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Sokolova O, Moročko-Bičevska I, Lācis G. Genetic Diversity of Venturia inaequalis in Latvia Revealed by Microsatellite Markers. Pathogens 2022; 11:pathogens11101165. [PMID: 36297222 PMCID: PMC9611756 DOI: 10.3390/pathogens11101165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 09/30/2022] [Accepted: 10/03/2022] [Indexed: 11/22/2022] Open
Abstract
Apple scab caused by the ascomycete Venturia inaequalis is an economically significant disease worldwide. The annual sexual reproduction of V. inaequalis leads to high variation, changes in the population's genetic structure and adaptations to the changing environment, including overcoming the host's resistance. The objective of this study is to characterise and assess the genetic diversity of V. inaequalis populations in two main apple-growing regions in Latvia. In total, 143 V. inaequalis isolates were collected from Latvia, six reference strains with known virulence were obtained from other countries, and all strains were genotyped by 12 SSR markers. The SSR markers were highly variable and informative, identifying 158 alleles that ranged from two to 29 per locus. The Bayesian clustering identified three genetic lineages among the Latvian isolates that did not correlate to the geographic origin, host genotype, organ (leaves or fruits) from which the pathogen was isolated, time of collection, and type of isolation (single conidium or ascospore). The possible relatedness to virulence was detected when reference strains with known virulence were included in the analysis. Our findings correspond with previous studies demonstrating that V. inaequalis in Europe has a high genetic diversity within populations, but low diversity among the populations.
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Affiliation(s)
- Olga Sokolova
- Institute of Horticulture, Latvia University of Life Sciences and Technologies, LV-3701 Dobele, Latvia
- Institute of Soil and Plant Sciences, Latvia University of Life Sciences and Technologies, Lielā str. 2, LV-3001 Jelgava, Latvia
- Correspondence:
| | - Inga Moročko-Bičevska
- Institute of Horticulture, Latvia University of Life Sciences and Technologies, LV-3701 Dobele, Latvia
| | - Gunārs Lācis
- Institute of Horticulture, Latvia University of Life Sciences and Technologies, LV-3701 Dobele, Latvia
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Genetic diversity of Venturia inaequalis isolates (Apple scab) in China and U.K. determined by SSR markers. PLoS One 2021; 16:e0252865. [PMID: 34111167 PMCID: PMC8191898 DOI: 10.1371/journal.pone.0252865] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2020] [Accepted: 05/24/2021] [Indexed: 11/21/2022] Open
Abstract
Apple scab caused by Venturia inaequalis is a serious disease of cultivated apple worldwide. In this study, we collected 132 V. inaequalis isolates from Shaanxi, Gansu, Xinjiang, and the U.K. and analyzed their genetic diversity by using 13 microsatellite markers. Cluster analysis based on population structure and genetic distances suggested high similarity among the four regions. Population differentiation values ranged from 0.044 to 0.155, indicating there is a high level of kinship among the four regions. All isolates could be divided into 5 lineages with a 0.76 similarity coefficient. Among the four regions, Shaanxi had only one lineage, Group II; Gansu had four lineages, Group I, Group II, Group IV, and Group V; Xinjiang had all five lineages, Group I, Group II, Group III, Group IV, and Group V; and the U.K. had three lineages, Group I, Group II and Group IV. High molecular variance was detected for populations in the four regions, with 91% of the variance occurring within the populations and 9% among the populations. Structure analysis there are three common ancestors of these four regions. The results of the present study shed light on the genetic diversity of V. inaequalis in Shaanxi, Gansu and Xinjiang, which will lead to the development of more effective management strategies and new resistant apple cultivars through molecular marker-assisted selection.
