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The Muller F element (4.2 Mb, ~80 protein-coding genes) is an unusual autosome of Drosophila melanogaster; it is mostly heterochromatic with a low recombination rate. To investigate how these properties impact the evolution of repeats and genes, we manually improved the sequence and annotated the genes on the D. erecta, D. mojavensis, and D. grimshawi F elements and euchromatic domains from the Muller D element. We find that F elements have greater transposon density (25–50%) than euchromatic reference regions (3–11%). Among the F elements, D. grimshawi has the lowest transposon density (particularly DINE-1: 2% vs. 11–27%). F element genes have larger coding spans, more coding exons, larger introns, and lower codon bias. Comparison of the Effective Number of Codons with the Codon Adaptation Index shows that, in contrast to the other species, codon bias in D. grimshawi F element genes can be attributed primarily to selection instead of mutational biases, suggesting that density and types of transposons affect the degree of local heterochromatin formation. F element genes have lower estimated DNA melting temperatures than D element genes, potentially facilitating transcription through heterochromatin. Most F element genes (~90%) have remained on that element, but the F element has smaller syntenic blocks than genome averages (3.4–3.6 vs. 8.4–8.8 genes per block), indicating greater rates of inversion despite lower rates of recombination. Overall, the F element has maintained characteristics that are distinct from other autosomes in the Drosophila lineage, illuminating the constraints imposed by a heterochromatic milieu.

Coffee is an important crop that assures a sustainable economy to farmers in tropical regions. A dramatic concern for coffee production is currently represented by climate change, which threatens the survival of Coffea arabica cultivation worldwide and imposes modifications of the agronomic practices to prevent this risk. The quality of coffee beans depends on optimized protocols of cultivation, ripe berries collection, and removal of the outer fruit layers by dry or wet processes and moisture reduction. Storage and shipment represent two steps where bean quality needs to be preserved by preventing fungal contamination that may impact the final product and form mycotoxins, mainly ochratoxin A. In this review, we describe the challenges faced by the coffee industry to guarantee quality from production to roasting and brewing. An overview of novel technologies, such as the application of starter cultures in fermentation and the exploitation of industrial enzymes in accelerating the process of flavour development in coffee beans, is given. Moreover, the results of studies on microbial populations on coffee and the differences found in fungi, yeasts and bacteria composition among the investigations, are summarized. In particular, this review describes new attempts to contain the development of mycotoxigenic fungi, through the application of antagonistic microorganisms such as S. cerevisiae. The new wave of specialty coffees, i.e., those with a cupping score higher than 85/100, is also presented. It is shown how, through careful coffee production methods and controlled fermentation processes, coffee producers may increase their income by assuring high standards of quality and high added value for the coffee experience sector.

Aims:  This study evaluated the quality and possible hygiene risks related to farm‐made silages by analysing the presence and number of micro‐organisms that influence the preservation and safety in samples from four Italian regions. Methods and Results:  Lactic acid bacteria, clostridia, lactate‐fermenting yeasts and propionibacteria (PAB) were isolated and identified by random amplified polymorphic DNA PCR, sequencing of the V2‐V3 16S rRNA gene region, 5·8S‐ITS rDNA RFLP and species‐specific PCR. The Lactobacillus plantarum cluster was the most numerous and comprised strains mostly isolated from alfalfa silage. The Lactobacillus buchneri cluster, second in number, comprised isolates from both alfalfa and maize silage. Anaerobic spore formers were assigned to the species Clostridium baratii, Clostridium beijerinkii, Clostridium butyricum, Clostridium perfringens, Clostridium saccharolyticum, Clostridium tyrobutyricum and Paenibacillus macerans. Yeast isolates were identified as Candida apicola, Candida mesenterica and Pichia fermentans. PAB strains, detected only in unifeed, were all identified as Propionibacterium acidipropionici. Conclusions:  The occurrence of spoiling micro‐organisms was frequent and the possibility of contamination by potentially pathogenic clostridia was demonstrated. Significance and Impact of the study:  The results suggest the need for improved ensiling practices and appropriate control measures to safeguard the hygienic and nutritional quality of silages produced in farms.