scholarly journals A high-quality grapevine downy mildew genome assembly reveals rapidly evolving and lineage-specific putative host adaptation genes

2018 ◽  
Author(s):  
Yann Dussert ◽  
Isabelle D. Mazet ◽  
Carole Couture ◽  
Jérôme Gouzy ◽  
Marie-Christine Piron ◽  
...  
Keyword(s):  
Downy Mildew ◽  
Genome Assembly ◽  
Population Genomics ◽  
Genome Project ◽  
Plant Diseases ◽  
Data Availability ◽  
Host Specialization ◽  
Grapevine Downy Mildew ◽  
Genes Encoding ◽  
Genome Assemblies

ABSTRACTDowny mildews are obligate biotrophic oomycete pathogens that cause devastating plant diseases on economically important crops. Plasmopara viticola is the causal agent of grapevine downy mildew, a major disease in vineyards worldwide. We sequenced the genome of Pl. viticola with PacBio long reads and obtained a new 92.94 Mb assembly with high continuity (359 scaffolds for a N50 of 706.5 kb) due to a better resolution of repeat regions. This assembly presented a high level of gene completeness, recovering 1,592 genes encoding secreted proteins involved in plant-pathogen interactions. Pl. viticola had a two-speed genome architecture, with secreted protein-encoding genes preferentially located in gene-sparse, repeat-rich regions and evolving rapidly, as indicated by pairwise dN/dS values. We also used short reads to assemble the genome of Plasmopara muralis, a closely related species infecting grape ivy (Parthenocissus tricuspidata). The lineage-specific proteins identified by comparative genomics analysis included a large proportion of RxLR cytoplasmic effectors and, more generally, genes with high dN/dS values. We identified 270 candidate genes under positive selection, including several genes encoding transporters and components of the RNA machinery potentially involved in host specialization. Finally, the Pl. viticola genome assembly generated here will allow the development of robust population genomics approaches for investigating the mechanisms involved in adaptation to biotic and abiotic selective pressures in this species.DATA AVAILABILITYRaw reads and genome assemblies have been deposited in GenBank (BioProjects PRJNA329579 for Pl. viticola and PRJNA448661 for Pl. muralis). Genome assemblies, gene annotations and analysis files (e.g. orthology relationships, full tables for GO enrichment analyses, pairwise dN/dS values and branch-site tests) have been deposited in Dataverse (Pl. viticola assembly and annotation: doi.org/10.15454/4NYHD6, Pl. muralis assembly and annotation: doi.org/10.15454/Q1QJYK, analysis files: doi.org/10.15454/8NZ8X9). Links to the data and information about the grapevine downy mildew genome project can be found at http://grapevine-downy-mildew-genome.com/.

scholarly journals A High-Quality Grapevine Downy Mildew Genome Assembly Reveals Rapidly Evolving and Lineage-Specific Putative Host Adaptation Genes

2019 ◽  
Vol 11 (3) ◽  
pp. 954-969 ◽  
Author(s):  
Yann Dussert ◽  
Isabelle D Mazet ◽  
Carole Couture ◽  
Jérôme Gouzy ◽  
Marie-Christine Piron ◽  
...  
Keyword(s):  
Downy Mildew ◽  
Genome Assembly ◽  
Population Genomics ◽  
Plasmopara Viticola ◽  
Plant Diseases ◽  
Host Specialization ◽  
Grapevine Downy Mildew ◽  
Downy Mildews ◽  
Genes Encoding ◽  
High Level

Abstract Downy mildews are obligate biotrophic oomycete pathogens that cause devastating plant diseases on economically important crops. Plasmopara viticola is the causal agent of grapevine downy mildew, a major disease in vineyards worldwide. We sequenced the genome of Pl. viticola with PacBio long reads and obtained a new 92.94 Mb assembly with high contiguity (359 scaffolds for a N50 of 706.5 kb) due to a better resolution of repeat regions. This assembly presented a high level of gene completeness, recovering 1,592 genes encoding secreted proteins involved in plant–pathogen interactions. Plasmopara viticola had a two-speed genome architecture, with secreted protein-encoding genes preferentially located in gene-sparse, repeat-rich regions and evolving rapidly, as indicated by pairwise dN/dS values. We also used short reads to assemble the genome of Plasmopara muralis, a closely related species infecting grape ivy (Parthenocissus tricuspidata). The lineage-specific proteins identified by comparative genomics analysis included a large proportion of RxLR cytoplasmic effectors and, more generally, genes with high dN/dS values. We identified 270 candidate genes under positive selection, including several genes encoding transporters and components of the RNA machinery potentially involved in host specialization. Finally, the Pl. viticola genome assembly generated here will allow the development of robust population genomics approaches for investigating the mechanisms involved in adaptation to biotic and abiotic selective pressures in this species.