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Kariyawasam GK, Wyatt N, Shi G, Liu S, Yan C, Ma Y, Zhong S, Rasmussen JB, Moolhuijzen P, Moffat CS, Friesen TL, Liu Z. A genome-wide genetic linkage map and reference quality genome sequence for a new race in the wheat pathogen Pyrenophora tritici-repentis. Fungal Genet Biol 2021; 152:103571. [PMID: 34015431 DOI: 10.1016/j.fgb.2021.103571] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 02/23/2021] [Accepted: 03/01/2021] [Indexed: 10/21/2022]
Abstract
Pyrenophora tritici-repentis is an ascomycete fungus that causes tan spot of wheat. The disease has a worldwide distribution and can cause significant yield and quality losses in wheat production. The fungal pathogen is homothallic in nature, which means it can undergo sexual reproduction by selfing to produce pseudothecia on wheat stubble for seasonal survival. Since homothallism precludes the development of bi-parental fungal populations, no genetic linkage map has been developed for P. tritici-repentis for mapping and map-based cloning of fungal virulence genes. In this work, we created two heterothallic strains by deleting one of the mating type genes in each of two parental isolates 86-124 (race 2) and AR CrossB10 (a new race) and developed a bi-parental fungal population between them. The draft genome sequences of the two parental isolates were aligned to the Pt-1C-BFP reference sequence to mine single nucleotide polymorphisms (SNPs). A total of 225 SNP markers were developed for genotyping the entire population. Additionally, 75 simple sequence repeat, and two gene markers were also developed and used in the genotyping. The resulting linkage map consisted of 13 linkage groups spanning 5,075.83 cM in genetic distance. Because the parental isolate AR CrossB10 is a new race and produces Ptr ToxC, it was sequenced using long-read sequencing platforms and de novo assembled into contigs. The majority of the contigs were further anchored into chromosomes with the aid of the linkage maps. The whole genome comparison of AR CrossB10 to the reference genome of M4 revealed a few chromosomal rearrangements. The genetic linkage map and the new AR CrossB10 genome sequence are valuable tools for gene cloning in P. tritici-repentis.
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Affiliation(s)
- Gayan K Kariyawasam
- Department of Plant Pathology, North Dakota State University, Fargo, ND 58108, USA
| | - Nathan Wyatt
- USDA-ARS Cereal Crops Research Unit, Edward T. Schafer Agricultural Research Center, Fargo, ND 58102, USA
| | - Gongjun Shi
- Department of Plant Pathology, North Dakota State University, Fargo, ND 58108, USA
| | - Sanzhen Liu
- Department of Plant Pathology, Kansas State University, Manhattan, KS 66506, USA
| | - Changhui Yan
- Department of Computer Science, North Dakota State University, Fargo, ND 58108, USA
| | - Yongchao Ma
- Department of Computer Science, North Dakota State University, Fargo, ND 58108, USA
| | - Shaobin Zhong
- Department of Plant Pathology, North Dakota State University, Fargo, ND 58108, USA
| | - Jack B Rasmussen
- Department of Plant Pathology, North Dakota State University, Fargo, ND 58108, USA
| | - Paula Moolhuijzen
- Center for Crop Disease and Management, Department of Environment and Agriculture, Curtin University, Bentley, Western Australia, Australia
| | - Caroline S Moffat
- Center for Crop Disease and Management, Department of Environment and Agriculture, Curtin University, Bentley, Western Australia, Australia
| | - Timothy L Friesen
- Department of Plant Pathology, North Dakota State University, Fargo, ND 58108, USA; USDA-ARS Cereal Crops Research Unit, Edward T. Schafer Agricultural Research Center, Fargo, ND 58102, USA
| | - Zhaohui Liu
- Department of Plant Pathology, North Dakota State University, Fargo, ND 58108, USA.
