scholarly journals A method for variant agnostic detection of SARS-CoV-2, rapid monitoring of circulating variants, detection of mutations of biological significance, and early detection of emergent variants such as Omicron

2022 ◽  
Author(s):  
Eric Lai ◽  
David Becker ◽  
Pius Brzoska ◽  
Tyler Cassens ◽  
Jeremy Davis-Turak ◽  
...  
Keyword(s):  
Sequence Data ◽  
Biological Significance ◽  
The United States ◽  
Nucleotide Polymorphisms ◽  
Panel Testing ◽  
Percent Agreement ◽  
Rapid Monitoring ◽  
Public Repositories ◽  
Detection Of Mutations ◽  
Next Generation Sequencing Ngs

The rapid emergence of new SARS-CoV-2 variants raises a number of public health questions including the capability of diagnostic tests to detect new strains, the efficacy of vaccines, and how to map the geographical distribution of variants to better understand patterns of transmission and possible load on healthcare resources. Next-Generation Sequencing (NGS) is the primary method for detecting and tracing the emergence of new variants, but it is expensive, and it can take weeks before sequence data is available in public repositories. Here, we describe a Polymerase Chain Reaction (PCR)-based genotyping approach that is significantly less expensive, accelerates reporting on SARS-CoV-2 variants, and can be implemented in any testing lab performing PCR. Specific Single Nucleotide Polymorphisms (SNPs) and indels are identified that have high positive percent agreement (PPA) and negative percent agreement (NPA) compared to NGS for the major genotypes that circulated in 2021. Using a 48-marker panel, testing on 1,128 retrospective samples yielded a PPA and NPA in the 96.3 to 100% and 99.2 to 100% range, respectively, for the top 10 most prevalent lineages. The effect on PPA and NPA of reducing the number of panel markers was also explored. In addition, with the emergence of Omicron, we also developed an Omicron genotyping panel that distinguishes the Delta and Omicron variants using four (4) highly specific SNPs. Data from testing demonstrates the capability to use the panel to rapidly track the growing prevalence of the Omicron variant in the United States in December 2021.

Frequent LOH of CYP2D6 in ER+ breast cancer determined by next-generation sequencing (NGS).

2013 ◽  
Vol 31 (15_suppl) ◽  
pp. 534-534
Author(s):  
Mark J. Ratain ◽  
James Sun ◽  
Yusuke Nakamura ◽  
Nancy J Cox ◽  
Tarek Sahmoud ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Sequence Data ◽  
Biological Significance ◽  
Gene Copy Number ◽  
Gene Copy ◽  
Full Cohort ◽  
Next Generation Sequencing Ngs ◽  
Apparent Association

534 Background: The role of CYP2D6 genetic variation in predicting response to tamoxifen in ER+ breast cancer is a subject of ongoing debate. There has been great variability in approaches to both genotyping and phenotyping, and in particular many investigators have extracted DNA from breast cancer samples rather than peripheral blood. We hypothesized that CYP2D6 gene copy number alterations are common in ER+ breast cancer, affecting genotype results, and used NGS to characterize CYP2D6 in patients with ER+ disease. Methods: CYP2D6 sequencing was performed as part of a comprehensive NGS profile of cancer-related genes for 261 predominantly relapsed and metastatic ER+ breast cancer FFPE specimens. Sequence data were resolved into genotypes according to the * allele nomenclature. Tumor LOH was determined at CYP2D6, and its error impact on genotyping methods was estimated. To assess biological significance, the prevalence of CYP2D6 alleles and LOH in ER+ disease was compared against a control set of 99 ER- tumors. Results: CYP2D6 allele frequencies in our full cohort (ER+, 261; ER-, 99) were consistent with prior studies; 64.4%, 16.8%, 9.0% vs. 63.1%, 17.2%, 7.0% for *1/*2, *4, and *41 respectively, and 1%-2% for the rarer alleles *9, *10, and *5. The rate of CYP2D6 LOH was higher in ER+ disease (41% vs. 26%, p<0.01), with all excess arising from copy-loss (as opposed to copy-neutral) changes (22% vs. 7%, p<0.002). The estimated impact of LOH on germline genotype assessment from tumor was considerable; an assay sensitive at >20% minor allele frequency (e.g., Sanger sequencing) can misclassify >10% of heterozygotes, leading to significant Hardy-Weinberg disequilibrium (e.g., p=8.3x10-8 for *4). Interestingly, an enrichment of reduced or non-functional CYP2D6 alleles in ER+ samples was observed (61% vs. 47%, p<0.03). Conclusions: Our results demonstrate the distorting effect of extensive LOH on genotype assessment of CYP2D6 in breast cancer. Therefore, tumor DNA should not be routinely used for determination of germline 2D6 genotype, although it appears possible to use NGS. The apparent association between reduced function CYP2D6 alleles and ER+ breast cancer in our dataset requires further investigation.

