Biology subjects

Gonzalez-Pech, R.

Publications and source records attributed to Gonzalez-Pech, R..

3 recordsLinked to original sources

bioRxiv2025

Evaluation of full-length 16S rRNA amplicon sequencing using Oxford Nanopore Technologies for diversity surveys of understudied microbiomes

O_LIThe use of long-read sequencing using portable Oxford Nanopore Technologies (ONT) is becoming increasingly popular in the study of host-associated microbiomes. However, its application has not yet been optimized for characterizing understudied microbiomes, such as those in marine environments. C_LIO_LIWe evaluated the accuracy and consistency of ONT sequencing of full-length 16S rRNA genes for diversity surveys of symbiotic dinoflagellate (family Symbiodiniaceae) microbiomes. C_LIO_LIWhen comparing amplicon sequencing of the full-length bacterial 16S rRNA gene with only its V4 hypervariable gene region using a known microbial community, the former recapitulated the bacterial taxonomic composition more accurately. C_LIO_LIONT sequencing was also highly consistent between sequencing runs and flow cells. C_LIO_LILong-read sequencing technologies enable microbiome surveys using the full-length 16S rRNA gene, achieving higher accuracy and resolution. C_LIO_LIThis work validates ONT long-read sequencing as a powerful tool for marine microbiome studies to catalyze advancements in the fields of ecology and evolution, resource management, and conservation. C_LI

ecology↗

bioRxiv2020

Comparative genomics supports that Brazilian bioethanol Saccharomyces cerevisiae comprise a unified group of domesticated strains related to cachaca spirit yeasts

Ethanol production from sugarcane is a key renewable fuel industry in Brazil. Major drivers of this alcoholic fermentation are Saccharomyces cerevisiae strains that originally were contaminants to the system and yet prevail in the industrial process. Here we present newly sequenced genomes (using Illumina short-read and PacBio long-read data) of two monosporic isolates (H3 and H4) of the S. cerevisiae PE-2, a predominant bioethanol strain in Brazil. The assembled genomes of H3 and H4, together with 42 draft genomes of sugarcane-fermenting (fuel ethanol plus cachaca) strains, were compared against those of the reference S288c and diverse S. cerevisiae. All genomes of bioethanol yeasts have amplified SNO2(3)/SNZ2(3) gene clusters for vitamin B1/B6 biosynthesis, and display ubiquitous presence of SAM-dependent methyl transferases, a gene family rare in S. cerevisiae. Widespread amplifications of quinone oxidoreductases YCR102C/YLR460C/YNL134C, and the structural or punctual variations among aquaporins and components of the iron homeostasis system, likely represent adaptations to industrial fermentation. Interesting is the pervasive presence among the bioethanol/cachaca strains of a five-gene cluster (Region B) that is a known phylogenetic signature of European wine yeasts. Combining genomes of H3, H4, and 195 yeast strains, we comprehensively assessed whole-genome phylogeny of these taxa using an alignment-free approach. The 197-genome phylogeny substantiates that bioethanol yeasts are monophyletic and closely related to the cachaca and wine strains. Our results support the hypothesis that biofuel-producing yeasts in Brazil may have been co-opted from a pool of yeasts that were pre-adapted to alcoholic fermentation of sugarcane for the distillation of cachaca spirit, which historically is a much older industry than the large-scale fuel ethanol production.

genomics↗

bioRxiv2017

Symbiodinium genomes reveal adaptive evolution of functions related to symbiosis

Symbiosis between dinoflagellates of the genus Symbiodinium and reef-building corals forms the trophic foundation of the worlds coral reef ecosystems. Here we present the first draft genome of Symbiodinium goreaui (Clade C, type C1: 1.03 Gbp), one of the most ubiquitous endosymbionts associated with corals, and an improved draft genome of Symbiodinium kawagutii (Clade F, strain CS-156: 1.05 Gbp), previously sequenced as strain CCMP2468, to further elucidate genomic signatures of this symbiosis. Comparative analysis of four available Symbiodinium genomes against other dinoflagellate genomes led to the identification of 2460 nuclear gene families that show evidence of positive selection, including genes involved in photosynthesis, transmembrane ion transport, synthesis and modification of amino acids and glycoproteins, and stress response. Further, we identified extensive sets of genes for meiosis and response to light stress. These draft genomes provide a foundational resource for advancing our understanding Symbiodinium biology and the coral-algal symbiosis.

genomics↗