Conservation of the Pal/Rim Pathway in Ustilaginomycetes.

The ability of fungi to effectively sense and internalize signals related to extracellular changing environments is essential for survival. This adaptability is particularly important for fungal pathogens of humans and plants that must sense and respond to drastic environmental changes when colonizing their hosts. One of the most important physicochemical factors affecting fungal growth and development is the pH. Ascomycota fungal species possess mechanisms such as the Pal/Rim pathway for external pH sensing and adaptation. However, the conservation of this mechanism in other fungi, such as Ustilaginomycetes is still little studied. To overcome this knowledge gap, we used a comparative genomic approach to explore the conservation of the Pal/Rim pathway in the 13 best sequenced and annotated Ustilaginomycetes. Our findings reveal that the Rim proteins and the Endosomal Sorting Complex Required for Transport (ESCRT) proteins are conserved in Ustilaginomycetes. They conserve the canonical domains present in Pal/Rim and ESCRT proteins of Ascomycota. This study sheds light on the molecular mechanisms used by these fungi for responding to extracellular stresses such as the pH, and open the door to further experimentations for understanding the molecular bases of the signaling in Ustilaginomycetes.

Genetic modification of Candida maltosa, a non-pathogenic CTG species, reveals EFG1 function.

Candida maltosa is closely related to important pathogenic Candida species, especially C. tropicalis and C. albicans, but it has been rarely isolated from humans. For this reason, through comparative studies, it could be a powerful model to understand the genetic underpinnings of the pathogenicity of Candida species. Here, we generated a cohesive assembly of the C. maltosa genome and developed genetic engineering tools that will facilitate studying this species at a molecular level. We used a combination of short and long-read sequencing to build a polished genomic draft composed of 14 Mbp, 45 contigs and close to 5700 genes. This assembly represents a substantial improvement from the currently available sequences that are composed of thousands of contigs. Genomic comparison with C. albicans and C. tropicalis revealed a substantial reduction in the total number of genes in C. maltosa. However, gene loss seems not to be associated to the avirulence of this species given that most genes that have been previously associated with pathogenicity were also present in C. maltosa. To be able to edit the genome of C. maltosa we generated a set of triple auxotrophic strains so that gene deletions can be performed similarly to what has been routinely done in pathogenic Candida species. As a proof of concept, we generated gene knockouts of EFG1, a gene that encodes a transcription factor that is essential for filamentation and biofilm formation in C. albicans and C. tropicalis. Characterization of these mutants showed that Efg1 also plays a role in biofilm formation and filamentous growth in C. maltosa, but it seems to be a repressor of filamentation in this species. The genome assembly and auxotrophic mutants developed here are a key step forward to start using C. maltosa for comparative and evolutionary studies at a molecular level.

Yeast diversity in open agave fermentations across Mexico.

Yeasts are a diverse group of fungal microorganisms that are widely used to produce fermented foods and beverages. In Mexico, open fermentations are used to obtain spirits from agave plants. Despite the prevalence of this traditional practice throughout the country, yeasts have only been isolated and studied from a limited number of distilleries. To systematically describe the diversity of yeast species from open agave fermentations, here we generate the YMX-1.0 culture collection by isolating 4524 strains from 68 sites with diverse climatic, geographical, and biological contexts. We used MALDI-TOF mass spectrometry for taxonomic classification and validated a subset of the strains by ITS and D1/D2 sequencing, which also revealed two potential novel species of Saccharomycetales. Overall, the composition of yeast communities was weakly associated with local variables and types of climate, yet a core set of six species was consistently isolated from most producing regions. To explore the intraspecific variation of the yeasts from agave fermentations, we sequenced the genomes of four isolates of the nonconventional yeast Kazachstania humilis. The genomes of these four strains were substantially distinct from a European isolate of the same species, suggesting that they may belong to different populations. Our work contributes to the understanding and conservation of an open fermentation system of great cultural and economic importance, providing a valuable resource to study the biology and genetic diversity of microorganisms living at the interface of natural and human-associated environments.

Draft Genome Sequence of a Kazachstania humilis Strain Isolated from Agave Fermentation.

The ascomycetous yeast Kazachstania humilis is an active species in backslopped sourdough and in the spontaneous fermentation of several traditional foods and beverages. Here, we report the draft genome sequence of a K. humilis strain isolated from agave must from a traditional distillery in Mexico.

Whole-Genome DNA Methylation Analysis in Hydrogen Peroxide Overproducing Transgenic Tobacco Resistant to Biotic and Abiotic Stresses.