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Mining and characterization of microsatellites from a genome of Venturia carpophila. Mycol Prog 2018. [DOI: 10.1007/s11557-018-1401-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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González-Domínguez E, Armengol J, Rossi V. Biology and Epidemiology of Venturia Species Affecting Fruit Crops: A Review. FRONTIERS IN PLANT SCIENCE 2017; 8:1496. [PMID: 28974954 PMCID: PMC5610699 DOI: 10.3389/fpls.2017.01496] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Accepted: 08/14/2017] [Indexed: 05/19/2023]
Abstract
The fungal genus Venturia Sacc. (anamorph Fusicladium Bonord.) includes plant pathogens that cause substantial economic damage to fruit crops worldwide. Although Venturia inaequalis is considered a model species in plant pathology, other Venturia spp. also cause scab on other fruit trees. Relative to the substantial research that has been conducted on V. inaequalis and apple scab, little research has been conducted on Venturia spp. affecting other fruit trees. In this review, the main characteristics of plant-pathogenic species of Venturia are discussed with special attention to V. inaequalis affecting apple, V. pyrina affecting European pear, V. nashicola affecting Asian pear, V. carpophila affecting peach and almond, Fusicladium oleagineum affecting olive, F. effusum affecting pecan, and F. eriobotryae affecting loquat. This review has two main objectives: (i) to identify the main gaps in our knowledge regarding the biology and epidemiology of Venturia spp. affecting fruit trees; and (ii) to identify similarities and differences among these Venturia spp. in order to improve disease management. A thorough review has been conducted of studies regarding the phylogenetic relationships, host ranges, biologies, and epidemiologies of Venturia spp. A multiple correspondence analysis (CA) has also been performed on the main epidemiological components of these Venturia spp. CA separated the Venturia spp. into two main groups, according to their epidemiological behavior: the first group included V. inaequalis, V. pyrina, V. nashicola, and V. carpophila, the second F. oleagineum and F. eriobotryae, with F. effusum having an intermediate position. This review shows that Venturia spp. affecting fruit trees are highly host-specific, and that important gaps in understanding the life cycle exist for some species, including V. pyrina; gaps include pseudothecia formation, ascospore and conidia germination, and mycelial growth. Considering the epidemiological information reviewed, this paper shows that the use of Mills tables to predict infection periods should be avoided for Venturia spp. other than V. inaequalis.
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Affiliation(s)
| | - Josep Armengol
- Instituto Agroforestal Mediterráneo, Universitat Politècnica de ValènciaValencia, Spain
| | - Vittorio Rossi
- Department of Sustainable Crop Protection, Università Cattolica del Sacro CuorePiacenza, Italy
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Bock CH, Grauke LJ, Conner P, Burrell SL, Hotchkiss MW, Boykin D, Wood BW. Scab Susceptibility of a Provenance Collection of Pecan in Three Different Seasons in the Southeastern United States. PLANT DISEASE 2016; 100:1937-1945. [PMID: 30682991 DOI: 10.1094/pdis-12-15-1398-re] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Pecan scab (caused by Fusicladium effusum) is the most economically destructive disease of pecan in the Southeast United States. Wet, humid conditions typical of the Southeast are known to provide conditions conducive to epidemics. A provenance collection of pecan from 19 locations representing the native range of the tree is located in Byron, Georgia, and was assessed for pecan scab severity in 1998, 2013, and 2014. There were significant differences among the 19 provenances (F = 5.6 to 62.5, P < 0.0001). Provenances from wetter locations (generally north of Texas) had the greatest proportion of scab resistant trees, while provenances from the drier southern areas (Texas and Mexico) tended to be the most susceptible to scab. The association with rainfall was borne out by correlation analysis (r = -0.625 to -0.823 [P < 0.0001 to 0.004]). Other factors consistently associated with scab severity included leaflet tilt and droop angle (r = -0.533 to -0.883 [P < 0.0001 to 0.02]). Multiple regression analysis demonstrated that leaflet droop angle was a particularly good predictor of provenance susceptibility. Leaflet characteristics vary with provenance location, and whether there is a direct relationship between scab severity and leaflet characteristics is not established. Estimates of heritability were not entirely consistent among years, but different methods were used to assess scab severity in 1998 (a 1 to 5 category scale) compared with 2013 and 2014 (the percent ratio scale). Despite using different methods, there was generally good agreement among years in regard to severity of disease on individual trees. In conclusion, trees from more northern populations (in areas with greater annual rainfall) are most likely to provide valuable and diverse sources of resistance to scab. The provenance collection contains a range of scab-resistant genotypes from diverse locations that can contribute to genetic improvement regarding scab resistance.
