the two spraying methodologies was effective for triatomine control in this area and our results point to a high likelihood of reinfestation after insecticide application. This underscores the importance of the implementation of physical barriers that prevent invasion and colonization of triatomines in households, such as home improvement initiatives, accompanied by a concerted effort to address the underlying socioeconomic issues that keep this population at risk of developing Chagas disease.
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Affiliation(s)
- Mario J Grijalva
- Infectious and Tropical Disease Institute, Department of Biomedical Sciences, Heritage College of Osteopathic Medicine, Ohio University, Athens, Ohio, USA.,Centro de Investigación para la Salud en América Latina, Escuela de Ciencias Biológicas, Facultad de Ciencias Exactas y Naturales, Pontificia Universidad Católica del Ecuador, Quito, Ecuador
| | - Anita G Villacís
- Centro de Investigación para la Salud en América Latina, Escuela de Ciencias Biológicas, Facultad de Ciencias Exactas y Naturales, Pontificia Universidad Católica del Ecuador, Quito, Ecuador
| | - Sofia Ocaña-Mayorga
- Centro de Investigación para la Salud en América Latina, Escuela de Ciencias Biológicas, Facultad de Ciencias Exactas y Naturales, Pontificia Universidad Católica del Ecuador, Quito, Ecuador
| | - César A Yumiseva
- Centro de Investigación para la Salud en América Latina, Escuela de Ciencias Biológicas, Facultad de Ciencias Exactas y Naturales, Pontificia Universidad Católica del Ecuador, Quito, Ecuador
| | - Claudia Nieto-Sanchez
- Infectious and Tropical Disease Institute, Department of Biomedical Sciences, Heritage College of Osteopathic Medicine, Ohio University, Athens, Ohio, USA.,Unit of Socio-Ecological Health Research, Department of Public Health, Institute of Tropical Medicine, Antwerp, Belgium
| | - Esteban G Baus
- Centro de Investigación para la Salud en América Latina, Escuela de Ciencias Biológicas, Facultad de Ciencias Exactas y Naturales, Pontificia Universidad Católica del Ecuador, Quito, Ecuador.,Facultad de Medicina, Pontificia Universidad Católica del Ecuador, Quito, Ecuador
| | - Ana L Moncayo
- Centro de Investigación para la Salud en América Latina, Escuela de Ciencias Biológicas, Facultad de Ciencias Exactas y Naturales, Pontificia Universidad Católica del Ecuador, Quito, Ecuador
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3
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Hernandez-Castro LE, Villacís AG, Jacobs A, Cheaib B, Day CC, Ocaña-Mayorga S, Yumiseva CA, Bacigalupo A, Andersson B, Matthews L, Landguth EL, Costales JA, Llewellyn MS, Grijalva MJ. Population genomics and geographic dispersal in Chagas disease vectors: Landscape drivers and evidence of possible adaptation to the domestic setting. PLoS Genet 2022; 18:e1010019. [PMID: 35120121 PMCID: PMC8849464 DOI: 10.1371/journal.pgen.1010019] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 02/16/2022] [Accepted: 01/06/2022] [Indexed: 12/19/2022] Open
Abstract
Accurate prediction of vectors dispersal, as well as identification of adaptations that allow blood-feeding vectors to thrive in built environments, are a basis for effective disease control. Here we adopted a landscape genomics approach to assay gene flow, possible local adaptation, and drivers of population structure in Rhodnius ecuadoriensis, an important vector of Chagas disease. We used a reduced-representation sequencing technique (2b-RADseq) to obtain 2,552 SNP markers across 272 R. ecuadoriensis samples from 25 collection sites in southern Ecuador. Evidence of high and directional gene flow between seven wild and domestic population pairs across our study site indicates insecticide-based control will be hindered by repeated re-infestation of houses from the forest. Preliminary genome scans across multiple population pairs revealed shared outlier loci potentially consistent with local adaptation to the domestic setting, which we mapped to genes involved with embryogenesis and saliva production. Landscape genomic models showed elevation is a key barrier to R. ecuadoriensis dispersal. Together our results shed early light on the genomic adaptation in triatomine vectors and facilitate vector control by predicting that spatially-targeted, proactive interventions would be more efficacious than current, reactive approaches. Re-infestation of recently insecticide-treated houses by wild/secondary triatomine, their potential adaptation to this new environment and capabilities to geographically disperse across multiple human communities jeopardise sustainable Chagas disease control. This is the first study in Chagas disease vectors that identifies genomic regions possibly linked to adaptations to the built environment and describes landscape drivers for accurate prediction of geographic dispersal. We sampled multiple domestic and wild Rhodnius ecuadoriensis population pairs across a mountainous terrain in southern Ecuador. We evidenced that triatomine movement from forest to built enviroments does occur at a high rate. In these highly connected population pairs we detected loci possibly linked to local adaptation among the genomic makers we evaluated and in doing so we pave the way for future triatomine genomic research. We highlighted that current haphazardous vector control in the zone will be hindered by reinfestation of triatomines from the forest. Instead, we recommend frequent and spatially-targeted vector control and provided a landacape genomic model that identifies highly connected and isolated triatomine populations to facilitate efficient vector control.