256 GENOMIC EVALUATION OF FERTILITY TRAITS AND DISCOVERY OF HAPLOTYPES THAT AFFECT FERTILITY OF US DAIRY CATTLE

2016 ◽  
Vol 28 (2) ◽  
pp. 260
Author(s):  
G. R. Wiggans ◽  
D. J. Null ◽  
J. B. Cole ◽  
H. D. Norman
Keyword(s):  
Dairy Cattle ◽  
Sequence Data ◽  
Reference Population ◽  
Bioinformatic Analysis ◽  
The United States ◽  
Conception Rate ◽  
National Database ◽  
Nucleotide Polymorphisms ◽  
Fertility Traits ◽  
Sire Conception Rate

Genomic evaluations of dairy cattle became official in the United States in January 2009 for Holsteins and Jerseys, and later for Brown Swiss, Ayrshires, and Guernseys. Up to 33 yield, fitness, calving, and conformation traits are evaluated, and the fertility traits included daughter pregnancy rate and heifer and cow conception rates. Additional fertility traits, such as age at first calving and days from calving to first insemination, also are being studied. Male fertility (sire conception rate) is evaluated phenotypically rather than through genomics. Over 1 million animals have genotypes in the national database, which reflects collaboration with Canada and Europe. Most of the genotypes are from females and are from genotyping chips with <30 000 single nucleotide polymorphisms (SNP). To combine data across chips, genotypes are imputed to a set of >77 000 SNP. The imputation process involves dividing the chromosome into segments of approximately equal length and determining the paternal or maternal origin of the alleles. Because some segments were never homozygous, they were assumed to contain an abnormality that resulted in early embryonic death. If a decrease in sire conception rate could be associated with a bull that was a carrier of such a chromosomal segment, the haplotype was designated as affecting fertility. Once the region was identified, bioinformatic analysis was used to discover the causative variant for many of those haplotypes. Accuracy of genomic evaluations is determined by size of the reference population and heritability of the trait. The reference population for Holsteins includes >180 000 bulls and cows. Because fertility traits have low heritabilities, genomic information is particularly useful in improving evaluation accuracy. Accuracy of fertility evaluations is expected to increase further by discovering causative variants for various aspects of conception and gestation through investigation of sequence data.

scholarly journals Challenges in evaluating the use of viral sequence data to identify HIV transmission networks for public health

2020 ◽  
Vol 12 (s1) ◽  
Author(s):  
Rami Kantor ◽  
John P. Fulton ◽  
Jon Steingrimsson ◽  
Vladimir Novitsky ◽  
Mark Howison ◽  
...  
Keyword(s):  
Public Health ◽  
United States ◽  
Hiv Transmission ◽  
Sequence Data ◽  
The United States ◽  
Viral Sequence ◽  
Transmission Networks ◽  
New Methods ◽  
Hiv Epidemic ◽  
The World

AbstractGreat efforts are devoted to end the HIV epidemic as it continues to have profound public health consequences in the United States and throughout the world, and new interventions and strategies are continuously needed. The use of HIV sequence data to infer transmission networks holds much promise to direct public heath interventions where they are most needed. As these new methods are being implemented, evaluating their benefits is essential. In this paper, we recognize challenges associated with such evaluation, and make the case that overcoming these challenges is key to the use of HIV sequence data in routine public health actions to disrupt HIV transmission networks.

scholarly journals PSI-40 Two mitochondrial lineages revealed in North American yak

2020 ◽  
Vol 98 (Supplement_4) ◽  
pp. 477-477
Author(s):  
Leah K Treffer ◽  
Edward S Rice ◽  
Anna M Fuller ◽  
Samuel Cutler ◽  
Jessica L Petersen
Keyword(s):  
Sequence Data ◽  
Haplotype Network ◽  
Ovis Aries ◽  
Similar Species ◽  
Nucleotide Polymorphisms ◽  
Mt Dna ◽  
Protein Coding ◽  
Sister Clade ◽  
Mtdna Sequence ◽  
The Impact

