Pectobacterium aquaticum sp. nov., isolated from waterways

International audienceThis work aimed to establish the taxonomic status of six strains (A212-S19-A16T, A127-S21-F16, A105-S21-F16, A104-S21-F16, A101-S19-F16 and A35-S23-M15) isolated from three different waterways in 2015 and 2016 in south-east France. Amplification and sequencing of the gapA housekeeping gene clustered these six strains together inside the genus Pectobacterium outside of already described or proposed Pectobacterium species and supspecies. Phenotypic analysis, using GENIII Biolog plates performed with strains A212-S19-A16T, A105-S21-F16, A101-S19-F16 and the closely related Pectobacterium polaris (CFBP 1403), Pectobacterium carotovorum subsp. odoriferum (CFBP 1878T), ‘ Pectobacterium carotovorum subsp. actinidiae’ (CFBP 7370), Pectobacterium carotovorum subsp. carotovorum (CFBP 2046T), ‘ Pectobacterium carotovorum subsp. brasiliense ’ (CFBP 6617) or the most distantly related Pectobacterium aroidearum (CFBP 8168T) failed to identify specific compounds metabolized by these three strains, but weak activity was specifically observed at pH 5 with these three strains. Illumina sequencing was used to sequence these six strains. Based on phylogenetic data, average nucleotide identity values and in silico DNA–DNA hybridization results, strains A212-S19-A16T, A127-S21-F16, A105-S21-F16, A101-S19-F16, A35-S23-M15 and A104-S21-F16 are suggested to represent a novel species of the genus Pectobacterium , for which the name Pectobacterium aquaticum sp. nov. is proposed. The type strain is A212-S19-A16 T (=CFBP 8637T=NCPPB 4640T)

Draft Genome Sequences of the Type Strains of Three Clavibacter Subspecies and Atypical Peach-Colored Strains Isolated from Tomato

Here, we present the draft genome sequences of 10 Clavibacter sp. strains, including the type strains of different subspecies of Clavibacter michiganensis and a potentially novel species within the genus. Genome lengths of the strains varied between 2,982,864 and 3,288,331 bp, with G+C contents of 72.23 to 73.50%

Gene expression profiles of bovine caruncular and intercaruncular endometrium at implantation

At implantation the endometrium undergoes modifications necessary for its physical interactions with the trophoblast as well as the development of the conceptus. We aim to identify endometrial factors and pathways essential for a successful implantation in the caruncular (C) and the intercaruncular (IC) areas in cattle. Using a 13,257-element bovine oligonucleotide array, we established expression profiles at day 20 of the estrous cycle or pregnancy (implantation), revealing 446 and 1,295 differentially expressed genes (DEG) in C and IC areas, respectively (false discovery rate = 0.08). The impact of the conceptus was higher on the immune response function in C but more prominent on the regulation of metabolism function in IC. The C vs. IC direct comparison revealed 1,177 and 453 DEG in cyclic and pregnant animals respectively (false discovery rate = 0.05), with a major impact of the conceptus on metabolism and cell adhesion. We selected 15 genes including C11ORF34, CXCL12, CXCR4, PLAC8, SCARA5, and NPY and confirmed their differential expression by quantitative RT-PCR. The cellular localization was analyzed by in situ hybridization and, upon pregnancy, showed gene-specific patterns of cell distribution, including a high level of expression in the luminal epithelium for C11ORF34 and MX1. Using primary cultures of bovine endometrial cells, we identified PTN, PLAC8, and CXCL12 as interferon-tau (IFNT) target genes and MSX1 and CXCR7 as IFNT-regulated genes, whereas C11ORF34 was not an IFNT-regulated gene. Our transcriptomic data provide novel molecular insights accounting for the biological functions related to the C or IC endometrial areas and may contribute to the identification of potential biomarkers for normal and perturbed early pregnancy

Massive dysregulation of genes involved in cell signaling and placental development in cloned cattle conceptus and maternal endometrium

A major unresolved issue in the cloning of mammals by somatic cell nuclear transfer (SCNT) is the mechanism by which the process fails after embryos are transferred to the uterus of recipients before or during the implantation window. We investigated this problem by using RNA sequencing (RNA-seq) to compare the transcriptomes in cattle conceptuses produced by SCNT and artificial insemination (AI) at day (d) 18 (preimplantation) and d 34 (postimplantation) of gestation. In addition, endometrium was profiled to identify the communication pathways that might be affected by the presence of a cloned conceptus, ultimately leading to mortality before or during the implantation window. At d 18, the effects on the transcriptome associated with SCNT were massive, involving more than 5,000 differentially expressed genes (DEGs). Among them are 121 genes that have embryonic lethal phenotypes in mice, cause defects in trophoblast and placental development, and/or affect conceptus survival in mice. In endometria at d 18, <0.4% of expressed genes were affected by the presence of a cloned conceptus, whereas at d 34, ∼36% and <0.7% of genes were differentially expressed in intercaruncular and caruncular tissues, respectively. Functional analysis of DEGs in placental and endometrial tissues suggests a major disruption of signaling between the cloned conceptus and the endometrium, particularly the intercaruncular tissue. Our results support a "bottleneck" model for cloned conceptus survival during the periimplantation period determined by gene expression levels in extraembryonic tissues and the endometrial response to altered signaling from clones