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Affiliation(s)
- Luis E. Hernandez-Castro
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, United Kingdom
- The Epidemiology, Economics and Risk Assessment Group, The Roslin Institute, Easter Bush Campus, The University of Edinburgh, Midlothian, United Kingdom
- * E-mail: (LEH-C); (MSL)
| | - Anita G. Villacís
- Centro de Investigación para la Salud en América Latina, Facultad de Ciencias Exactas y Naturales, Pontificia Universidad Católica del Ecuador, Quito, Ecuador
| | - Arne Jacobs
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, United Kingdom
- Department of Natural Resources and the Environment, Cornell University, Ithaca, New York, United States of America
| | - Bachar Cheaib
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, United Kingdom
| | - Casey C. Day
- Computational Ecology Lab, School of Public and Community Health Sciences, University of Montana, Missoula, Montana, United States of America
| | - Sofía Ocaña-Mayorga
- Centro de Investigación para la Salud en América Latina, Facultad de Ciencias Exactas y Naturales, Pontificia Universidad Católica del Ecuador, Quito, Ecuador
| | - Cesar A. Yumiseva
- Centro de Investigación para la Salud en América Latina, Facultad de Ciencias Exactas y Naturales, Pontificia Universidad Católica del Ecuador, Quito, Ecuador
| | - Antonella Bacigalupo
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, United Kingdom
| | - Björn Andersson
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Louise Matthews
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, United Kingdom
| | - Erin L. Landguth
- Computational Ecology Lab, School of Public and Community Health Sciences, University of Montana, Missoula, Montana, United States of America
- Center for Population Health Research, School of Public and Community Health Sciences, University of Montana, Missoula, Montana, United States of America
| | - Jaime A. Costales
- Centro de Investigación para la Salud en América Latina, Facultad de Ciencias Exactas y Naturales, Pontificia Universidad Católica del Ecuador, Quito, Ecuador
| | - Martin S. Llewellyn
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, United Kingdom
- * E-mail: (LEH-C); (MSL)
| | - Mario J. Grijalva
- Centro de Investigación para la Salud en América Latina, Facultad de Ciencias Exactas y Naturales, Pontificia Universidad Católica del Ecuador, Quito, Ecuador
- Infectious and Tropical Disease Institute, Department of Biomedical Sciences, Heritage College of Osteopathic Medicine, Ohio University, Athens, Ohio, United States of America
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Abad-Franch F, Monteiro FA, Pavan MG, Patterson JS, Bargues MD, Zuriaga MÁ, Aguilar M, Beard CB, Mas-Coma S, Miles MA. Under pressure: phenotypic divergence and convergence associated with microhabitat adaptations in Triatominae. Parasit Vectors 2021; 14:195. [PMID: 33832518 PMCID: PMC8034103 DOI: 10.1186/s13071-021-04647-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Accepted: 02/16/2021] [Indexed: 12/20/2022] Open
Abstract
Background Triatomine bugs, the vectors of Chagas disease, associate with vertebrate hosts in highly diverse ecotopes. It has been proposed that occupation of new microhabitats may trigger selection for distinct phenotypic variants in these blood-sucking bugs. Although understanding phenotypic variation is key to the study of adaptive evolution and central to phenotype-based taxonomy, the drivers of phenotypic change and diversity in triatomines remain poorly understood. Methods/results We combined a detailed phenotypic appraisal (including morphology and morphometrics) with