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High-quality Illumina assemblies were produced from 284 Xanthomonas citri pv. citri pathotype A strains mostly originating from the Southwest Indian Ocean region, a subset of which was also sequenced using MinION technology. Some strains hosted chromosomally encoded transcription activator-like effector (TALE) genes, an atypical feature for this bacterium.

International audience

International audience; The Comoros Archipelago is constituted of four islands. These islands are located in the North Mozambique Channel in the Indian Ocean, one of the world’s hotspots of biodiversity. Despite this status of hotspot, only one species of Phytoseiidae was known from this Archipelago, from Mayotte: Phytoseius mayottae. No species were recorded from the three other islands. We report in this paper the results of a preliminary survey in Great Comoro or “Grande Comore” Island also called Ngazidja in the Comorian language (= Shikomori) with five species recorded.

Cassava is the most important vegetatively propagated food staple crop in Africa. Even if its vegetative propagation through stem cuttings has many advantages, it also represents its Achilles heel. Pathogens are passed from one generation to the next and can easily accumulate, threatening cassava production. Two viral diseases are currently considered to be the greatest global threat to cassava production in Africa. Faced with the gravity of this situation, 43 scientists from African national and regional institutions and international agricultural research centres met in Saint-Pierre, La Réunion Island from 10 to 13 June 2014, to contribute to the surveillance and control of cassava diseases and pests that threaten the food security and livelihoods of millions Africans. The main action was to consolidate and develop a global alliance against cassava diseases in Africa and a strategic action plan with several international initiatives for the coming years. Firstly, the establishment of a Pan-African Cassava Surveillance Network (PACSUN) with an interactive website and an International Cassava Transit Site (ICTS) in La Réunion. Secondly, the development of diagnostic technologies to better identifying viruses, bacteria and vectors, and a comprehensive educational and training plan to support all these activities. (Texte intégral)

The Ralstonia solanacearum species complex (Rssc) encompasses strains that are highly destructive worldwide on a wide hast range. This soilborne bacterial plant pathogen invades the roots and colonizes the xylem vessels causing bacterial wilt (BW) diseases. Strains are distributed into four phylogenetic groups, called phylotypes, differing in geographical origin of the strains: phylotype I (Asia), phylotype II (America), phylotype III (Africa) and phylotype IV (Australia - lndonesia - Japan). Each phylotype is subdivided into sequevars based on partial sequencing of the endoglucanase (egl) gene (Fegan and Prior, 2005). In the South-West lndian Ocean (SWIO) islands, although the Rssc is regularly reported no recent data is available about its genetic diversity and population structure. To thoroughly analyze the genetic diversity of the Rssc in the SWIO, we collected a significant collection of Rssc strains mainly from Solanaceae: Reunion (n=789, 41 sites), Mauritius (n=785, 30 sites), Rodrigues (n=S1, 3 sites), Mayotte (n=166, 24 sites), Seychelles (n=92, 9 sites) and Comoros (n=S, to be completed). Using the Multiplex-PCR (Fegan and Prior, 2005), we revealed that the four phylotypes are present with variable distribution depending on the SWIO islands and variable proportions: phylotype 1 (86.7%), phylotype II (9.7%), phylotype Ill (3.5%) and two strains from phylotype IV (0.1%). Partial egl sequencing based on a selection of strains that covered the geographic and hast diversity showed the unexpected overrepresentation of one sequevar (1-31). Further characterizations are ongoing through (i) a MLSA/MLST (Multilocus sequence analysis/typing) based on partial amplification of 7 genes (gdhA, mutS, adK, feus, rp/B, gyrB, and egl) and (ii) the development of a new MLVA (Multilocus variable number of tandem repeat analysis) scheme. Results of bath approaches will be discussed du ring the presentation.

