scholarly journals Genome Resource forNeocamarosporium betae(syn.Pleospora betae), the Cause of Phoma Leaf Spot and Root Rot onBeta vulgaris

2019 ◽  
Vol 32 (7) ◽  
pp. 787-789 ◽  
Author(s):  
Niloofar Vaghefi ◽  
Alex Silva ◽  
Lori B. Koenick ◽  
Sarah J. Pethybridge
Keyword(s):  
Leaf Spot ◽  
Root Rot ◽  
Population Biology ◽  
De Novo ◽  
Underlying Disease ◽  
Economic Importance ◽  
Genetic Studies ◽  
Root Decay ◽  
Genetic Mechanisms ◽  
Phoma Betae

Neocamarosporium betae (syn. Phoma betae, Pleospora betae) is the cause of Phoma leaf spot and root decay on Beta vulgaris worldwide. Despite the economic importance of the pathogen, many aspects of its life cycle and population biology remain unknown. The first genome assembly of N. betae was constructed to facilitate identification of mating-type loci and development of microsatellite markers for population genetics studies. The de novo assembled genome is provided as a resource for future genetic studies to understand the genetic mechanisms underlying disease development and host-pathogen interactions.

scholarly journals Pathogenicity of Phoma betae isolates from red beet (Beta vulgaris) at seed farms in Canterbury, New Zealand

2019 ◽  
Vol 72 ◽  
pp. 21-26
Author(s):  
Nitesh Chand ◽  
E. Eirian Jones ◽  
Seona Casonato
Keyword(s):  
New Zealand ◽  
Beta Vulgaris ◽  
Leaf Spot ◽  
Root Rot ◽  
Economic Importance ◽  
The Other ◽  
Fodder Beet ◽  
Leaf Spots ◽  
Red Beet ◽  
Phoma Betae

Phoma betae is an economically important pathogen of red beet causing preemergence seedling damping, leaf spot and root rot. However, the pathogenicity of P. betae is unknown in New Zealand despite the economic importance of this pathogen. Twenty-five isolates were collected from a survey of red beet seed farms in Canterbury, New Zealand during 2016/2017 and three of these PB101 (from seeds), PB103 (from roots) and PB106 (from leaves) were used for pathogenicity testing of two red-beet cultivars. Isolate PB106 was further used to investigate its effects on spinach and fodder beet as well as red beet under greenhouse conditions. All three P. betae isolates were pathogenic on both red-beet cultivars tested, causing leaf-spot symptoms. Isolates PB101 and PB106 produced significantly larger leaf-spot lesions (P<0.001) compared with PB103. Phoma betae isolate PB106 was pathogenic to both red-beet cultivars, spinach and fodder beet but fodder beet was less susceptible than the other species tested. Regardless of cultivar, <i>P. betae </i>is an important pathogen of beets and is capable of causing leaf spots.

scholarly journals Phytotoxicity of the new metabolites produced by Phoma betae, the cause of phoma root rot and leaf spot in sugar beet (Beta vulgaris L.).

1985 ◽  
Vol 51 (2) ◽  
pp. 219-222 ◽  
Author(s):  
Ryutaro SAKAI ◽  
Yosuke MINO ◽  
Akitami ICHIHARA ◽  
Sadao SAKAMURA
Keyword(s):  
Sugar Beet ◽  
Beta Vulgaris ◽  
Leaf Spot ◽  
Root Rot ◽  
Phoma Betae ◽  
New Metabolites

scholarly journals RNA-Seq reveals divergent gene expression between larvae with contrasting trophic modes in the poecilogonous polychaete Boccardia wellingtonensis

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Álvaro Figueroa ◽  
Antonio Brante ◽  
Leyla Cárdenas
Keyword(s):  
De Novo ◽  
Juvenile Stage ◽  
Type I ◽  
Rna Seq ◽  
Mrna Synthesis ◽  
De Novo Transcriptome ◽  
Larval Stages ◽  
Divergent Gene ◽  
Genetic Mechanisms ◽  
Planktotrophic Larvae