mitochondrial cytb and nuclear ITS2 DNA sequence analyses to study Rhodnius ecuadoriensis populations from across the species’ range. We found three major, naked-eye phenotypic variants. Southern-Andean bugs primarily from vertebrate-nest microhabitats (Ecuador/Peru) are typical, light-colored, small bugs with short heads/wings. Northern-Andean bugs from wet-forest palms (Ecuador) are dark, large bugs with long heads/wings. Finally, northern-lowland bugs primarily from dry-forest palms (Ecuador) are light-colored and medium-sized. Wing and (size-free) head shapes are similar across Ecuadorian populations, regardless of habitat or phenotype, but distinct in Peruvian bugs. Bayesian phylogenetic and multispecies-coalescent DNA sequence analyses strongly suggest that Ecuadorian and Peruvian populations are two independently evolving lineages, with little within-lineage phylogeographic structuring or differentiation. Conclusions We report sharp naked-eye phenotypic divergence of genetically similar Ecuadorian R. ecuadoriensis (nest-dwelling southern-Andean vs palm-dwelling northern bugs; and palm-dwelling Andean vs lowland), and sharp naked-eye phenotypic similarity of typical, yet genetically distinct, southern-Andean bugs primarily from vertebrate-nest (but not palm) microhabitats. This remarkable phenotypic diversity within a single nominal species likely stems from microhabitat adaptations possibly involving predator-driven selection (yielding substrate-matching camouflage coloration) and a shift from palm-crown to vertebrate-nest microhabitats (yielding smaller bodies and shorter and stouter heads). These findings shed new light on the origins of phenotypic diversity in triatomines, warn against excess reliance on phenotype-based triatomine-bug taxonomy, and confirm the Triatominae as an informative model system for the study of phenotypic change under ecological pressure. ![]()
Supplementary Information The online version contains supplementary material available at 10.1186/s13071-021-04647-z.
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Affiliation(s)
- Fernando Abad-Franch
- Núcleo de Medicina Tropical, Faculdade de Medicina, Universidade de Brasília, Brasília, Brazil. .,Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK.
| | - Fernando A Monteiro
- Laboratório de Epidemiologia e Sistemática Molecular, Instituto Oswaldo Cruz-Fiocruz, Rio de Janeiro, Brazil. .,Division of Vector-Borne Diseases, Centers for Disease Control and Prevention, Fort Collins, USA.
| | - Márcio G Pavan
- Laboratório de Mosquitos Transmissores de Hematozoários, Instituto Oswaldo Cruz-Fiocruz, Rio de Janeiro, Brazil
| | - James S Patterson
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - M Dolores Bargues
- Departamento de Parasitología, Facultad de Farmacia, Universidad de Valencia, Valencia, Spain
| | - M Ángeles Zuriaga
- Departamento de Parasitología, Facultad de Farmacia, Universidad de Valencia, Valencia, Spain
| | - Marcelo Aguilar
- Facultad de Ciencias Médicas, Universidad Central del Ecuador, Quito, Ecuador.,Instituto Juan César García, Quito, Ecuador
| | - Charles B Beard
- Division of Vector-Borne Diseases, Centers for Disease Control and Prevention, Fort Collins, USA
| | - Santiago Mas-Coma
- Departamento de Parasitología, Facultad de Farmacia, Universidad de Valencia, Valencia, Spain
| | - Michael A Miles
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
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5