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Affiliation(s)
- Clive H Bock
- United States Department of Agriculture - Agriculture Research Service, Southeastern Fruit and Tree Nut Research Lab (USDA-ARS, SEFTNRL), Byron, GA 31008
| | - Larry J Grauke
- USDA-ARS Pecan Breeding and Genetics, Somerville, TX 77845
| | - Patrick Conner
- Horticulture Department, University of Georgia, Tifton, GA 31794
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Thakur K, Chawla V, Bhatti S, Swarnkar MK, Kaur J, Shankar R, Jha G. De novo transcriptome sequencing and analysis for Venturia inaequalis, the devastating apple scab pathogen. PLoS One 2013; 8:e53937. [PMID: 23349770 PMCID: PMC3547962 DOI: 10.1371/journal.pone.0053937] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2012] [Accepted: 12/04/2012] [Indexed: 11/28/2022] Open
Abstract
Venturia inaequalis is the causal agent of apple scab, one of the most devastating diseases of apple. Due to several distinct features, it has emerged as a model fungal pathogen to study various aspects of hemibiotrophic plant pathogen interactions. The present study reports de novo assembling, annotation and characterization of the transcriptome of V. inaequalis. Venturia transcripts expressed during its growth on laboratory medium and that expressed during its biotrophic stage of infection on apple were sequenced using Illumina RNAseq technology. A total of 94,350,055 reads (50 bp read length) specific to Venturia were obtained after filtering. The reads were assembled into 62,061 contigs representing 24,571 unique genes. GO analysis suggested prevalence of genes associated with biological process categories like metabolism, transport and response to stimulus. Genes associated with molecular function like binding, catalytic activities and transferase activities were found in majority. EC and KEGG pathway analyses suggested prevalence of genes encoding kinases, proteases, glycoside hydrolases, cutinases, cytochrome P450 and transcription factors. The study has identified several putative pathogenicity determinants and candidate effectors in V. inaequalis. A large number of transcripts encoding membrane transporters were identified and comparative analysis revealed that the number of transporters encoded by Venturia is significantly more as compared to that encoded by several other important plant fungal pathogens. Phylogenomics analysis indicated that V. inaequalis is closely related to Pyrenophora tritici-repentis (the causal organism of tan spot of wheat). In conclusion, the findings from this study provide a better understanding of the biology of the apple scab pathogen and have identified candidate genes/functions required for its pathogenesis. This work lays the foundation for facilitating further research towards understanding this host-pathogen interaction.
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Affiliation(s)
- Karnika Thakur
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology (Council of Scientific and Industrial Research), Palampur, Himachal Pradesh, India
- Department of Biotechnology, Panjab University, Chandigarh, India
| | - Vandna Chawla
- Studio of Computational Biology & Bioinformatics, CSIR-Institute of Himalayan Bioresource Technology (Council of Scientific and Industrial Research), Palampur, Himachal Pradesh, India
| | - Shammi Bhatti
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology (Council of Scientific and Industrial Research), Palampur, Himachal Pradesh, India
| | - Mohit Kumar Swarnkar
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology (Council of Scientific and Industrial Research), Palampur, Himachal Pradesh, India
| | - Jagdeep Kaur
- Department of Biotechnology, Panjab University, Chandigarh, India
| | - Ravi Shankar
- Studio of Computational Biology & Bioinformatics, CSIR-Institute of Himalayan Bioresource Technology (Council of Scientific and Industrial Research), Palampur, Himachal Pradesh, India
| | - Gopaljee Jha
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology (Council of Scientific and Industrial Research), Palampur, Himachal Pradesh, India
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Foulongne-Oriol M. Genetic linkage mapping in fungi: current state, applications, and future trends. Appl Microbiol Biotechnol 2012; 95:891-904. [PMID: 22743715 DOI: 10.1007/s00253-012-4228-4] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2012] [Revised: 06/04/2012] [Accepted: 06/05/2012] [Indexed: 10/28/2022]
Abstract
Genetic mapping is a basic tool for eukaryotic genomic research. Linkage maps provide insights into genome organization and can be used for genetic studies of traits of interest. A genetic linkage map is a suitable support for the anchoring of whole genome sequences. It allows the localization of genes of interest or quantitative trait loci (QTL) and map-based cloning. While genetic mapping has been extensively used in plant or animal models, this discipline is more recent in fungi. The present article reviews the current status of genetic linkage map research in fungal species. The process of linkage mapping is detailed, from the development of mapping populations to the construction of the final linkage map, and illustrated based on practical examples. The range of specific applications in fungi is browsed, such as the mapping of virulence genes in pathogenic species or the mapping of agronomically relevant QTL in cultivated edible mushrooms. Future prospects are finally discussed in the context of the most recent advances in molecular techniques and the release of numerous fungal genome sequences.