International audience; no abstract

Bacterial spot of Solanaceae is present in most areas of the world where tomato and pepper are cultivated. Its incidence is especially high in tropical and subtropical regions, such as the islands of South West Indian Ocean. This desease can be caused by five taxa: X. vesicatoria , X. perforans , X. gardneri , X. euvesicatoria et X. campestris pv. raphani, but recent studies suggest that some of those species are synonymous or actually correspond to other species of Xanthomonas. The objectives of this work were (1) to assess the genetic diversity of a word collection of strains using two high throughput molecular techniques: AFLP and MLSA; (2) to describe the phylogenetic relationships between the different taxa caising bacterial spot and other Xanthomonas; (3) to develop a rapid identification method based on SCAR markers identified by AFLP, which would take into account the global diversity of the pathogen. Tree topologies derived from the sequences of four housekeeping genes were not congruent and recombination events could be detected in three of them. A survey of bacterial spot of tomato and pepper in the South West Indian Ocean showed a broad diversity of the species causing this disease in the region. Our data confirmed the strong genetic similarity between, X. alfalfae , X. euvesicatoria et X. perforans, as well as between X. cynarae and X. gardneri, which are probably synonymous species.; La gale bactérienne des Solanées à graines est une maladie répandue dans la plupart des aires de production de tomate et des Capsicum spp. (piment, poivron) du monde. Elle est très sévère dans les régions tropicales et subtropicales et sa présence est récurrente dans la région Sud-Ouest de l’océan Indien. Cette maladie est complexe car cinq taxons sont actuellement reconnus comme agents causaux, X. vesicatoria , X. perforans , X. gardneri , X. euvesicatoria et X. campestris pv. raphani . Néanmoins certaines études récentes suggèrent des synonymies de certaines de ces espèces entre elles et également avec d’autres Xanthomonas. Les objectifs principaux de la thèse étaient (1) l’analyse de la diversité sur une collection mondiale à l’aide des deux techniques moléculaires à haut débit, AFLP et MLSA, avec un accent particulier sur la diversité génétique et pathologique régionale (2) la description des relations phylogénétiques entre ces taxons et les autres Xanthomonas (3) la mise au point d’un outil d’identification rapide qui tienne compte de la diversité de l’agent pathogène et basé sur des marqueurs SCAR identifiés par AFLP. Une absence de congruence entre les topologies d’arbres dérivées des séquences de 4 gènes de ménage étudiés a été mise en évidence, de même que plusieurs évènements de recombinaison sur trois d’entre eux. Un inventaire des espèces trouvées dans les îles SWIO a pu être dressé, mettant à jour une grande diversité dans cette région. Nos données ont confirmé de fortes similarités génétiques entre X. alfalfae , X. euvesicatoria et X. perforans d’une part et de X. cynarae et X. gardneri d’autre part, qui ont probablement le statut d’espèces-synonyme.

La tomate et le piment sont infectés par plusieurs espèces de Xanthomonas dont certaines ont fait l'objet d'une reclassification récente, ayant abouti à la création de trois nouvelles espèces : X. euvesicatoria, X gardneri et X perforans, auxquelles s'ajoutent X. vesicatoria et X. campestris pv. raphani de description plus ancienne. X. euvesicatoria, X perforans et X vesicatoria sont considérées comme organisme de quarantaine en Europe. La caractérisation par AFLP et MLSA sur la base de quatre portions de gènes de ménage (atpD, dnaK, efp et gyrB) d'une collection mondiale de souches associées à la gale bactérienne de la tomate et du piment et d'une collection de référence comprenant l'ensemble des souches-type des espèces valides au sein du genre Xanthomonas suggère les points suivants : 1) Les espèces X alfalfae, X. euvesicatoria et X. perforans sont probablement des espèces-synonyme qui doivent être dénommées X euvesicatoria. 2) L'espèce X. gardneri est synonyme de X. cynarae. 3) Quelques souches isolées de tomate aux USA et en Zambie appartiennent à l'espèce X. campestris et sont génétiquement très proches de X. campestris pv. raphani. L'étude du pouvoir pathogène de X. gardneri et de X. cynarae sur tomate, piment et artichaut a montré que toutes les souches étudiées provoquent une réaction de type compatible sur l'ensemble des espèces étudiées. Aucune spécialisation d'hôte apparente n'a été mise en évidence. De même, les souches de X. campestris isolées de tomate sont pathogènes du radis, sans aucune différence par rapport aux souches de X. campestris pv. raphani ni dans la morphologie des symptômes produits ni dans les niveaux de population mesurés. Ceci confirme que la tomate est un hôte naturel du pathovar raphani. Ce schéma de typage est en cours d'application pour connaître la diversité de souches isolées de Solanées à graines dans la région Sud-ouest de l'Océan Indien.

Bacterial spot of tomato and pepper (BSTP), a major problem in tropical and subtropical climates, can be caused by several #Xanthomonas genospecies#, #X. euvesicatoria#, #X. vesicatoria#, #X. perforans#, and #X. gardneri.# #X. campestris# pv. #raphani# strains primarily pathogenic to #Brassicaceae# have also been associated with outbreaks of BSTP on tomato. BSTP has been observed in the South West Indian Ocean (SWIO) region but no data is available about the status of #Xanthomonas# species associated with BSTP in this region. A total of 72 strains collected from Comoros, Madagascar, Mauritius, Réunion and the Seychelles were characterized using AFLP (Amplified Fragment Length Polymorphism) and MLSA (MultiLocus Sequence Analysis) based on four housekeeping genes. AFLP and MLSA consistently assigned strains at the species level. All strains were unambiguously classified in one species, namely: #X. euvesicatoria#, #X. vesicatoria#, #X. perforans# and #X. gardneri#. MLSA identified two to three sequence types per genospecies. No #X. campestris# pv. #raphani# strains were identified in the collection. Most of the strains were identified as #X. euvesicatoria# (65 %). MLSA data suggested that sequence variations primarily consisted of synonymous mutations, although a recombination event spanning several hundreds nucleotides was detected for some strains of #X. euvesicatoria# on the atpD gene coding for the F1-F0-ATPase ß subunit. Pathogenicity tests were also performed with pathogenicity profiles of strains consistent with the classification in genospecies. Some pathological variations were primarily observed among strains identified as #X. euvesicatoria#. This study provides for the first time a comprehensive description of the status in the SWIO region of #Xanthomonas# species causing BSTP.