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Kieran TJ, Bayona-Vásquez NJ, Varian CP, Saldaña A, Samudio F, Calzada JE, Gottdenker NL, Glenn TC. Population genetics of two chromatic morphs of the Chagas disease vector Rhodnius pallescens Barber, 1932 in Panamá. INFECTION GENETICS AND EVOLUTION 2020; 84:104369. [PMID: 32442632 DOI: 10.1016/j.meegid.2020.104369] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Revised: 05/13/2020] [Accepted: 05/15/2020] [Indexed: 12/29/2022]
Abstract
Rhodnius pallescens is the principal vector of Chagas disease in Panama. Recently a dark chromatic morph has been discovered in the highlands of Veraguas Province. Limited genetic studies have been conducted with regards to the population structure and dispersal potential of Triatominae vectors, particularly in R. pallescens. Next generation sequencing methods such as RADseq and complete mitochondrial DNA (mtDNA) genome sequencing have great potential for examining vector biology across space and time. Here we utilize a RADseq method (3RAD), along with complete mtDNA sequencing, to examine the population structure of the two chromatic morpho types of R. pallescens in Panama. We sequenced 105 R. pallescens samples from five localities in Panama. We generated a 2216 SNP dataset and 6 complete mtDNA genomes. RADseq showed significant differentiation among the five localities (FCT = 0.695; P = .004), but most of this was between localities with the dark vs. light chromatic morphs (Veraguas vs. Panama Oeste). The mtDNA genomes showed a 97-98% similarity between dark and light chromatic morphs across all genes and a 502 bp insert in light morphs. Thus, both the RADseq and mtDNA data showed highly differentiated clades with essentially no gene flow between the dark and light chromatic morphs from Veraguas and central Panama respectively. We discuss the growing evidence showing clear distinctions between these two morpho types with the possibility that these are separate species, an area of research that requires further investigation. Finally, we discuss the cost-effectiveness of 3RAD which is a third of the cost compared to other RADseq methods used recently in Chagas disease vector research.
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Affiliation(s)
- Troy J Kieran
- Department of Environmental Health Science, College of Public Health, University of Georgia, Athens, GA, USA
| | - Natalia J Bayona-Vásquez
- Department of Environmental Health Science, College of Public Health, University of Georgia, Athens, GA, USA; Institute of Bioinformatics, The University of Georgia, Athens, GA, USA
| | - Christina P Varian
- Center for the Ecology of Infectious Diseases, The University of Georgia, Athens, GA, USA; Department of Veterinary Pathology, College of Veterinary Medicine, The University of Georgia, Athens, GA, USA
| | - Azael Saldaña
- Instituto Conmemorativo Gorgas de Estudios de la Salud (ICGES), Panama City, Panama; Centro de Investigación y Diagnóstico de Enfermedades Parasitarias (CIDEP), Facultad de Medicina, Universidad de Panamá, Panama
| | - Franklyn Samudio
- Instituto Conmemorativo Gorgas de Estudios de la Salud (ICGES), Panama City, Panama
| | - Jose E Calzada
- Instituto Conmemorativo Gorgas de Estudios de la Salud (ICGES), Panama City, Panama
| | - Nicole L Gottdenker
- Center for the Ecology of Infectious Diseases, The University of Georgia, Athens, GA, USA; Department of Veterinary Pathology, College of Veterinary Medicine, The University of Georgia, Athens, GA, USA; Odum School of Ecology, The University of Georgia, Athens, GA, USA
| | - Travis C Glenn
- Department of Environmental Health Science, College of Public Health, University of Georgia, Athens, GA, USA; Institute of Bioinformatics, The University of Georgia, Athens, GA, USA; Center for the Ecology of Infectious Diseases, The University of Georgia, Athens, GA, USA.
