Genome sequencing provides new insights on the distribution of Erwinia amylovora lineages in northern Italy

Erwinia amylovora is a Gram-negative bacterium that colonizes a wide variety of plant species causing recurrent local outbreaks of fire blight in crops of the Rosaceae family. Recent genomic surveys have documented the limited genomic diversity of this species, possibly related to a recent evolutionary bottleneck and a strong correlation between geography and phylogenetic structure of the species. Despite its economic importance, little is known about the genetic variability of co-circulating strains during local outbreaks. Here, we report the genome sequences of 82 isolates of E. amylovora, collected from different host plants in a period of 16 years in Trentino, a small region in the Northeastern Italian Alps that has been characterized by recurrent outbreaks of fire blight in apple orchards. While the genome isolated before 2018 are closely related to other strains already present in Europe, we found a novel subclade composed only by isolates that were sampled starting from 2018 and demonstrate that the endemic population of this pathogen can be composed by mixture of strain

Breeding strategy shapes the composition of bacterial communities in female Nile tilapia reared in a recirculating aquaculture system

publishedVersio

Grapevine (Vitis vinifera L.) varietal assortment and evolution in the Marche region (central Italy)

14openInternationalItalian coauthor/editorItaly is one of the richest countries in terms of grapevine varietal assortment, and the Marche region in central Italy has an ancient winegrowing tradition. Increasing interest in autochthonous grapevine varieties prompted efforts to recover and identify local minor germplasm also in this region, and to search for pedigree relationships and determine the evolution of varietal assortment. In the present study this was done using nuclear and chloroplast microsatellite markers and SNP markers from the Vitis18kSNP chip. Eighteen new genotypes were found, of which seventeen belonged to well-known, less known and even unknown vines found to be specific to the Marche region. The rearranged pedigree highlighted the complex intertwining relationships between Marche varieties. Second-degree relationships were also derived. Some minor Marche varieties have increased the number of parent-offspring related members of Garganega, Sangiovese, Crepolino/Visparola and Sciaccarello, which are varieties already recognised as founders or recurrent parents of many Italian cultivars. Crepolino/Visparola was shown to be a key variety in the evolution of the Marche varietal assortment, having played the role of parent and grandparent, as explained by the presence of this genotype in the region in ancient times. Surprisingly, Semidano, a well-known Sardinian variety, played a clear role as parent or grandparent of three minor Marche varieties, testifying to its presence in central Italy in ancient times. Incrocio Bruni 54 was confirmed as an offspring of Sauvignon and Verdicchio, as declared by the breeder. The parentage of Lacrima was completed: this variety was found to be a spontaneous cross between Nera Rada and Aleatico. A dendrogram of genetic similarity clearly resembled the groups defined with the pedigree reconstruction and it gave an indication of the genetic similarity of the varieties excluded from the strictest parentage links.openCrespan, Manna; Migliaro, Daniele; Larger, Simone; Pindo, Massimo; Palmisano, Massimo; Manni, Alvise; Manni, Elisa; Polidori, Enzo; Sbaffi, Francesco; Silvestri, Quintilio; Silvestroni, Oriana; Velasco, Riccardo; Virgili, Settimio; Camilli, GiuseppeCrespan, M.; Migliaro, D.; Larger, S.; Pindo, M.; Palmisano, M.; Manni, A.; Manni, E.; Polidori, E.; Sbaffi, F.; Silvestri, Q.; Silvestroni, O.; Velasco, R.; Virgili, S.; Camilli, G

Absence of increased genomic variants in the cyanobacterium Chroococcidiopsis exposed to Mars-like conditions outside the space station

Despite the increasing interest in using microbial‑based technologies to support human space exploration, many unknowns remain not only on bioprocesses but also on microbial survivability and genetic stability under non‑Earth conditions. Here the desert cyanobacterium Chroococcidiopsis sp. CCMEE 029 was investigated for robustness of the repair capability of DNA lesions accumulated under Mars‑like conditions (UV radiation and atmosphere) simulated in low Earth orbit using the EXPOSE‑R2 facility installed outside the International Space Station. Genomic alterations were determined in a space‑derivate of Chroococcidiopsis sp. CCMEE 029 obtained upon reactivation on Earth of the space‑exposed cells. Comparative analysis of whole‑genome sequences showed no increased variant numbers in the space‑derivate compared to triplicates of the reference strain maintained on the ground. This result advanced cyanobacteria‑based technologies to support human space exploratio