scholarly journals Draft Genome Sequence of Plasmopara viticola , the Grapevine Downy Mildew Pathogen

2016 ◽  
Vol 4 (5) ◽  
Author(s):  
Yann Dussert ◽  
Jérôme Gouzy ◽  
Sylvie Richart-Cervera ◽  
Isabelle D. Mazet ◽  
Laurent Delière ◽  
...  
Keyword(s):  
Downy Mildew ◽  
Genome Sequence ◽  
Genome Analysis ◽  
Plant Pathogen ◽  
Host Resistance ◽  
Draft Genome ◽  
Plasmopara Viticola ◽  
Host Specialization ◽  
Grapevine Downy Mildew ◽  
Plant Pathogen Interactions

Plasmopara viticola is a biotrophic pathogenic oomycete responsible for grapevine downy mildew. We present here the first draft of the P. viticola genome. Analysis of this sequence will help in understanding plant-pathogen interactions in oomycetes, especially pathogen host specialization and adaptation to host resistance.

scholarly journals Identification of the first oomycete mating-type locus sequence in the grapevine downy mildew pathogen, Plasmopara viticola

2020 ◽  
Author(s):  
Yann Dussert ◽  
Ludovic Legrand ◽  
Isabelle D. Mazet ◽  
Carole Couture ◽  
Marie-Christine Piron ◽  
...  
Keyword(s):  
Downy Mildew ◽  
Mating Type ◽  
Type Systems ◽  
Plasmopara Viticola ◽  
Plant Diseases ◽  
Mating Types ◽  
Type Locus ◽  
Grapevine Downy Mildew ◽  
Mating Type Locus ◽  
A Genome

ABSTRACTMating types are self-incompatibility systems that promote outcrossing in plants, fungi and oomycetes. Mating-type genes have been widely studied in plants and fungi, but have yet to be identified in oomycetes, eukaryotic organisms closely related to brown algae that cause many destructive animal and plant diseases. We identified the mating-type locus of Plasmopara viticola, the oomycete responsible for grapevine downy mildew, one of the most damaging grapevine diseases worldwide. Using a genome-wide association approach, we identified a 570 kb repeat-rich non-recombining region controlling mating types, with two highly divergent alleles. We showed that one mating type was homozygous, whereas the other was heterozygous at this locus. The mating-type locus encompassed 40 genes, including one encoding a putative hormone receptor. Our findings have fundamental implications for our understanding of the evolution of mating types, as they reveal a unique determinism involving an asymmetry of heterozygosity, as in sex chromosomes and unlike other mating-type systems. This identification of the mating-type locus in such an economically important crop pathogen also has applied implications, as outcrossing facilitates rapid evolution and resistance to harsh environmental conditions.

scholarly journals Genome sequencing of four culinary herbs reveals terpenoid genes underlying chemodiversity in the Nepetoideae

DNA Research ◽  
2020 ◽  
Vol 27 (3) ◽  
Author(s):  
Nolan Bornowski ◽  
John P Hamilton ◽  
Pan Liao ◽  
Joshua C Wood ◽  
Natalia Dudareva ◽  
...  
Keyword(s):  
Leaf Tissue ◽  
Terpene Synthases ◽  
Genomic Analyses ◽  
Genes Encoding ◽  
Medicinal Properties ◽  
Culinary Herbs ◽  
Rosmarinus Officinalis L ◽  
Origanum Majorana ◽  
Genome Assemblies ◽  
High Quality Genome

Abstract Species within the mint family, Lamiaceae, are widely used for their culinary, cultural, and medicinal properties due to production of a wide variety of specialized metabolites, especially terpenoids. To further our understanding of genome diversity in the Lamiaceae and to provide a resource for mining biochemical pathways, we generated high-quality genome assemblies of four economically important culinary herbs, namely, sweet basil (Ocimum basilicum L.), sweet marjoram (Origanum majorana L.), oregano (Origanum vulgare L.), and rosemary (Rosmarinus officinalis L.), and characterized their terpenoid diversity through metabolite profiling and genomic analyses. A total 25 monoterpenes and 11 sesquiterpenes were identified in leaf tissue from the 4 species. Genes encoding enzymes responsible for the biosynthesis of precursors for mono- and sesqui-terpene synthases were identified in all four species. Across all 4 species, a total of 235 terpene synthases were identified, ranging from 27 in O. majorana to 137 in the tetraploid O. basilicum. This study provides valuable resources for further investigation of the genetic basis of chemodiversity in these important culinary herbs.

