0000000000634076
AUTHOR
Pedro Gómez
De novoassembly of the zucchini genome reveals a whole-genome duplication associated with the origin of theCucurbitagenus
Summary The Cucurbita genus (squashes, pumpkins and gourds) includes important domesticated species such as C. pepo, C. maxima and C. moschata. In this study, we present a high-quality draft of the zucchini (C. pepo) genome. The assembly has a size of 263 Mb, a scaffold N50 of 1.8 Mb and 34 240 gene models. It includes 92% of the conserved BUSCO core gene set, and it is estimated to cover 93.0% of the genome. The genome is organized in 20 pseudomolecules that represent 81.4% of the assembly, and it is integrated with a genetic map of 7718 SNPs. Despite the small genome size, three independent lines of evidence support that the C. pepo genome is the result of a whole-genome duplication: the …
Natural Hosts and Genetic Diversity of the Emerging Tomato Leaf Curl New Delhi Virus in Spain
Knowledge about the host range and genetic structure of emerging plant viruses provides insights into fundamental ecological and evolutionary processes, and from an applied perspective, facilitates the design and implementation of sustainable disease control measures. Tomato leaf curl New Delhi virus (ToLCNDV) is an emerging whitefly transmitted begomovirus that is rapidly spreading and inciting economically important diseases in cucurbit crops of the Mediterranean basin. Genetic characterization of the ToLCNDV Mediterranean populations has shown that they are monophyletic in cucurbit plants. However, the extent to which other alternative (cultivated and wild) hosts may affect ToLCNDV genet…
Additional file 5: of An SNP-based saturated genetic map and QTL analysis of fruit-related traits in Zucchini using Genotyping-by-sequencing
Phenotypic values of RILs carrying Zucchini and Scallop alleles in the detected QTL regions. Means and standard errors of the phenotypic value of RILs belonging to the alternative allelic classes (Zuchini versus Scallop) for the markers in the LOD peak regions of each significant QTL are shown. Data of the three environments, combined and separate, are shown to validate the effects of the different QTLs (Paip2014, Paip2015, and UPV2015). (DOCX 39 kb)
Modelling temperature-dependent dynamics of single and mixed infections in a plant virus
Multiple viral infection is an important issue in health and agriculture with strong impacts on society and the economy. Several investigations have dealt with the population dynamics of viruses with different dynamic properties, focusing on strain competition during multiple infections and the effects on viruses’ hosts. Recent interest has been on how multiple infections respond to abiotic factors such as temperature (T). This is especially important in the case of plant pathogens, whose dynamics could be affected significantly by global warming. However, few mathematical models incorporate the effect of T on parasite fitness, especially in mixed infections. Here, we investigate simple mat…
Increasing growth temperature alters the within-host competition of viral strains and influences virus genetic variation
AbstractThe emergence of viral diseases in plant crops hamper the sustainability of food production, and this may be boosted by global warming. Concurrently, mixed viral infections are becoming common in plants, of which epidemiology are unpredictable due to within-host virus-virus interactions. However, the extent in which the combined effect of variations in the abiotic components of the plant ecological niche (e.g., temperature) and the prevalence of mixed infections (i.e., within-host interactions among viruses) affect the evolutionary dynamics of viral populations is not well understood. Here, we explore the interplay between ecological and evolutionary factors during viral infections,…
Additional file 2: of An SNP-based saturated genetic map and QTL analysis of fruit-related traits in Zucchini using Genotyping-by-sequencing
Average percentage of genome covered with the GBS reads with a read depth from > 1 to > 20. (PPTX 713 kb)
An SNP-based saturated genetic map and QTL analysis of fruit-related traits in Zucchini using Genotyping-by-sequencing
[EN] Background: Cucurbita pepo is a cucurbit with growing economic importance worldwide. Zucchini morphotype is the most important within this highly variable species. Recently, transcriptome and Simple Sequence Repeat (SSR)- and Single Nucleotide Polymorphism (SNP)-based medium density maps have been reported, however further genomic tools are needed for efficient molecular breeding in the species. Our objective is to combine currently available complete transcriptomes and the Zucchini genome sequence with high throughput genotyping methods, mapping population development and extensive phenotyping to facilitate the advance of genomic research in this species. Results: We report the Genoty…
Increasing temperature alters the within-host competition of viral strains and influences virus genetic variability
Environmental conditions can affect viral accumulation, virulence and adaptation, which have implications in the disease outcomes and efficiency of control measures. Concurrently, mixed viral infections are relevant in plants, being their epidemiology shaped by within-host virus–virus interactions. However, the extent in which the combined effect of variations in abiotic components of the plant ecological niche and the prevalence of mixed infections affect the evolutionary dynamics of viral populations is not well understood. Here, we explore the interplay between ecological and evolutionary factors during viral infections and show that isolates of two strains of Pepino mosaic potexvirus co…
Additional file 1: of An SNP-based saturated genetic map and QTL analysis of fruit-related traits in Zucchini using Genotyping-by-sequencing
Phenotyped traits in the RIL population. (DOCX 13 kb)
Additional file 4: of An SNP-based saturated genetic map and QTL analysis of fruit-related traits in Zucchini using Genotyping-by-sequencing
a) LOD peaks of the QTLs identified in the RIL population for vine, flowering and fruit traits. Lines represent the thresholds p 0.01 and 0.05. Results of CIM analysis with a 20 cM windows are shown for each trait. First box show QTL results with data from all the environments and the other three boxes show the QTL results for single environments Paip2014, Paip2015 and UPV2015. b) Means and errors of the phenotype of alternative allelic classes, homozygous Zucchini (AA) and homozygous Scallop (BB), are shown for each QTL, calculated with the full set of data and with the data form each environment separately. c) Genetic correlations (r x,y) between locations for each trait (*p
Additional file 6: of An SNP-based saturated genetic map and QTL analysis of fruit-related traits in Zucchini using Genotyping-by-sequencing
List of genes underlying the significant QTLs involved in vine, flowering and fruit traits variation annotated in the last version of the C. pepo genome (v 3.2) available [13]. (XLSX 146 kb)
Additional file 3: of An SNP-based saturated genetic map and QTL analysis of fruit-related traits in Zucchini using Genotyping-by-sequencing
a) Genetic map developed using the GBS approach with the RIL population derived from the cross Zucchini x Scallop. The genetic and physical position of each of the the 7,718 SNP markers (in the C. pepo genome version 3.2) is indicated and the flanking sequenced of each SNPs is also included. b) Physical position and annotation (in the C. pepo genome version 3.2) of the SNPs that showed statistically significant distorted segregation. Chi-square p-values were corrected for multiple testing using Benjamini and Yekutieli correction [36]. Distorted SNPs are integrated with the 7,718 non-distorted SNPs used for the map construction for which the genetic position is also indicated. c) Main region…