AbstractThe polychaete Boccardia wellingtonensis is a poecilogonous species that produces different larval types. Females may lay Type I capsules, in which only planktotrophic larvae are present, or Type III capsules that contain planktotrophic and adelphophagic larvae as well as nurse eggs. While planktotrophic larvae do not feed during encapsulation, adelphophagic larvae develop by feeding on nurse eggs and on other larvae inside the capsules and hatch at the juvenile stage. Previous works have not found differences in the morphology between the two larval types; thus, the factors explaining contrasting feeding abilities in larvae of this species are still unknown. In this paper, we use a transcriptomic approach to study the cellular and genetic mechanisms underlying the different larval trophic modes of B. wellingtonensis. By using approximately 624 million high-quality reads, we assemble the de novo transcriptome with 133,314 contigs, coding 32,390 putative proteins. We identify 5221 genes that are up-regulated in larval stages compared to their expression in adult individuals. The genetic expression profile differed between larval trophic modes, with genes involved in lipid metabolism and chaetogenesis over expressed in planktotrophic larvae. In contrast, up-regulated genes in adelphophagic larvae were associated with DNA replication and mRNA synthesis.

scholarly journals Comparative Analysis of SNP Discovery and Genotyping in Fagus sylvatica L. and Quercus robur L. Using RADseq, GBS, and ddRAD Methods

Forests ◽  
2021 ◽  
Vol 12 (2) ◽  
pp. 222
Author(s):  
Bartosz Ulaszewski ◽  
Joanna Meger ◽  
Jaroslaw Burczyk
Keyword(s):  
Population Genomics ◽  
De Novo ◽  
Genetic Studies ◽  
Genomic Libraries ◽  
Reduced Representation ◽  
Large Numbers ◽  
Broadleaved Tree Species ◽  
Fagus Sylvatica L ◽  
Reference Genomes ◽  
Future Population

Next-generation sequencing of reduced representation genomic libraries (RRL) is capable of providing large numbers of genetic markers for population genetic studies at relatively low costs. However, one major concern of these types of markers is the precision of genotyping, which is related to the common problem of missing data, which appears to be particularly important in association and genomic selection studies. We evaluated three RRL approaches (GBS, RADseq, ddRAD) and different SNP identification methods (de novo or based on a reference genome) to find the best solutions for future population genomics studies in two economically and ecologically important broadleaved tree species, namely F. sylvatica and Q. robur. We found that the use of ddRAD method coupled with SNP calling based on reference genomes provided the largest numbers of markers (28 k and 36 k for beech and oak, respectively), given standard filtering criteria. Using technical replicates of samples, we demonstrated that more than 80% of SNP loci should be considered as reliable markers in GBS and ddRAD, but not in RADseq data. According to the reference genomes’ annotations, more than 30% of the identified ddRAD loci appeared to be related to genes. Our findings provide a solid support for using ddRAD-based SNPs for future population genomics studies in beech and oak.

Root rot damage in naturally regenerated stands of spruce and balsam fir in Ontario

1989 ◽  
Vol 19 (3) ◽  
pp. 295-308 ◽  
Author(s):  
R. D. Whitney
Keyword(s):  
Root Rot ◽  
Black Spruce ◽  
Basal Area ◽  
Ground Level ◽  
White Spruce ◽  
Balsam Fir ◽  
Tree Age ◽  
Stand Age ◽  
Root Decay ◽  
Forest Region

In an 11-year study in northern Ontario, root rot damage was heaviest in balsam fir, intermediate in black spruce, and least in white spruce. As a result of root rot, 16, 11, and 6%, respectively, of dominant or codominant trees of the three species were killed or experienced premature windfall. Butt rot, which resulted from the upward extension of root rot into the boles of living trees, led to a scaled cull of 17, 12, and 10%, respectively, of gross merchantable volume of the remaining living trees in the three species. The total volume of wood lost to rot was, therefore, 33, 23, and 16%, respectively. Of 1108 living dominant and codominant balsam fir, 1243 black spruce, and 501 white spruce in 165 stands, 87, 68, and 63%, respectively, exhibited some degree of advanced root decay. Losses resulting from root rot increased with tree age. Significant amounts of root decay and stain (>30% of root volume) first occurred at 60 years of age in balsam fir and 80 years in black spruce and white spruce. For the three species together, the proportion of trees that were dead and windfallen as a result of root rot increased from an average of 3% at 41–50 years to 13% at 71–80 years and 26% at 101–110 years. The root rot index, based on the number of dead and windfallen trees and estimated loss of merchantable volume, also increased, from an average of 17 at 41–50 years to 40 at 71–80 years and 53 at 101–110 years. Death and windfall of balsam fir and black spruce were more common in northwestern Ontario than in northeastern Ontario. Damage to balsam fir was greater in the Great Lakes–St. Lawrence Forest region than in the Boreal Forest region. In all three tree species, the degree of root rot (decay and stain) was highly correlated with the number of dead and windfallen trees, stand age, and root decay at ground level (as a percentage of basal area) for a 10-tree sample.