Epigenetic regulation is a key component of stress responses, acclimatization and adaptation processes in plants. DNA methylation is a stable mark plausible for the inheritance of epigenetic traits, such that it is a potential scheme for plant breeding. However, the effect of modulators of stress responses, as hydrogen peroxide (H2O2), in the methylome status has not been elucidated. A transgenic tobacco model to the CchGLP gene displayed high H2O2 endogen levels correlated with biotic and abiotic stresses resistance. The present study aimed to determine the DNA methylation status changes in the transgenic model to obtain more information about the molecular mechanism involved in resistance phenotypes. The Whole-genome bisulfite sequencing analysis revealed a minimal impact of overall levels and distribution of methylation. A total of 9432 differential methylated sites were identified in distinct genome regions, most of them in CHG context, with a trend to hypomethylation. Of these, 1117 sites corresponded to genes, from which 83 were also differentially expressed in the plants. Several genes were associated with respiration, energy, and calcium signaling. The data obtained highlighted the relevance of the H2O2 in the homeostasis of the system in stress conditions, affecting at methylation level and suggesting an association of the H2O2 in the physiological adaptation to stress functional linkages may be regulated in part by DNA methylation.

Response of transgenic tobacco overexpressing the CchGLP gene to cadmium and aluminium: phenotypic and microRNAs expression changes.

Transgenic tobacco (N. tabacum cv. Xanthi nc) expressing Capsicum chinense CchGLP gene that encodes an Mn-SOD, constitutively produces hydrogen peroxide that increase endogenous ROS levels. Previous studies using these plants against geminivirus infections as well as drought stress confirmed that CchGLP expression conferred resistance against biotic and abiotic stresses. Cadmium (Cd) and Aluminium (Al) contamination in soils are a major ecological concern since they are two of the most widespread toxic elements in terrestrial environments. Trying to explore additional possible tolerance to another stresses in these plants, the aim of this work was to analyse the response to cadmium and aluminium salts during germination and early stages of plantlet development and a differential transcriptome of microRNAs (miRNAs) expression in expressing CchGLP transgenic lines and an azygote non-CchGLP expressing line. Plants were grown in vitro with addition of CdCl2 and AlCl3 at three different concentrations: 100, 300 and 500 µM and 50, 150 and 300 µM, respectively. The results showed higher tolerance to Cd and Al salts evaluated in two CchGLP-expressing transgenic lines L8 and L26 in comparison with the azygous non-CchGLP expressing line L1. Interestingly, L8 under Al stress presented vigorous roots and development of radicular hairs in comparison with azygous control (L1). Differentially expressed miRNAs in the comparison between L8 and L1 were associated with up and down-regulation of target genes related with structural molecule activity and ribosome constituents, as well as down-regulation in proton-transporting V-type ATPase (Vacuolar ATPase or V-ATPase). Moreover, KEGG analysis of the target genes for the differentially expressed miRNAs, led to identification of genes related with metabolic pathways and biosynthesis of secondary metabolites. One possible explanation of the tolerance to Cd and Al displayed in the transgenic tobaccos evaluated, might involve the fact that several down-regulated miRNAs, were found associated with target genes expressing V-ATPase. Specifically, miR7904-5p was down regulated and related with the up-regulation of one V-ATPase. The expression levels of these genes was confirmed by qRT-PCR assays, thus suggesting that a cation transport activity driven by the V-ATPases-dependent proton motive force, might significantly contribute as one mechanism for Cd and Al detoxification by vacuolar compartmentation in these transgenic tobacco plants.

Transcriptional landscapes of Axolotl (Ambystoma mexicanum).

The axolotl (Ambystoma mexicanum) is the vertebrate model system with the highest regeneration capacity. Experimental tools established over the past 100 years have been fundamental to start unraveling the cellular and molecular basis of tissue and limb regeneration. In the absence of a reference genome for the Axolotl, transcriptomic analysis become fundamental to understand the genetic basis of regeneration. Here we present one of the most diverse transcriptomic data sets for Axolotl by profiling coding and non-coding RNAs from diverse tissues. We reconstructed a population of 115,906 putative protein coding mRNAs as full ORFs (including isoforms). We also identified 352 conserved miRNAs and 297 novel putative mature miRNAs. Systematic enrichment analysis of gene expression allowed us to identify tissue-specific protein-coding transcripts. We also found putative novel and conserved microRNAs which potentially target mRNAs which are reported as important disease candidates in heart and liver.