Decoding the chromosome-scale genome of the nutrient-rich Agaricus subrufescens: a resource for fungal biology and biotechnology.

Agaricus subrufescens, also known as the "sun mushroom," has significant nutritional and medicinal value. However, its short shelf life due to the browning process results in post-harvest losses unless it's quickly dehydrated. This restricts its availability to consumers in the form of capsules. A genome sequence of A. subrufescens may lead to new cultivation alternatives or the application of gene editing strategies to delay the browning process. We assembled a chromosome-scale genome using a hybrid approach combining Illumina and Nanopore sequencing. The genome was assembled into 13 chromosomes and 31 unplaced scaffolds, totaling 44.5 Mb with 96.5% completeness and 47.24% GC content. 14,332 protein-coding genes were identified, with 64.6% of the genome covered by genes and 23.41% transposable elements. The mitogenome was circularized and encoded fourteen typical mitochondrial genes. Four polyphenol oxidase (PPO) genes and the Mating-type locus were identified. Phylogenomic analysis supports the placement of A. subrufescens in the Agaricomycetes clade. This is the first available genome sequence of a strain of the "sun mushroom." Results are available through a Genome Browser (https://plantgenomics.ncc.unesp.br/gen.php?id=Asub) and can support further fungal biological and genomic studies.

Comparative genomics study of Staphylococcus aureus isolated from cattle and humans reveals virulence patterns exclusively associated with bovine clinical mastitis strains.

Staphylococcus aureus causes nosocomial and intramammary infections in humans and cattle, respectively. A large number of virulence factors are thought to play important roles in the pathogenesis of this bacterium. Currently, genome-wide and data-analysis studies are being used to better understand its epidemiology. In this study, we conducted a genome wide comparison and phylogenomic analyses of S. aureus to find specific virulence patterns associated with clinical and subclinical mastitis strains in cattle and compare them with those of human origin. The presence/absence of key virulence factors such as adhesin, biofilm, antimicrobial resistance, and toxin genes, as well as the phylogeny and sequence type of the isolates were evaluated. A total of 248 genomes (27 clinical mastitis, 43 subclinical mastitis, 21 milk, 53 skin-related abscesses, 49 skin infections, and 55 pus from cellulitis) isolated from 32 countries were evaluated. We found that the cflA, fnbA, ebpS, spa, sdrC, coa, emp, vWF, atl, sasH, sasA, and sasF adhesion genes, as well as the aur, hglA, hglB, and hglC toxin genes were highly associated in clinical mastitis strains. The strains had diverse genetic origins (72 protein A and 48 sequence types with ST97, ST8 and ST152 being frequent in isolates from clinical mastitis, abscess, and skin infection, respectively). Further, our phylogenomic analyses suggested that zoonotic and/or zooanthroponotic transmission may have occurred. These findings contribute to a better understanding of S. aureus epidemiology and the relationships between adhesion mechanisms, biofilm formation, antimicrobial resistance, and toxins and could aid in the development of improved vaccines and strain genotyping methods.

The complete mitochondrial genome of carnivorous Genlisea tuberosa (Lentibulariaceae): Structure and evolutionary aspects.

Sequenced genomic data for carnivorous plants are scarce, especially regarding the mitogenomes (MTs) and further studies are crucial to obtain a better understanding of the topic. In this study, we sequenced and characterized the mitochondrial genome of the tuberous carnivorous plant Genlisea tuberosa, being the first of its genus to be sequenced. The genome comprises 729,765 bp, encoding 80 identified genes of which 36 are protein-coding, 40 tRNA, four rRNA genes, and three pseudogenes. An intronic region from the cox1 gene was identified that encodes an endonuclease enzyme that is present in the other sequenced species of Lentibulariaceae. Chloroplast genes (pseudogene and complete) inserted in the MT genome were identified, showing possible horizontal transfer between organelles. In addition, 50 pairs of long repeats from 94 to 274 bp are present, possibly playing an important role in the maintenance of the MT genome. Phylogenetic analysis carried out with 34 coding mitochondrial genes corroborated the positioning of the species listed here within the family. The molecular dynamism in the mitogenome (e.g. the loss or pseudogenization of genes, insertion of foreign genes, the long repeats as well as accumulated mutations) may be reflections of the carnivorous lifestyle where a significant part of cellular energy was shifted for the adaptation of leaves into traps molding the mitochondrial DNA. The sequence and annotation of G. tuberosa's MT will be useful for further studies and serve as a model for evolutionary and taxonomic clarifications of the group as well as improving our comprehension of MT evolution.