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Barbanti A, Torrado H, Macpherson E, Bargelloni L, Franch R, Carreras C, Pascual M. Helping decision making for reliable and cost-effective 2b-RAD sequencing and genotyping analyses in non-model species. Mol Ecol Resour 2020; 20. [PMID: 32061018 DOI: 10.1111/1755-0998.13144] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 02/04/2020] [Accepted: 02/10/2020] [Indexed: 12/18/2022]
Abstract
High-throughput sequencing has revolutionized population and conservation genetics. RAD sequencing methods, such as 2b-RAD, can be used on species lacking a reference genome. However, transferring protocols across taxa can potentially lead to poor results. We tested two different IIB enzymes (AlfI and CspCI) on two species with different genome sizes (the loggerhead turtle Caretta caretta and the sharpsnout seabream Diplodus puntazzo) to build a set of guidelines to improve 2b-RAD protocols on non-model organisms while optimising costs. Good results were obtained even with degraded samples, showing the value of 2b-RAD in studies with poor DNA quality. However, library quality was found to be a critical parameter on the number of reads and loci obtained for genotyping. Resampling analyses with different number of reads per individual showed a trade-off between number of loci and number of reads per sample. The resulting accumulation curves can be used as a tool to calculate the number of sequences per individual needed to reach a mean depth ≥20 reads to acquire good genotyping results. Finally, we demonstrated that selective-base ligation does not affect genomic differentiation between individuals, indicating that this technique can be used in species with large genome sizes to adjust the number of loci to the study scope, to reduce sequencing costs and to maintain suitable sequencing depth for a reliable genotyping without compromising the results. Here, we provide a set of guidelines to improve 2b-RAD protocols on non-model organisms with different genome sizes, helping decision-making for a reliable and cost-effective genotyping.
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Affiliation(s)
- Anna Barbanti
- Department of Genetics, Microbiology and Statistics and IRBio, University of Barcelona, Barcelona, Spain
| | - Hector Torrado
- Department of Genetics, Microbiology and Statistics and IRBio, University of Barcelona, Barcelona, Spain.,Center for Advanced Studies of Blanes (CEAB-CSIC), Blanes, Girona, Spain
| | - Enrique Macpherson
- Center for Advanced Studies of Blanes (CEAB-CSIC), Blanes, Girona, Spain
| | - Luca Bargelloni
- Department of Comparative Biomedicine and Food Science, University of Padova, Legnaro, Italy
| | - Rafaella Franch
- Department of Comparative Biomedicine and Food Science, University of Padova, Legnaro, Italy
| | - Carlos Carreras
- Department of Genetics, Microbiology and Statistics and IRBio, University of Barcelona, Barcelona, Spain
| | - Marta Pascual
- Department of Genetics, Microbiology and Statistics and IRBio, University of Barcelona, Barcelona, Spain
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7
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Khan S, Zhao X, Hou Y, Yuan C, Li Y, Luo X, Liu J, Feng X. Analysis of genome-wide SNPs based on 2b-RAD sequencing of pooled samples reveals signature of selection in different populations of Haemonchus contortus. J Biosci 2019; 44:97. [PMID: 31502575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The parasitic nematode Haemonchus contortus is one of the world's most important parasites of small ruminants that causes significant economic losses to the livestock sector. The population structure and selection in its various strains are poorly understood. No study so far compared its different populations using genome-wide data. Here, we focused on different geographic populations of H. contours from China (Tibet, TB; Hubei, HB; Inner Mongolia, IM; Sichuan, SC), UK and Australia (AS), using genome-wide population-genomic approaches, to explore genetic diversity, population structure and selection. We first performed next-generation high-throughput 2b RAD pool sequencing using Illumina technology, and identified single-nucleotide polymorphisms (SNPs) in all the strains. We identified 75,187 SNPs for TB, 82,271 for HB, 82,420 for IM, 79,803 for SC, 83,504 for AS and 78,747 for UK strain. The SNPs revealed low-nucleotide diversity (pi= 0.0092-0.0133) within each strain, and a significant differentiation level (average Fst = 0.34264) among them. Chinese populations TB and SC, along with the UK strain, were more divergent populations. Chinese populations IM and HB showed affinities to the Australian strain. We then analysed signature of selection and detected 44 (UK) and 03 (AS) private selective sweeps containing 49 and 05 genes, respectively. Finally, we performed the functional annotation of selective sweeps and proposed biological significance to signature of selection. Our data suggest that 2b-RAD pool sequencing can be used to assess the signature of selection in H. contortus.
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Affiliation(s)
- Sawar Khan
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Key Laboratory of Animal Parasitology, Ministry of Agriculture of China, Shanghai 200241, People's Republic of China
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8
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Khan S, Zhao X, Hou Y, Yuan C, Li Y, Luo X, Liu J, Feng X. Analysis of genome-wide SNPs based on 2b-RAD sequencing of pooled samples reveals signature of selection in different populations of Haemonchus contortus. J Biosci 2019. [DOI: 10.1007/s12038-019-9917-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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