Abstract Domestic yak (Bos grunniens) are bovids native to the Asian Qinghai-Tibetan Plateau. Studies of Asian yak have revealed that introgression with domestic cattle has contributed to the evolution of the species. When imported to North America (NA), some hybridization with B. taurus did occur. The objective of this study was to use mitochondrial (mt) DNA sequence data to better understand the mtDNA origin of NA yak and their relationship to Asian yak and related species. The complete mtDNA sequence of 14 individuals (12 NA yak, 1 Tibetan yak, 1 Tibetan B. indicus) was generated and compared with sequences of similar species from GeneBank (B. indicus, B. grunniens (Chinese), B. taurus, B. gaurus, B. primigenius, B. frontalis, Bison bison, and Ovis aries). Individuals were aligned to the B. grunniens reference genome (ARS_UNL_BGru_maternal_1.0), which was also included in the analyses. The mtDNA genes were annotated using the ARS-UCD1.2 cattle sequence as a reference. Ten unique NA yak haplotypes were identified, which a haplotype network separated into two clusters. Variation among the NA haplotypes included 93 nonsynonymous single nucleotide polymorphisms. A maximum likelihood tree including all taxa was made using IQtree after the data were partitioned into twenty-two subgroups using PartitionFinder2. Notably, six NA yak haplotypes formed a clade with B. indicus; the other four haplotypes grouped with B. grunniens and fell as a sister clade to bison, gaur and gayal. These data demonstrate two mitochondrial origins of NA yak with genetic variation in protein coding genes. Although these data suggest yak introgression with B. indicus, it appears to date prior to importation into NA. In addition to contributing to our understanding of the species history, these results suggest the two major mtDNA haplotypes in NA yak may functionally differ. Characterization of the impact of these differences on cellular function is currently underway.

scholarly journals 130. increase in Multidrug Resistance (2011–2018) and the Emergence of Extensive Drug Resistance (2020) in shigella Sonnei in the United States

2020 ◽  
Vol 7 (Supplement_1) ◽  
pp. S195-S195
Author(s):  
Naeemah Z Logan ◽  
Beth E Karp ◽  
Kaitlin A Tagg ◽  
Claire Burns-Lynch ◽  
Jessica Chen ◽  
...  
Keyword(s):  
United States ◽  
Multidrug Resistance ◽  
Disease Surveillance ◽  
Sequence Data ◽  
The United States ◽  
Multidrug Resistant ◽  
Shigella Sonnei ◽  
Short Read ◽  
Men 2 ◽  
The Us

Abstract Background Multidrug-resistant (MDR) Shigella sonnei infections are a serious public health threat, and outbreaks are common among men who have sex with men (MSM). In February 2020, Australia’s Department of Health notified CDC of extensively drug-resistant (XDR) S. sonnei in 2 Australian residents linked to a cruise that departed from Florida. We describe an international outbreak of XDR S. sonnei and report on trends in MDR among S. sonnei in the United States. Methods Health departments (HDs) submit every 20th Shigella isolate to CDC’s National Antimicrobial Resistance Monitoring System (NARMS) laboratory for susceptibility testing. We defined MDR as decreased susceptibility to azithromycin (MIC ≥32 µg/mL) with resistance to ampicillin, ciprofloxacin, and cotrimoxazole, and XDR as MDR with additional resistance to ceftriaxone. We used PulseNet, the national subtyping network for enteric disease surveillance, to identify US isolates related to the Australian XDR isolates by short-read whole genome sequencing. We screened these isolates for resistance determinants (ResFinder v3.0) and plasmid replicons (PlasmidFinder) and obtained patient histories from HDs. We used long-read sequencing to generate closed plasmid sequences for 2 XDR isolates. Results NARMS tested 2,781 S. sonnei surveillance isolates during 2011–2018; 80 (2.9%) were MDR, including 1 (0.04%) that was XDR. MDR isolates were from men (87%), women (9%), and children (4%). MDR increased from 0% in 2011 to 15.3% in 2018 (Figure). In 2020, we identified XDR isolates from 3 US residents on the same cruise as the Australians. The US residents were 41–42 year-old men; 2 with available information were MSM. The US and Australian isolates were highly related (0–1 alleles). Short-read sequence data from all 3 US isolates mapped to the blaCTX-M-27 harboring IncFII plasmids from the 2 Australian isolates with &gt;99% nucleotide identity. blaCTX-M-27 genes confer ceftriaxone resistance. Increase in Percentage of Shigella sonnei Isolates with Multidrug Resistance* in the United States, 2011–2018† Conclusion MDR S. sonnei is increasing and is most often identified among men. XDR S. sonnei infections are emerging and are resistant to all recommended antibiotics, making them difficult to treat without IV antibiotics. This outbreak illustrates the alarming capacity for XDR S. sonnei to disseminate globally among at-risk populations, such as MSM. Disclosures All Authors: No reported disclosures

scholarly journals PSV-13 Genetic parameters and quantitative trait loci for heat stress related traits in sheep