The first complete plastome of Mimusops coriacea (A. DC.) Miq. (Sapotaceae).

Mimusops coriacea (A. DC.) Miq. (Sapotoideae, Sapotaceae, Ericales) is native to Madagascar and the Comoro Islands. This species is cultivated in many countries around the world and grows on sand in coastal vegetation. Here we sequenced, assembled, and annotated the first complete chloroplast genome of M. coriacea. The newly assembled chloroplast was analyzed with other available chloroplasts of Sapotaceae. Our results found a general conserved structure. The complete chloroplast genome has 159,689 bp, including 133 genes distributed in four regions: a large single-copy region of 88,887 bp, a small single-copy region of 18,618 bp, and two inverted repeats of 26,092 bp each. Our maximum likelihood phylogenetic tree was generated with 80 protein-coding genes and recovered a monophyletic Sapotaceae sister to a clade formed by Ebenaceae + Primulaceae. In our analysis, Mimusops coriacea clustered with the other eight species of Sapotaceae included in the study.

Calophyllaceae plastomes, their structure and insights in relationships within the clusioids.

A complete chloroplast genome is not yet available for numerous species of plants. Among the groups that lack plastome information is the clusioid clade (Malpighiales), which includes five families: Bonnetiaceae, Calophyllaceae, Clusiaceae, Hypericaceae, and Podostemaceae. With around 2200 species, it has few published plastomes and most of them are from Podostemaceae. Here we assembled and compared six plastomes from members of the clusioids: five from Calophyllaceae (newly sequenced) and one from Clusiaceae. Putative regions for evolutionary studies were identified and the newly assembled chloroplasts were analyzed with other available chloroplasts for the group, focusing on Calophyllaceae. Our results mostly agree with recent studies which found a general conserved structure, except for the two Podostemaceae species that have a large inversion (trnK-UUU-rbcL) and lack one intron from ycf3. Within Calophyllaceae we observed a longer LSC and reduced IRs in Mahurea exstipulata, resulting in some genic rearrangement, and a short inversion (psbJ-psbE) in Kielmeyera coriacea. Phylogenetic analyses recovered the clusioids and the five families as monophyletic and revealed that conflicts in relationships reported in the literature for the group agree with nodes concentrating uninformative or conflicting gene trees. Our study brings new insights about clusioid plastome architecture and its evolution.

Genomic comparisons and phylogenetic analysis of mastitis-related staphylococci with a focus on adhesion, biofilm, and related regulatory genes.

Mastitis is a common and costly disease on dairy farms, commonly caused by Staphylococcus spp. though the various species are associated with different clinical outcomes. In the current study, we performed genomic analyses to determine the prevalence of adhesion, biofilm, and related regulatory genes in 478 staphylococcal species isolated from clinical and subclinical mastitis cases deposited in public databases. The most prevalent adhesin genes (ebpS, atl, pls, sasH and sasF) were found in both clinical and subclinical isolates. However, the ebpS gene was absent in subclinical isolates of Staphylococcus arlettae, S. succinus, S. sciuri, S. equorun, S. galinarum, and S. saprophyticus. In contrast, the coa, eap, emp, efb, and vWbp genes were present more frequently in clinical (vs. subclincal) mastitis isolates and were highly correlated with the presence of the biofim operon (icaABCD) and its transcriptional regulator, icaR. Co-phylogenetic analyses suggested that many of these adhesins, biofilm, and associated regulatory genes could have been horizontally disseminated between clinical and subclinical isolates. Our results further suggest that several adhesins, biofilm, and related regulatory genes, which have been overlooked in previous studies, may be of use for virulence profiling of mastitis-related Staphylococcus strains or as potential targets for vaccine development.

Genlisea hawkingii (Lentibulariaceae), a new species from Serra da Canastra, Minas Gerais, Brazil.

Genlisea hawkingii, which is a new species of Genlisea subgen. Tayloria (Lentibulariaceae) from cerrado in southwest Brazil, is described and illustrated. This species has been found in only one locality thus far, in the Serra da Canastra, which is located in the Delfinópolis municipality in Minas Gerais, Brazil. The new species is morphologically similar to Genlisea violacea and G. flexuosa, but differs from them in having a corolla with a conical and curved spur along with sepals with an acute apex and reproductive organs that only have glandular hairs. Moreover, it is similar to G. uncinata's curved spur. G. hawkingii is nested within the subgen. Tayloria clade as a sister group to all the other species of this subgenus. Therefore, both morphological and phylogenetic results strongly support G. hawkingii as a new species in the subgen. Tayloria.