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International audience; We report the complete and circularized genome sequences of two strains of Xanthomonas citri pv. glycines causing bacterial pustule on soybean and one strain of Xanthomonas euvesicatoria pv. alfalfae causing bacterial leaf and stem spot on alfalfa. These assemblies provide high-quality material for functional and evolutionary studies of these legume pathogens.

Background Xanthomonas citri pv. fuscans (Xcf) and Xanthomonas phaseoli pv. phaseoli (Xpp) are the causal agents of common bacterial blight of bean (CBB), an important disease worldwide that remains difficult to control. These pathogens belong to distinct species within the Xanthomonas genus and have undergone a dynamic evolutionary history including the horizontal transfer of genes encoding factors probably involved in adaptation to and pathogenicity on common bean. Seed transmission is a key point of the CBB disease cycle, favouring both vertical transmission of the pathogen and worldwide distribution of the disease through global seed trade. Taxonomy Kingdom: Bacteria; phylum: Proteobacteria; class: Gammaproteobacteria; order: Lysobacterales (also known as Xanthomonadales); family: Lysobacteraceae (also known as Xanthomonadaceae); genus: Xanthomonas; species: X. citri pv. fuscans and X. phaseoli pv. phaseoli (Xcf‐Xpp). Host range The main host of Xcf‐Xpp is the common bean (Phaseolus vulgaris). Lima bean (Phaseolus lunatus) and members of the Vigna genus (Vigna aconitifolia, Vigna angularis, Vigna mungo, Vigna radiata, and Vigna umbellata) are also natural hosts of Xcf‐Xpp. Natural occurrence of Xcf‐Xpp has been reported for a handful of other legumes such as Calopogonium sp., Pueraria sp., pea (Pisum sativum), Lablab purpureus, Macroptilium lathyroides, and Strophostyles helvola. There are conflicting reports concerning the natural occurrence of CBB agents on tepary bean (Phaseolus acutifolius) and cowpea (Vigna unguiculata subsp. unguiculata). Symptoms CBB symptoms occur on all aerial parts of beans, that is, seedlings, leaves, stems, pods, and seeds. Symptoms initially appear as water‐soaked spots evolving into necrosis on leaves, pustules on pods, and cankers on twigs. In severe infections, defoliation and wilting may occur. Distribution CBB is distributed worldwide, meaning that it is frequently encountered in most places where bean is cultivated in the Americas, Asia, Africa, and Oceania, except for arid tropical areas. Xcf‐Xpp are regulated nonquarantine pathogens in Europe and are listed in the A2 list by the European and Mediterranean Plant Protection Organization (EPPO). Genome The genome consists of a single circular chromosome plus one to four extrachromosomal plasmids of various sizes, for a total mean size of 5.27 Mb with 64.7% GC content and an average predicted number of 4,181 coding sequences. Disease control Management of CBB is based on integrated approaches that comprise measures aimed at avoiding Xcf‐Xpp introduction through infected seeds, cultural practices to limit Xcf‐Xpp survival between host crops, whenever possible the use of tolerant or resistant bean genotypes, and chemical treatments, mainly restricted to copper compounds. The use of pathogen‐free seeds is essential in an effective management strategy and requires appropriate sampling, detection, and identification methods. Useful websites https://gd.eppo.int/taxon/XANTPH, https://gd.eppo.int/taxon/XANTFF, and http://www.cost.eu/COST_Actions/ca/CA16107., This pathogen profile summarizes the current knowledge on Xanthomonas phaseoli pv. phaseoli and Xanthomonas citri pv. fuscans, two phylogenetically distant groups of strains that cause common bacterial blight of bean. ​

Additional file 2: Figure S2. Validation of RNA-Seq results by RT-qPCR analysis in BAT93 (A) and JaloEEP558 (B). Gene expression data were expressed according to the 2–ΔΔCt method (Vandesompele et al. 2002) [145], relatively to three housekeeping genes: Act11, EF1-α and IDE, and to the value of water inoculated plants.

Additional file 4: Figure S4. KEGG orthology map for plant hormone signal transduction. The KEGG orthology maps (pvu04075) of BAT93 (A) and JaloEEP558 (B) highlight DEGs that were induced (red), repressed (blue), or both induced and repressed (green) 48 h after inoculation with Xanthomonas phaseoli pv. phaseoli. The number of DEGs (colored numbers) and the average Log2FC (black numbers) are indicated above the boxes.

Additional file 1: Figure S1 Statistical analysis of RNA-Seq data. Statistics were performed by using the total number of RNA-Seq reads mapped on the 20,787 homologs shared by BAT93 and JaloEEP558. Principal component analysis (A). Triangles and dots represent the barycenters of RNA-Seq data from BAT93 and JaloEEP558, respectively. Data from plants inoculated with H2O are in orange while data from plants inoculated with Xanthomonas strain CFBP6546R are in black. Pearson correlation matrix (B). Numbers represent the means of Pearson correlation coefficients calculated using three biological replicates per condition.

Additional file 3 Figure S3 Numbers of DEGs in the different families of transcription factors. The list of common bean transcription factors was retrieved from the iTAK database ( http://itak.feilab.net , Zheng et al. 2016) [142]. The numbers of induced and repressed genes are represented by red and blue bars respectively, in the specific transcriptomes of BAT93 (solid) or JaloEEP558 (hatched). Only families with at least 10 DEGs were represented.

Gel photograph showing the sizes obtained for tal23A_CFBP4885 (Xfutal1) and tal18H_CFBP4885 (Xfutal2) after PCR amplification. Amplification was performed using XapF2 and XapR primers on plasmidic DNA from the CFBP4885 strain (Additional file 18: Table S11). Expected PCR product sizes for tal23A_CFBP4885 and tal18H_CFBP4885 were 4604 bp and 3074 bp for Sanger sequencing of the entire genome, respectively, and 3686 bp and 3176 bp for SMRT sequencing of the entire genome, respectively. (DOCX 2788 kb)