scholarly journals Climate change and the occurrence of downy mildew in Brazilian grapevines

2017 ◽  
Vol 52 (6) ◽  
pp. 426-434 ◽  
Author(s):  
Francislene Angelotti ◽  
Emília Hamada ◽  
Edineide Elisa Magalhães ◽  
Raquel Ghini ◽  
Lucas da Ressureição Garrido ◽  
...  
Keyword(s):  
Climate Change ◽  
Latent Period ◽  
Downy Mildew ◽  
Temporal Distribution ◽  
Gas Emission ◽  
Grapevine Downy Mildew ◽  
Diseased Leaf Area ◽  
The Mean ◽  
Potential Impact ◽  
Logic Functions

Abstract: The objective of this work was to evaluate the potential impact of climate change on the occurrence of grapevine downy mildew in Brazil. Seedlings containing four to six leaves were sprayed with a sporangia suspension containing 105 sporangia per milliliter. After spraying, the seedlings were subjected to temperatures of 26, 28, 29.1, 30.4, and 31.8°C for 24 hours. The percentage of diseased leaf area and the latent period were evaluated. Maps of the geographic and temporal distribution of the disease were made considering the monthly average of the mean air temperature and leaf wetness duration for the reference climate or climate normal (1961-1990) and the future climates (2011-2040, 2041-2070, and 2071-2100), considering the A2 and B1 gas emission scenarios, designed by the Intergovernamental Panel on Climate Change (IPCC). Favorability ranges were set and used in logic functions of the geografical information system (GIS) to generate monthly maps for grapevine downy mildew. Rising temperatures interfered with the grapevine downy mildew infections, reduced the disease severity, and increased the latent period. Future climate scenarios indicate a reduction of favorability of downy mildew in Brazil, with variability in the different grape producing regions.

scholarly journals Timing of Grape Downy Mildew Onset in Bordeaux Vineyards

2019 ◽  
Vol 109 (5) ◽  
pp. 787-795 ◽  
Author(s):  
Mathilde Chen ◽  
François Brun ◽  
Marc Raynal ◽  
David Makowski
Keyword(s):  
Downy Mildew ◽  
Severe Disease ◽  
Survival Analyses ◽  
Fungicide Treatment ◽  
Grapevine Downy Mildew ◽  
Local Characteristics ◽  
South West ◽  
Disease Surveys ◽  
Grape Downy Mildew ◽  
Regional Disease

Grapevine downy mildew (GDM) is a severe disease of grapevines. Because of the lack of reliable information about the dates of GDM symptom onset, many vine growers begin fungicide treatments early in the season. We evaluate the extent to which such preventive treatments are justified. Observational data for 266 untreated sites for the years between 2010 and 2017 were used to estimate the timing of GDM onset on vines and bunches of grapes in South West France (Bordeaux region) through survival analyses. The onset of GDM was not apparent on vines and bunches before early to mid-May, and the rate of GDM symptom appearance was highly variable across years. Depending on the year, 50% of the plots displayed symptoms between mid-May and late June for vines. For several years, our statistical analysis revealed that the proportion of plots with no symptoms was high in early August on vines (27.5 and 43.7% in 2013 and 2016) and on bunches (between 23 and 79% in 2011, 2013, and 2016). We found a significant effect of the amount of rainfall in spring on the date of symptom appearance. These results indicate that preventive fungicide application is unjustified in many vineyards, and that regional disease surveys should be used to adjust fungicide treatment dates according to local characteristics, in particular according to rainfall conditions in spring.

scholarly journals A highly contiguous nuclear genome assembly of the mandarinfish Synchiropus splendidus (Syngnathiformes: Callionymidae)

2021 ◽  
Author(s):  
Martin Stervander ◽  
William A Cresko
Keyword(s):  
Genome Assembly ◽  
Nuclear Genome ◽  
Phylogenetic Position ◽  
Blue Color ◽  
Long Reads ◽  
The Family ◽  
Commercially Important ◽  
Genomic Resource ◽  
Genome Assemblies ◽  
Important Fish