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Bus VG, Rikkerink EH, Caffier V, Durel CE, Plummer KM. Revision of the Nomenclature of the Differential Host-Pathogen Interactions of Venturia inaequalis and Malus. ANNUAL REVIEW OF PHYTOPATHOLOGY 2011; 49:391-413. [PMID: 0 DOI: 10.1146/annurev-phyto-072910-095339] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
The apple scab (Venturia inaequalis–Malus) pathosystem was one of the first systems for which Flor's concept of gene-for-gene (GfG) relationships between the host plant and the pathogen was demonstrated. There is a rich resource of host resistance genes present in Malus germplasm that could potentially be marshalled to confer durable resistance against this most important apple disease. A comprehensive understanding of the host-pathogen interactions occurring in this pathosystem is a prerequisite for effectively manipulating these host resistance factors. An accurate means of identification of specific resistance and consistent use of gene nomenclature is critical for this process. A set of universally available, differentially resistant hosts is described, which will be followed by a set of defined pathogen races at a later stage. We review pertinent aspects of the history of apple scab research, describe the current status and future directions of this research, and resolve some outstanding issues.
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Affiliation(s)
- Vincent G.M. Bus
- The Plant and Food Research Institute of New Zealand, Private Bag 1401, Havelock North 4157, New Zealand
| | - Erik H.A. Rikkerink
- The Plant and Food Research Institute of New Zealand, Private Bag 92169, Auckland 1142, New Zealand
| | - Valérie Caffier
- INRA, UMR77 Pathologie Végétale – PaVé, INRA/ACO/UA, IFR QUASAV, BP 60057, F-49071 Beaucouzé, France
| | - Charles-Eric Durel
- INRA, UMR 1259 Genetics and Horticulture – GenHort, INRA/ACO/UA, IFR QUASAV, BP 60057, F-49071 Beaucouzé, France
| | - Kim M. Plummer
- La Trobe University, Department of Botany, Bundoora, Vic. 3086, Australia
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Genetic mapping of 14 avirulence genes in an EU-B04×1639 progeny of Venturia inaequalis. Fungal Genet Biol 2011; 48:166-76. [DOI: 10.1016/j.fgb.2010.09.001] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2010] [Revised: 09/03/2010] [Accepted: 09/05/2010] [Indexed: 02/01/2023]
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Bowen JK, Mesarich CH, Bus VGM, Beresford RM, Plummer KM, Templeton MD. Venturia inaequalis: the causal agent of apple scab. MOLECULAR PLANT PATHOLOGY 2011; 12:105-22. [PMID: 21199562 PMCID: PMC6640350 DOI: 10.1111/j.1364-3703.2010.00656.x] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
UNLABELLED The fungus Venturia inaequalis infects members of the Maloideae, and causes the disease apple scab, the most important disease of apple worldwide. The early elucidation of the gene-for-gene relationship between V. inaequalis and its host Malus has intrigued plant pathologists ever since, with the identification of 17 resistance (R)-avirulence (Avr) gene pairings. The Avr gene products are presumably a subset of the total effector arsenal of V. inaequalis (predominantly proteins secreted in planta assumed to facilitate infection). The supposition that effectors from V. inaequalis act as suppressors of plant defence is supported by the ability of the pathogen to penetrate the cuticle and differentiate into large pseudoparenchymatous structures, termed stromata, in the subcuticular space, without the initiation of an effective plant defence response. If effectors can be identified that are essential for pathogenicity, the corresponding R genes will be durable and would add significant value to breeding