A dual sgRNA-directed CRISPR/Cas9 construct for editing the fruit-specific β-cyclase 2 gene in pigmented citrus fruits

CRISPR/Cas9 genome editing is a modern biotechnological approach used to improve plant varieties, modifying only one or a few traits of a specific variety. However, this technology cannot be easily used to improve fruit quality traits in citrus, due to the lack of knowledge of key genes, long juvenile stage, and the difficulty regenerating whole plants of specific varieties. Here, we introduce a genome editing approach with the aim of producing citrus plantlets whose fruits contain both lycopene and anthocyanins. Our method employs a dual single guide RNA (sgRNA)-directed genome editing approach to knockout the fruit-specific β-cyclase 2 gene, responsible for the conversion of lycopene to beta-carotene. The gene is targeted by two sgRNAs simultaneously to create a large deletion, as well as to induce point mutations in both sgRNA targets. The EHA105 strain of Agrobacterium tumefaciens was used to transform five different anthocyanin-pigmented sweet oranges, belonging to the Tarocco and Sanguigno varietal groups, and ‘Carrizo’ citrange, a citrus rootstock as a model for citrus transformation. Among 58 plantlets sequenced in the target region, 86% of them were successfully edited. The most frequent mutations were deletions (from -1 to -74 nucleotides) and insertions (+1 nucleotide). Moreover, a novel event was identified in six plantlets, consisting of the inversion of the region between the two sgRNAs. For 20 plantlets in which a single mutation occurred, we excluded chimeric events. Plantlets did not show an altered phenotype in vegetative tissues. To the best of our knowledge, this work represents the first example of the use of a genome editing approach to potentially improve qualitative traits of citrus fruit

IA et Enseignement Supérieur : quels enjeux et impacts ?

LE NUMÉRIQUE DANS L'ESR + LA COLLECTION NUMÉRIQUEL’IA au sommaire de la collection numérique de Noël Pour les fêtes, nous vous offrons… le dernier numéro de la collection numérique de l’année. Le #30 ! Et pour l’alimenter, l’enrichir, lui apporter prospective et réflexion, de grands auteurs ont répondu à notre sollicitation et ont accepté de se pencher sur le berceau de l'IA de l'ESR. Nous vous laissons les découvrir au fil du numéro, approcher l’IA dans sa globalité, prendre conscience des enjeux et écueils, trouver des solutions, réfléchir à demain

Urgence sur les sobriétés numériques !

LE NUMÉRIQUE DANS L'ESR + LA COLLECTION NUMÉRIQUELa collection numérique + Urgence sur les sobriétés numériquesLes mots sont posés dès l’édito par le GDS EcoInfo « Ce numéro consacré à la sobriété numérique est là pour rappeler à la fois l'urgence d'agir, mais également présenter des axes sur lesquels nous pouvons le faire. »Et les ressources sont nombreuses et variées, car les contributeurs ont été nombreux à répondre présent sur un sujet aussi capital.Nous allons donc parler sobriété numérique, Bilan des émissions de gaz à effet de serre, numérique responsable, climat, empreinte environnementale, mais aussi actions concertées, low-tech, régulation, réduction de l’empreinte carbone, écoconception, mooc, obsolescence et décroissance. Encore un numéro riche de sens, d’initiatives, de constats et d’innovations, qui porte un œil attentif et constructif sur une situation critique, mais apporte également la richesse de ceux qui ne se résignent pas et œuvrent au quotidien à un monde meilleur.Et on partage largement ! A lire pour s’enrichir

Bibliographie critique

Pinto Roger, Ferrier Jean-Pierre, Deniniolle Sylvie, van der Essen Alfred, Dreyfus Simone, Larger Dominique, Flory Thiébaut, Feuer Guy, Goy Raymond, Pellet Alain, Labouz Marie-Françoise. Bibliographie critique. In: Annuaire français de droit international, volume 29, 1983. pp. 959-1059