Background: Due to the accessibility of underlying technologies the 'Omics', in particular genomics, are becoming commonplace in several fields of research, including the study of agricultural pests. The weed community is starting to embrace these approaches; genome sequences have been made available in the past years, with several other sequencing projects underway, as promoted by the International Weed Genome Consortium. Chromosome-scale sequences are essential to fully exploit the power of genetics and genomics.Results: We report such an assembly for Conyza canadensis, an important agricultural weed. Third-generation sequencing technology was used to create a genome assembly of 426 megabases, of which nine chromosome-scale scaffolds cover more than 98% of the entire assembled sequence. As this weed was the first to be identified with glyphosate resistance, and since we do not have a firm handle on the genetic mechanisms responsible for several herbicide resistances in the species, the genome sequence was annotated with genes known to be associated with herbicide resistance. A high number of ABC-type transporters, cytochrome P450 and glycosyltransferases (159, 352 and 181, respectively) were identified among the list of ab initio predicted genes.Conclusion: As C. canadensis has a small genome that is syntenic with other Asteraceaes, has a short life cycle and is relatively easy to cross, it has the potential to become a model weed species and, with the chromosome-scale genome sequence, contribute to a paradigm shift in the way non-target site resistance is studied.

Background: The introgression of a transgene conferring glyphosate resistance from Brassica napus (rapeseed, canola) to Brassica rapa weeds (bird rape) was documented at a single location in 2007. In 2015, several cases of glyphosate resistant mustard were reported by growers in areas where rapeseed was seldom grown.Results: Survey result indicated glyphosate resistant bird rape mustard is present in areas where glyphosate tolerant corn and soybean are often grown in rotation. Genetic analyses reveal that hybridization followed by introgression and progressive loss of chromosome is the likely mechanism for the horizontal gene transfer (HGT) of glyphosate resistance.Conclusion: Introgression of the glyphosate-resistance conferring transgene in the populations studied appears to have occurred several times, consistent with the ease for B. rapa to form hybrids with B. napus. The introduction of a transgene into a crop should therefore take into account the weediness of the species that share a common genome and their ability to form hybrids. We provide here such an example between B. napus and B. rapa, and potentially between B. napus and Raphanistrum raphanistrum.

Erwinia amylovora and Pseudomonas syringae are bacterial phytopathogens responsible for considerable yield losses in commercial pome fruit production. The pathogens, if left untreated, can compromise tree health and economically impact entire commercial fruit productions. Historically, the choice of effective control methods has been limited. The use of antibiotics was proposed as an effective control method. The identification of these pathogens and screening for the presence of antibiotic resistance is paramount in the adoption and implementation of disease control methods. Molecular tests have been developed and accepted for identification and characterization of these disease-causing organisms. We improved existing molecular tests by developing methods that are equal or superior in robustness for identifying E. amylovora or P. syringae while being faster to execute. In addition, the real-time PCR-based detection method for E. amylovora provided complementary information on the susceptibility or resistance to streptomycin of individual isolates. Finally, we describe a methodology and results that compare the aggressiveness of the different bacterial isolates on four apple cultivars. We show that bacterial isolates exhibit different behaviors when brought into contact with various apple varieties and that the hierarchical clustering of symptom severity indicates a population structure, suggesting a genetic basis for host cultivar specificity.

Cultivation of lowbush blueberry (Vaccinium angustifolium Aiton), an important crop in the eastern part of North America, is unique as it is done over the course of two consecutive growing seasons. Pest management, and in particular weed management, is impacted by the biennial cultural practice. The choice of methods to control weeds is limited and such a system relies heavily on herbicides for weed management. Availability of unique herbicide active ingredients for weed management is limited, and ones that are available are repeatedly used and the risk of developing resistance is acute. Hair fescue (Festuca filiformis Pourr.), a perennial grass weed, has evolved resistance to hexazinone, a frequently used photosystem II inhibitor in lowbush blueberry production. We show that substitution of phenylalanine to isoleucine at position 255 is responsible for a decreased sensitivity to hexazinone by a factor of 6.12. Early diagnosis of resistance based on the detection of the mutation will inform growers to use alternative control methods and thus help to increase the sustainability of the cropping system.

Ambrosia artemisiifolia and Ambrosia trifida (Asteraceae) are important pest species and the two greatest sources of aeroallergens globally. Here we took advantage of a hybrid to simplify genome assembly and present high quality chromosome level assemblies for both species. These assemblies show high levels completeness with BUSCOs of 94.5% for A. artemisiifolia and 96.1% for A. trifida and LTR Assembly Index values of 26.6 and 23.6, respectively. The genomes were annotated using RNA data identifying 41,642 genes in A. artemisiifolia and 50,203 in A. trifida. More than half the genome is comprised of repetitive elements, with 62% in A. artemisiifolia and 69% in A. trifida, and this is similar to other species in the Heliantheae alliance . Single copies of herbicide resistance associated genes PPX2L, HPPD, and ALS where found, while 2 copies of the EPSPS gene were identified; this latter observation may reveal a possible mechanism of resistance to the herbicide glyphosate. The evolution of genome structure has differed among these two Ambrosia species. The genome of A. trifida has undergone greater rearrangement, possibly the result of cataclysmic reorganization through chromoplexy. In contrast, the genome of A. artemisiifolia retains a structure that makes the allotetraploidization of the most recent common ancestor of the Heliantheae alliance the clearest feature of its genome. When compared other Heliantheae alliance species, this allowed us to reconstruct the common ancestor’s karyotype – a key step for further development of our understanding of the evolution and diversification of this economically and allergenically important group.