2020 ◽  
Vol 98 (Supplement_3) ◽  
pp. 163-164
Author(s):  
Devin R Jacobs ◽  
Claudia E Silvera-Rojas ◽  
Jennifer M Bormann ◽  
Terry A Gipson ◽  
Arthur L Goetsch ◽  
...  
Keyword(s):  
Heat Stress ◽  
Quantitative Trait Loci ◽  
Rectal Temperature ◽  
Quantitative Trait ◽  
Fixed Effects ◽  
Univariate Analysis ◽  
Average Daily Gain ◽  
The United States ◽  
Nucleotide Polymorphisms ◽  
Trait Loci

Abstract Greater selection emphasis has been placed on efficiency than on fitness in livestock populations over the last several decades. Heat stress is a concern in production systems due to the negative effects on production, reproduction, and immunity. The objective of the study was to estimate variance components and identify quantitative trait loci (QTL) for heat stress related traits in sheep. A total of 125 Dorper, Katahdin, and St. Croix ewes originating from four regions of the United States were selected for the experiment. Animals were separated into four trials due to facility limitations. Data were collected for each trial over four consecutive two-week periods in an environmentally controlled facility with targeted heat load index (HLI) for daytime/nighttime of 70/70, 85/77, 90/77, and 95/81. Body weight was collected three times per week and rectal temperature was collected weekly. Black globe temperature and humidity were measured every 15 minutes. Animals were genotyped using the Illumina OvineSNP50 BeadChip. After quality control, 49,396 effective single nucleotide polymorphisms were included in the univariate analysis performed with the BLUPF90 suite of programs. Fixed effects in the models included region of origin, breed, trial, and age as a covariate. Traits analyzed included rectal temperature at 95 HLI (RT95), feed intake at 95 HLI (FI95), and average daily gain for the period for HLI between 90 and 95 (ADG). Heritabilities for RT95, FI95, and ADG were 0.35, 0.10, and 0.10, respectively. Largest effect QTL were identified on chromosomes 23, 9, and 6 for RT95, chromosomes 9, 2, and 20 for FI95, and chromosomes 6, 1, and 5 for ADG. Many of the regions identified have also been associated with weight and carcass traits in other studies, but few had obvious connections to the heat stress related response. In conclusion, results suggest selection could improve heat tolerance in sheep.

scholarly journals Optimization of a WGA-Free Molecular Tagging-Based NGS Protocol for CTCs Mutational Profiling

2020 ◽  
Vol 21 (12) ◽  
pp. 4364
Author(s):  
Giuseppa De Luca ◽  
Barbara Cardinali ◽  
Lucia Del Mastro ◽  
Sonia Lastraioli ◽  
Franca Carli ◽  
...  
Keyword(s):  
Substantial Reduction ◽  
Breast Cancer Patients ◽  
Dna Templates ◽  
Molecular Tagging ◽  
Mutational Profiling ◽  
Optimized Protocol ◽  
Set Up ◽  
Detection Of Mutations ◽  
Almost All ◽  
Next Generation Sequencing Ngs

Molecular characterization of Circulating Tumor Cells (CTCs) is still challenging, despite attempts to minimize the drawbacks of Whole Genome Amplification (WGA). In this paper, we propose a Next-Generation Sequencing (NGS) optimized protocol based on molecular tagging technology, in order to detect CTCs mutations while skipping the WGA step. MDA-MB-231 and MCF-7 cell lines, as well as leukocytes, were sorted into pools (2–5 cells) using a DEPArray™ system and were employed to set up the overall NGS procedure. A substantial reduction of reagent volume for the preparation of libraries was performed, in order to fit the limited DNA templates directly derived from cell lysates. Known variants in TP53, KRAS, and PIK3CA genes were detected in almost all the cell line pools (35/37 pools, 94.6%). No additional alterations, other than those which were expected, were found in all tested pools and no mutations were detected in leukocytes. The translational value of the optimized NGS workflow is confirmed by sequencing CTCs pools isolated from eight breast cancer patients and through the successful detection of variants. In conclusion, this study shows that the proposed NGS molecular tagging approach is technically feasible and, compared to traditional NGS approaches, has the advantage of filtering out the artifacts generated during library amplification, allowing for the reliable detection of mutations and, thus, making it highly promising for clinical use.

