Although pathogenic bacteria are the targets of antibiotics, these drugs also affect hundreds of commensal or mutualistic species. Moreover, the use of antibiotics is not only restricted to the treatment of infections but is also largely applied in agriculture and in prophylaxis. During this work, we tested the hypothesis that there is a correlation between the number and the genomic location of antibiotic resistance (AR) genes and virulence factor (VF) genes. We performed a comprehensive study of 16,632 reference bacterial genomes in which we identified and counted all orthologues of AR and VF genes in each of the locations: chromosomes, plasmids, or in both locations of the same genome. We found that, on a global scale, no correlation emerges. However, some categories of AR and VF genes co-occur preferentially, and in the mobilome, which supports the hypothesis that some bacterial pathogens are under selective pressure to be resistant to specific antibiotics, a fact that can jeopardize antimicrobial therapy for some human-threatening diseases.

The slow-melting flesh (SMF) trait in peach [Prunus persica (L.) Batsch] defines a slower process of postharvest fruit-softening than the prevalent melting flesh (MF) types. This gives a longer shelf life and a delayed harvest-time resulting in better fruit quality. Unlike other known fruit texture traits, SMF is difficult to measure and has a complex inheritance. We examined this character over 2 years in the offspring of two crosses, both with “Big Top,” an SMF nectarine, as the female parent, and with a melting flesh (MF) nectarine as the male parent (“Armking” and “Nectaross”). Following harvest, a texturometer was used to provide a textural profile analysis, and fruit firmness evolution was measured with a penetrometer over a period of 5 days’ storage at 20 °C. Linkage maps were constructed with a high-density SNP chip, and a phenotype-genotype analysis allowed the detection of three independent genomic regions where most QTLs (quantitative trait loci) were located. Two of these, on linkage groups 4 and 5, explained the variability for two characters—maturity date and firmness loss—that is, the QTL on linkage group 4 found in the MF parents and that on linkage group 5 in Big Top. A third region on linkage group 6, which identified a QTL for maturity date only in Armking, has no apparent association to the softening process. The relationship between maturity date and fruit-firmness loss and a hypothesis on the inheritance of the SMF character are discussed.

Cork oak (Quercus suber L.) is an ecologically and economically important evergreen tree species native to the Mediterranean region and widespread in southwest Europe and northwest Africa. An improved genome assembly of cork oak using a combination of Illumina and PacBio sequencing is presented in this study. The assembled genome contains 2351 scaffolds longer than 1000 bp, accounting for 765.7 Mbp of genome size, L90 of 755, and a N50 of 1.0 Mbp, with 40,131 annotated genes. The repetitive sequences constitute 53.6% of the genome. The genome sequences of chloroplast and mitochondrion were determined for the first time, with a genome size of 161,179 bp and 531,858 bp, respectively. Phylogenetic analysis based on complete chloroplast genome sequence showed that Q. suber is closely related to Quercus variabilis, two cork-producing species with commercial use. All data generated are available through the public databases, being ready to be used without restrictions. This study provides an improved nuclear genome assembly together with the organelle genomes of cork oak. These resources will be useful for further breeding strategies and conservation programs and for comparative genomic studies in oak species.

This study aimed to analyse the chemical profile and biological activities of 29 accessions of Brassica rapa (turnips) and 9 of Brassica napus (turnips and seeds) collections, maintained ex situ in Portugal. HPLC-HRMS allowed the determination of glucosinolates (GLS) and polyphenolic compounds. The antioxidant and antimicrobial activities were determined by using relevant assays. The chemical profiles showed that glucosamine, gluconasturtiin, and neoglucobrassin were the most abundant GLS in the extracts from the turnip accessions. Minor forms of GLS include gluconapoleiferin, glucobrassicanapin, glucoerucin, glucobrassin, and 4-hydroxyglucobrassin. Both species exhibited strong antioxidant activity, attributed to glucosinolates and phenolic compounds. The methanol extracts of Brassica rapa accessions were assessed against a panel of five Gram-negative bacteria (Enterobacter cloacae, Escherichia coli, Pseudomonas aeruginosa, Salmonella enterica subsp. enterica serovar, and Yersinia enterocolitica) and three Gram-positive bacteria (Bacillus cereus, Listeria monocytogenes, and Staphylococcus aureus). The extracts exhibited activity against S. enterica and S. aureus, and two showed inhibitory activity against E. coli and Y. enterocolitica. This study provides valuable insights into the chemical composition and biological properties of Brassica rapa and Brassica napus collections in Portugal. The selected accessions can constitute potential sources of natural antioxidants and bioactive compounds, which can be used in breeding programs and improving human health and to promote healthy food systems.