Abstract The fish order Syngnathiformes has been referred to as a collection of misfit fishes, comprising commercially important fish such as red mullets as well as the highly diverse seahorses, pipefishes, and seadragons—the well-known family Syngnathidae, with their unique adaptations including male pregnancy. Another ornate member of this order is the species mandarinfish. No less than two types of chromatophores have been discovered in the spectacularly colored mandarinfish: the cyanophore (producing blue color) and the dichromatic cyano-erythrophore (producing blue and red). The phylogenetic position of mandarinfish in Syngnathiformes, and their promise of additional genetic discoveries beyond the chromatophores, made mandarinfish an appealing target for whole genome sequencing. We used linked sequences to create synthetic long reads, producing a highly contiguous genome assembly for the mandarinfish. The genome assembly comprises 483 Mbp (longest scaffold 29 Mbp), has an N50 of 12 Mbp, and an L50 of 14 scaffolds. The assembly completeness is also high, with 92.6% complete, 4.4% fragmented, and 2.9% missing out of 4,584 BUSCO genes found in ray-finned fishes. Outside the family Syngnathidae, the mandarinfish represents one of the most contiguous syngnathiform genome assemblies to date. The mandarinfish genomic resource will likely serve as a high-quality outgroup to syngnathid fish, and furthermore for research on the genomic underpinnings of the evolution of novel pigmentation.

scholarly journals The hormone neuroparsin seems essential in Lepidoptera but not in domesticated silkworms

2019 ◽  
Author(s):  
Jan A. Veenstra
Keyword(s):  
Bombyx Mori ◽  
Genome Assembly ◽  
Galleria Mellonella ◽  
Sequence Similarity ◽  
Neuroendocrine Cells ◽  
Primary Sequence ◽  
Genome Assemblies ◽  
Limited Sequence ◽  
Wax Moth

AbstractThe primary sequence of the Arthropod neurohormone neuroparsin is so variable that so far no orthologs from moths and butterflies have been characterized, even though classical neurosecretory stains identify cells that are homologous to those producing this hormone in other insect species. Here Lepidopteran cDNAs showing limited sequence similarity to other insect neuroparsins are described. That these cDNAs do indeed code for authentic neuroparsins was confirmed by in situ hybridization in the wax moth, Galleria mellonella, which labeled the neuroparsin neuroendocrine cells. Although in virtually all genome assemblies from Lepidoptera a neuroparsin gene could be identified, the genome assembly from the silkworm, Bombyx mori, has a neuroparsin gene containing a 16 nucleotide deletion that renders this gene nonfunctional. Although only a small number of all silkworm strains carry this deletion, it suggests that the domestication of the silkworm has rendered the function of this neurohormone dispensable.

scholarly journals Identifying the causes and consequences of assembly gaps using a multiplatform genome assembly of a bird-of-paradise

2019 ◽  
Author(s):  
Valentina Peona ◽  
Mozes P.K. Blom ◽  
Luohao Xu ◽  
Reto Burri ◽  
Shawn Sullivan ◽  
...  
Keyword(s):  
Dark Matter ◽  
Genome Assembly ◽  
Sex Chromosome ◽  
De Novo ◽  
Model Organism ◽  
Technology Choice ◽  
High Quality ◽  
Sequencing Technologies ◽  
Downstream Analysis ◽  
Genome Assemblies

AbstractGenome assemblies are currently being produced at an impressive rate by consortia and individual laboratories. The low costs and increasing efficiency of sequencing technologies have opened up a whole new world of genomic biodiversity. Although these technologies generate high-quality genome assemblies, there are still genomic regions difficult to assemble, like repetitive elements and GC-rich regions (genomic “dark matter”). In this study, we compare the efficiency of currently used sequencing technologies (short/linked/long reads and proximity ligation maps) and combinations thereof in assembling genomic dark matter starting from the same sample. By adopting different de-novo assembly strategies, we were able to compare each individual draft assembly to a curated multiplatform one and identify the nature of the previously missing dark matter with a particular focus on transposable elements, multi-copy MHC genes, and GC-rich regions. Thanks to this multiplatform approach, we demonstrate the feasibility of producing a high-quality chromosome-level assembly for a non-model organism (paradise crow) for which only suboptimal samples are available. Our approach was able to reconstruct complex chromosomes like the repeat-rich W sex chromosome and several GC-rich microchromosomes. Telomere-to-telomere assemblies are not a reality yet for most organisms, but by leveraging technology choice it is possible to minimize genome assembly gaps for downstream analysis. We provide a roadmap to tailor sequencing projects around the completeness of both the coding and non-coding parts of the genomes.

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