148 Multiple Dysregulated Novel Pathways and Genes in Aleutian Mink Disease Revealed by Selection Signatures and Gene Network Analyses Using Whole-genome Sequence Data

2021 ◽  
Vol 99 (Supplement_3) ◽  
pp. 76-76
Author(s):  
Seyed Milad Vahedi ◽  
Karim Karimi ◽  
Siavash Salek Ardestani ◽  
Younes Miar
Keyword(s):  
Sequence Data ◽  
American Mink ◽  
Enrichment Analysis ◽  
Whole Genome Sequence ◽  
Fixation Index ◽  
Pathway Enrichment Analysis ◽  
Whole Genome ◽  
Nucleotide Polymorphisms ◽  
Network Analyses ◽  
Genome Level

Abstract Aleutian disease (AD) is a chronic persistent infection in domestic mink caused by Aleutian mink disease virus (AMDV). Female mink’s fertility and pelt quality depression are the main reasons for the AD’s negative economic impacts on the mink industry. A total number of 79 American mink from the Canadian Center for Fur Animal Research at Dalhousie University (Truro, NS, Canada) were classified based on the results of counter immunoelectrophoresis (CIEP) tests into two groups of positive (n = 48) and negative (n = 31). Whole-genome sequences comprising 4,176 scaffolds and 8,039,737 single nucleotide polymorphisms (SNPs) were used to trace the selection footprints for response to AMDV infection at the genome level. Window-based fixation index (Fst) and nucleotide diversity (θπ) statistics were estimated to compare positive and negative animals’ genomes. The overlapped top 1% genomic windows between two statistics were considered as potential regions underlying selection pressures. A total of 98 genomic regions harboring 33 candidate genes were detected as selective signals. Most of the identified genes were involved in the development and functions of immune system (PPP3CA, SMAP2, TNFRSF21, SKIL, and AKIRIN2), musculoskeletal system (COL9A2, PPP1R9A, ANK2, AKAP9, and STRIT1), nervous system (ASCL1, ZFP69B, SLC25A27, MCF2, and SLC7A14), reproductive system (CAMK2D, GJB7, SSMEM1, C6orf163), liver (PAH and DPYD), and lung (SLC35A1). Gene-expression network analysis showed the interactions among 27 identified genes. Moreover, pathway enrichment analysis of the constructed genes network revealed significant oxytocin (KEGG: hsa04921) and GnRH signaling (KEGG: hsa04912) pathways, which are likely to be impaired by AMDV leading to dams’ fecundity reduction. These results provided a perspective to the genetic architecture of response to AD in American mink and novel insight into the pathogenesis of AMDV.

scholarly journals Phylogeographic Analysis Reveals Multiple International transmission Events Have Driven the Global Emergence of Escherichia coli O157:H7

2018 ◽  
Vol 69 (3) ◽  
pp. 428-437 ◽  
Author(s):  
Eelco Franz ◽  
Ovidiu Rotariu ◽  
Bruno S Lopes ◽  
Marion MacRae ◽  
James L Bono ◽  
...  
Keyword(s):  
United States ◽  
Disease Outbreaks ◽  
The United States ◽  
Human Case ◽  
Whole Genome Sequencing Data ◽  
Nucleotide Polymorphisms ◽  
Sequencing Data ◽  
E Coli ◽  
Phylogeographic Analysis ◽  
International Distribution

AbstractBackgroundShiga toxin–producing Escherchia coli (STEC) O157:H7 is a zoonotic pathogen that causes numerous food and waterborne disease outbreaks. It is globally distributed, but its origin and the temporal sequence of its geographical spread are unknown.MethodsWe analyzed whole-genome sequencing data of 757 isolates from 4 continents, and performed a pan-genome analysis to identify the core genome and, from this, extracted single-nucleotide polymorphisms. A timed phylogeographic analysis was performed on a subset of the isolates to investigate its worldwide spread.ResultsThe common ancestor of this set of isolates occurred around 1890 (1845–1925) and originated from the Netherlands. Phylogeographic analysis identified 34 major transmission events. The earliest were predominantly intercontinental, moving from Europe to Australia around 1937 (1909–1958), to the United States in 1941 (1921–1962), to Canada in 1960 (1943–1979), and from Australia to New Zealand in 1966 (1943–1982). This pre-dates the first reported human case of E. coli O157:H7, which was in 1975 from the United States.ConclusionsInter- and intra-continental transmission events have resulted in the current international distribution of E. coli O157:H7, and it is likely that these events were facilitated by animal movements (eg, Holstein Friesian cattle). These findings will inform policy on action that is crucial to reduce the further spread of E. coli O157:H7 and other (emerging) STEC strains globally.