programmes. An R gene cluster in Malus has been cloned, but no V. inaequalis effectors have been characterized at the molecular level. However, the identification of effectors is likely to be facilitated by the resolution of the whole genome sequence of V. inaequalis. TAXONOMY Teleomorph: Venturia inaequalis Cooke (Wint.); Kingdom Fungi; Phylum Ascomycota; Subphylum Euascomycota; Class Dothideomycetes; Family Venturiaceae; genus Venturia; species inaequalis. Anamorph: Fusicladium pomi (Fr.) Lind or Spilocaea pomi (Fr.). LIFE CYCLE: V. inaequalis is a hemibiotroph and overwinters as pseudothecia (sexual fruiting bodies) following a phase of saprobic growth in fallen leaf tissues. The primary inoculum consists of ascospores, which germinate and penetrate the cuticle. Stromata are formed above the epidermal cells but do not penetrate them. Cell wall-degrading enzymes are only produced late in the infection cycle, raising the as yet unanswered question as to how V. inaequalis gains nutrients from the host. Conidia (secondary inoculum) arise from the upper surface of the stromata, and are produced throughout the growing season, initiating multiple rounds of infection. VENTURIA INAEQUALIS AS A MODEL PATHOGEN OF A WOODY HOST: V. inaequalis can be cultured and is amenable to crossing in vitro, enabling map-based cloning strategies. It can be transformed readily, and functional analyses can be conducted by gene silencing. Expressed sequence tag collections are available to aid in gene identification. These will be complemented by the whole genome sequence, which, in turn, will contribute to the comparative analysis of different races of V. inaequalis and plant pathogens within the Dothideomycetes.
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Affiliation(s)
- Joanna K Bowen
- The New Zealand Institute for Plant & Food Research Limited, Mt. Albert Research Centre, Private Bag 92 169, Auckland 1142, New Zealand.
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Celton JM, Christoffels A, Sargent DJ, Xu X, Rees DJG. Genome-wide SNP identification by high-throughput sequencing and selective mapping allows sequence assembly positioning using a framework genetic linkage map. BMC Biol 2010; 8:155. [PMID: 21192788 PMCID: PMC3024234 DOI: 10.1186/1741-7007-8-155] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2010] [Accepted: 12/30/2010] [Indexed: 11/24/2022] Open
Abstract
Background Determining the position and order of contigs and scaffolds from a genome assembly within an organism's genome remains a technical challenge in a majority of sequencing projects. In order to exploit contemporary technologies for DNA sequencing, we developed a strategy for whole genome single nucleotide polymorphism sequencing allowing the positioning of sequence contigs onto a linkage map using the bin mapping method. Results The strategy was tested on a draft genome of the fungal pathogen Venturia inaequalis, the causal agent of apple scab, and further validated using sequence contigs derived from the diploid plant genome Fragaria vesca. Using our novel method we were able to anchor 70% and 92% of sequences assemblies for V. inaequalis and F. vesca, respectively, to genetic linkage maps. Conclusions We demonstrated the utility of this approach by accurately determining the bin map positions of the majority of the large sequence contigs from each genome sequence and validated our method by mapping single sequence repeat markers derived from sequence contigs on a full mapping population.
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Affiliation(s)
- Jean-Marc Celton
- Biotechnology Department, University of the Western Cape, Private Bag X17, Bellville 7535, South Africa.
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