First report of Sclerotium rolfsii (=Athelia rolfsii) associated with root rot and leaf spot on clove basil (Ocimum gratissimum L.) in India

2021 ◽  
Author(s):  
Shivannegowda Mahadevakumar ◽  
Yelandur Somaraju Deepika ◽  
Kandikere Ramaiah Sridhar ◽  
Kestur Nagaraj Amruthesh ◽  
Nanjaiah Lakshmidevi
Keyword(s):  
Leaf Spot ◽  
Root Rot ◽  
Sclerotium Rolfsii ◽  
First Report ◽  
Ocimum Gratissimum ◽  
Athelia Rolfsii

scholarly journals Genotypic and Phenotypic Characterization of Lettuce Bacterial Pathogen Xanthomonas hortorum pv. vitians Populations Collected in Quebec, Canada

Agronomy ◽  
2021 ◽  
Vol 11 (12) ◽  
pp. 2386
Author(s):  
Pierre-Olivier Hébert ◽  
Martin Laforest ◽  
Dong Xu ◽  
Marie Ciotola ◽  
Mélanie Cadieux ◽  
...  
Keyword(s):  
Leaf Spot ◽  
Genome Wide Association Study ◽  
De Novo ◽  
Association Studies ◽  
Genome Wide Association ◽  
Phenotypic Characterization ◽  
Genome Wide Association Studies ◽  
Bacterial Leaf Spot ◽  
Eastern Canada ◽  
Genome Wide

Bacterial leaf spot of lettuce, caused by Xanthomonas hortorum pv. vitians, is an economically important disease worldwide. For instance, it caused around 4 million CAD in losses in only a few months during the winter of 1992 in Florida. Because only one pesticide is registered to control this disease in Canada, the development of lettuce cultivars tolerant to bacterial leaf spot remains the most promising approach to reduce the incidence and severity of the disease in lettuce fields. The lack of information about the genetic diversity of the pathogen, however, impairs breeding programs, especially when disease resistance is tested on newly developed lettuce germplasm lines. To evaluate the diversity of X. hortorum pv. vitians, a multilocus sequence analysis was performed on 694 isolates collected in Eastern Canada through the summers of 2014 to 2017 and two isolates in 1996 and 2007. All isolates tested were clustered into five phylogroups. Six pathotypes were identified following pathogenicity tests conducted in greenhouses, but when phylogroups were compared with pathotypes, no correlation could be drawn. However, in vitro production of xanthan and xanthomonadins was investigated, and isolates with higher production of xanthomonadins were generally causing less severe symptoms on the tolerant cultivar Little Gem. Whole-genome sequencing was undertaken for 95 isolates belonging to the pathotypes identified, and de novo assembly made with reads unmapped to the reference strain’s genome sequence resulted in 694 contigs ranging from 128 to 120,795 bp. Variant calling was performed prior to genome-wide association studies computed with single-nucleotide polymorphisms (SNPs), copy-number variants and gaps. Polymorphisms with significant p-values were only found on the cultivar Little Gem. Our results allowed molecular identification of isolates likely to cause bacterial leaf spot of lettuce, using two SNPs identified through genome-wide association study.

scholarly journals A Systematic Review on Extreme Phenotype Strategies to Search for Rare Variants in Genetic Studies of Complex Disorders

2020 ◽  
Author(s):  
Sana Amanat ◽  
Teresa Requena ◽  
Jose Antonio Lopez-Escamez
Keyword(s):  
Systematic Review ◽  
Candidate Genes ◽  
Rare Variants ◽  
De Novo ◽  
Complex Diseases ◽  
De Novo Mutations ◽  
Genetic Studies ◽  
Complex Disorders ◽  
Extreme Phenotype ◽  
Age Related

Exome sequencing has been commonly used in rare diseases by selecting multiplex families or singletons with an extreme phenotype (EP) to search for rare variants in coding regions. The EP strategy covers both extreme ends of a disease spectrum and it has been also used to investigate the contribution of rare variants to heritability in complex clinical traits. We have conducted a systematic review to find evidence supporting the use of EP strategies to search for rare variants in genetic studies of complex diseases, to highlight the contribution of rare variation to the genetic structure of multiallelic conditions. After performing the quality assessment of the retrieved records, we selected 19 genetic studies considering EP to demonstrate genetic association. All the studies successfully identified several rare variants, de novo mutations and many novel candidate genes were also identified by selecting an EP. There is enough evidence to support that the EP approach in patients with an early onset of the disease can contribute to the identification of rare variants in candidate genes or pathways involved in complex diseases. EP patients may contribute to a better understanding of the underlying genetic architecture of common heterogeneous disorders such as tinnitus or age-related hearing loss.

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