scholarly journals First Report of Leptosphaeria biglobosa (Blackleg) on Brassica oleracea (Cabbage) in Mexico

Plant Disease ◽  
2010 ◽  
Vol 94 (6) ◽  
pp. 791-791 ◽  
Author(s):  
A. Dilmaghani ◽  
M. H. Balesdent ◽  
T. Rouxel ◽  
O. Moreno-Rico
Keyword(s):  
Brassica Oleracea ◽  
Sequence Data ◽  
Leptosphaeria Maculans ◽  
The United States ◽  
Internal Transcribed Spacers ◽  
First Report ◽  
5.8S Rdna ◽  
Single Location ◽  
Leptosphaeria Biglobosa ◽  
Β Tubulin

Broccoli (Brassica oleracea var. italica), cauliflower (B. oleracea var. botrytis), and cabbage (B. oleracea var. capitata) have been grown in central Mexico since 1970, with 21,000 ha cropped in 2001. In contrast, areas grown with oilseed rape (B. napus) are very limited in Mexico (<8,000 ha). Blackleg, a destructive disease of B. napus in most parts of the world, was first observed in Mexico in Zacatecas and Aguascalientes in 1988 on B. oleracea, causing as much as 70% yield loss. A species complex of two closely related Dothideomycete species, Leptosphaeria maculans and L. biglobosa, is associated with this disease of crucifers (1), but leaf symptoms on susceptible plants are different, with L. maculans typically causing >15-mm pale gray lesions with numerous pycnidia, whereas L. biglobosa causes dark and smaller lesions only containing a few pycnidia. Having a similar epidemiology, both species can be present on the same plants at the same time, and symptom confusion can occur as a function of the physiological condition of the plant or expression of plant resistance responses. A total of 209 isolates from symptomatic B. oleracea leaves were collected from three fields in central states of Mexico (58 to 71 isolates per location). All leaves showed similar symptoms, including a 10- to 15-mm tissue collapse with an occasional dark margin. Cotyledons of seven B. napus differentials were inoculated with conidia of all the isolates as described by Dilmaghani et al. (1). Two hundred isolates caused tissue collapse typical of L. maculans. However, nine obtained from white cabbage in a single location in Aguascalientes caused <5-mm dark lesions. When inoculated onto cotyledons of three B. oleracea genotypes commonly grown in Mexico (cvs. Domador, Monaco, and Iron Man), the nine isolates caused a range of symptoms characterized by tissue collapse (maximum 10 to 15 mm), showing the presence of patches of black necrotic spots within the collapse. The occasional presence of a few pycnidia allowed us to reisolate the fungus for molecular identification. ITS1-5.8S-ITS2, (internal transcribed spacers and 5.8S rDNA), actin, and β-tubulin sequences were obtained as described previously (4). Multiple gene genealogies based on these sequence data showed two subclades of L. biglobosa: L. biglobosa ‘occiaustralensis’ (one isolate; ITS [AM410082], actin [AM410084], and β-tubulin [AM410083]) and L. biglobosa ‘canadensis’ (eight isolates; ITS [AJ550868], actin [AY748956], and β-tubulin [AY749004]) (3,4), which were previously described on B. napus in the United States, Canada, and Chile. To our knowledge, this is the first report of L. biglobosa in Mexico. Previously, this species has only been reported once on B. oleracea without discrimination into subclades (2). In the Aguascalientes sampling, 24% of the isolates were L. biglobosa, similar to Canadian locations where this species is still common as compared with L. maculans (1). The large proportion of sampled L. biglobosa ‘canadensis’, highlights the prevalence of this subclade throughout the American continent (1). References: (1) A. Dilmaghani et al. Plant Pathol. 58:1044, 2009. (2) E. Koch et al. Mol. Plant-Microbe Interact. 4:341, 1991. (3) E. Mendes-Pereira et al. Mycol Res. 107:1287, 2003. (4) L. Vincenot et al. Phytopathology 98:321, 2008.

Sign in / Sign up

Export Citation Format

Share Document