Geographical and temporal distribution of SARS-CoV-2 clades in the WHO European Region, January to June 2020

We show the distribution of SARS-CoV-2 genetic clades over time and between countries and outline potential genomic surveillance objectives. We applied three available genomic nomenclature systems for SARS-CoV-2 to all sequence data from the WHO European Region available during the COVID-19 pandemic until 10 July 2020. We highlight the importance of real-time sequencing and data dissemination in a pandemic situation. We provide a comparison of the nomenclatures and lay a foundation for future European genomic surveillance of SARS-CoV-2.Peer reviewe

Disease resistance gene homologs correlate with disease resistance loci of Arabidopsis thaliana

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A Comparison of Peronospora parasitica (Downy mildew) Isolates from Arabidopsis thaliana and Brassica oleracea Using Amplified Fragment Length Polymorphism and Internal Transcribed Spacer 1 Sequence Analyses

Amplified fragment length polymorphism (AFLP) fingerprints and internal transcribed spacer 1 (ITS1) sequences from 27 Peronospora parasitica isolates (collected from Arabidopsis thaliana or Brassica oleracea), 5 Albugo candida isolates (from the same hosts and from Capsella bursa-pastoris), and 1 Bremia lactucae isolate (from Lactuca sativa) were compared. The AFLP analysis divided the isolates into five groups that correlated with taxonomic species and, in most cases, with host origin. The only exception was a group consisting of A. candida isolates from both B. oleracea and C. bursa-pastoris. ITS1 sequence analysis divided the isolates into the same five groups, demonstrated the divergence between P. parasitica isolates from A. thaliana and B. oleracea, and, using previously published ITS1 sequences, clearly showed the relationship between A. candida isolates from different hosts

Phenotypic and Genotypic Variation in the Interaction between Arabidopsls thaliana and Albugo candida

Two biotrophic parasites of the wild crucifer Arabidopsis thaliana (L.) Heynh. are being used to explore the molecular basis and evolution of genotype-specific recognition and host defense. Genes for recognition of Peronospora parasitica (downy mildew) are numerous in A. thaliana and located on four of the five chromosomes as described previously. Genes for recognition of the closely related parasite Albugo Candida (white blister) are described here. In contrast to the former parasite, less than 15% of the host accessions tested were capable of recognizing either of two isolates of A. Candida. The geographic regions represented by these accessions included countries in eastern and western Europe, Asia, North America and Africa. Extensive collections from England and Germany were required to identify examples of incompatible interactions. Phenotypic variation among incompatible interactions included reduced blister formation or complete lack of asexual reproduction by the parasite. Variation in the extent of the host response was also observed. Three host genes for recognition of A. Candida (RAC), each associated with different interaction phenotypes, were identified through inheritance studies with three accessions. One of these genes at locus RACI appeared to be completely dominant, whereas the other two genes were only partially dominant or recessive under certain conditions, possibly including the effect of genetic background. One of the latter two genes defined a second locus RAC2. RACI was mapped to the top arm of chromosome 1 in the 1 cM interval between RFLP markers M254 and M253

Downy mildew (Peronospora parasitica) resistance genes in Arabidopsis vary in functional requirements for NDR1, EDS1, NPR1 and salicylic acid accumulation

PubMedID: 10886772To better understand the genetic requirements for R gene-dependent defense activation in Arabidopsis, we tested the effect of several defense response mutants on resistance specified by eight RPP genes (for resistance to Peronospora parasitica) expressed in the Col-0 background. In most cases, resistance was not suppressed by a mutation in the SAR regulatory gene NPR1 or by expression of the NahG transgene. Thus, salicylic acid accumulation and NPR1 function are not necessary for resistance mediated by these RPP genes. In addition, resistance conferred by two of these genes, RPP7 and RPP8, was not significantly suppressed by mutations in either EDS1 or NDR1. RPP7 resistance was also not compromised by mutations in EIN2, JAR1 or COI1 which affect ethylene or jasmonic acid signaling. Double mutants were therefore tested. RPP7 and RPP8 were weakly suppressed in an eds1-2/ndr1-1 background, suggesting that these RPP genes operate additively through EDS1, NDR1 and as-yet-undefined signaling components. RPP7 was not compromised in coi1/npr1 or coi1/NahG backgrounds. These observations suggest that RPP7 initiates resistance through a novel signaling pathway that functions independently of salicylic acid accumulation or jasmonic acid response components