Biology subjects

Delaye, L.

Publications and source records attributed to Delaye, L..

5 recordsLinked to original sources

bioRxiv2026

Phylogenetic correlation between the Type IV Secretion System and HIP1 suggest an adaptation for horizontal gene transfer conserved at the phylum level

Most cyanobacterial genomes are rich in the GCGATCGC octamer, also known as Highly Iterated Palindrome 1 (HIP1). Despite its description over three decades ago, the biological function of this highly abundant sequence is only beginning to be elucidated. HIP1 is recognized by two DNA methylases, DmtA and DmtC, and is characterized by its evolutionary conservation and a quasi-periodic distribution within genomes. However, whether the phylogenetic distribution of HIP1 correlates with the presence of functional categories of protein families remains unknown. Here we investigated whether certain protein families share a phylogenetic distribution with this abundant palindromic sequence across cyanobacterial genomes. Our analysis revealed a strong phylogenetic correlation between several proteins of the Type IV secretion system (T4SS) and the abundance of HIP1. This finding aligns with recent discoveries demonstrating that HIP1 enhances DNA transformation in a methylation-dependent manner in two distinct cyanobacterial species. Consequently, we hypothesize that HIP1 function as a conserved adaptation for horizontal gene transfer (HGT) at the phylum level, potentially by serving as a DNA-uptake recognition sequence in cyanobacteria. Significance statementScientists have long been baffled by the HIP1 sequence, a short, highly common, repetitive DNA pattern found across almost all cyanobacterial genomes. Our study used a whole-genome evolutionary approach and found that the presence of this repetitive pattern is tightly linked to the presence of a cells external DNA uptake system. This tight co-evolutionary relationship suggests that HIP1 isnt just random genomic feature, but a conserved evolutionary adaptation used by the entire cyanobacterial phylum to specifically enhance their ability to acquire new genes from one another.

evolutionary biology↗

bioRxiv2025

Hanseniaspora yeasts from agave fermentations provide insight into intraspecific gene loss

Hanseniaspora species stand out among yeasts for having the smallest genomes, marked by extensive gene family contractions. Consequently, they have been proposed as model organisms for studying the evolution of free-living cells lacking genes otherwise considered essential. Here, we show that Hanseniaspora yeasts are prevalent in agave fermentations used to produce traditional spirits across Mexico. We sequenced the genomes of 15 strains, unambiguously identifying them as H. lachancei, H. pseudoguilliermondii, H. guilliermondii, and H. opuntiae. Comparative genomic analyses revealed dynamic shifts in gene family sizes and compositions, suggesting ongoing gene loss within the fast-evolving branch of this genus. Notably, gene losses varied across functional categories, even among isolates of the same species. Growth assays across diverse stress conditions and carbon sources indicated that these genomic disparities do not directly translate into phenotypic differences. Together, our findings suggest that differential gene loss within species is an active evolutionary process shaping Hanseniaspora genomes, highlighting agave-fermentation populations as valuable models for studying genome reduction in a natural context.

genomics↗

bioRxiv2023

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 4,524 strains from 68 sites in diverse climatic, geographical, and biological contexts. We used MALDI-TOF mass spectrometry for taxonomic classification and a subset of the strains was verified by ITS and D1/D2 sequencing. The most abundant species isolated from all producing regions were Saccharomyces cerevisiae, Pichia kudriavzevii, Pichia manshurica, and Kluyveromyces marxianus. Despite the great diversity of environmental conditions and production practices the composition of yeast communities remained largely homogeneous throughout locations and fermentation stages, even if less abundant but commonly occurring yeasts were considered. Furthermore, ITS and D1/D2 sequencing revealed two candidate new species of Saccharomycetales. To explore the intraspecific variation of the yeasts from agave fermentations, we conducted genome sequencing on four isolates of the non-conventional yeast Kazachstania humilis. The genomes of these four strains were considerably distinct from other genomes of the same species, suggesting that they belong to a different population. 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. TAKE AWAYO_LIWe isolated and identified 4,524 yeast strains from open agave fermentations in Mexico. C_LIO_LIYeast communities remained largely homogeneous throughout diverse locations. C_LIO_LIKazachstania humilis genomes differed significantly from isolates in other regions of the world. C_LIO_LIWe report two candidate new species related to the Pichia clade. C_LI

microbiology↗

bioRxiv2022

Comparing the evolutionary dynamics of predominant SARS-CoV-2 virus lineages co-circulating in Mexico

Over 200 different SARS-CoV-2 lineages have been observed in Mexico by November 2021. To investigate lineage replacement dynamics, we applied a phylodynamic approach and explored the evolutionary trajectories of five dominant lineages that circulated during the first year of local transmission. For most lineages, peaks in sampling frequencies coincided with different epidemiological waves of infection in Mexico. Lineages B.1.1.222 and B.1.1.519 exhibited similar dynamics, constituting clades that likely originated in Mexico and persisted for >12 months. Lineages B.1.1.7, P.1 and B.1.617.2 also displayed similar dynamics, characterized by multiple introduction events leading to a few successful extended local transmission chains that persisted for several months. For the largest B.1.617.2 clades, we further explored viral lineage movements across Mexico. Many clades were located within the south region of the country, suggesting that this area played a key role in the spread of SARS-CoV-2 in Mexico.

evolutionary biology↗

bioRxiv2020

Tracking evolutionary trends towards increasing complexity: a case study in Cyanobacteria

Progressive evolution, the tendency towards increasing complexity, is a controversial issue in Biology, whose resolution requires a proper measurement of complexity. Genomes are the best entities to address this challenge, as they record the history and information gaining of organisms in their ongoing biotic and environmental interactions. Using six metrics of genome complexity, none of which is primarily associated to biological function, we measure genome complexity in 91 genomes from the phylum Cyanobacteria. Several phylogenetic analyses reveal the existence of progressive evolution towards higher genome complexity: 1) all the metrics detect strong phylogenetic signals; 2) ridge regressions detect positive trends towards higher complexity; and 3) classical proofs for progressive evolution (the minimum, the ancestor-descendent and the sub-clade tests), show that some of these positive trends are driven, being mainly due to natural selection. These findings support the existence of progressive genome evolution in this ancient and diverse group of organisms.

evolutionary biology↗