Biology subjects

Alvarez-Ponce, D.

Publications and source records attributed to Alvarez-Ponce, D..

7 recordsLinked to original sources

bioRxiv2025

Comparative genomic analyses shed light on the introduction routes of rice-pathogenic Burkholderia gladioli strains into Bangladesh

BackgroundThe gram-negative bacterium Burkholderia gladioli can cause diseases in a wide range of hosts, including humans and plants. In rice, it produces Bacterial Panicle Blight (BPB), an emerging disease that is threatening the production of this staple food worldwide. Recently, BPB has affected several rice fields in Bangladesh, and B. gladioli has been reported as the causative agent in one of these fields, raising questions about how the pathogen was introduced into the country. Understanding the introduction routes into Bangladesh and the pathogenicity mechanisms of B. gladioli is essential to develop sustainable management strategies to control BPB. ResultsTo investigate the origin of pathogenic B. gladioli strains and their introduction routes into Bangladesh, we sequenced the complete genomes of 19 strains isolated from symptomatic rice panicles from four major rice-growing districts of the country (Rangpur, Faridpur, Natore, and Mymensingh). A phylogenetic analysis encompassing all 320 publicly available B. gladioli genomes along with the 19 newly sequenced genomes revealed five independent introduction events into Bangladesh--four of which showed close phylogenetic links to clinical isolates from the USA--and no evidence of inter-district dissemination within the country. Many host transitions (35 human-to-plant and 1 plant-to-human) were inferred across the phylogeny, highlighting the pathogens versatile and cross-kingdom transmission dynamics. Analysis of the presence/absence patterns of 37 virulence-related genes across all 339 B. gladioli strains indicated that human-to-plant host transitions often coincided with loss of the tsr and motB genes--which are associated with bacterial motility--, suggesting convergent adaptive shifts in response to host switches. ConclusionOur findings shed light on the introduction pathways of pathogenic B. gladioli strains into Bangladesh and highlight specific virulence-related genes as potentially responsible for cross-kingdom host shifts.

genomics↗

bioRxiv2025

The publication and citation gender gap in Biology: bibliometric analysis of Biology faculty at top United States universities

Women are underrepresented in academia, especially in top research institutions, STEM departments, and senior positions. A number of studies have shown that, on average, female academics publish fewer articles per year, are less cited, and are promoted more slowly than their male peers. Other studies, however, have found that these gender differences are absent or even reversed in certain fields and social contexts, highlighting the importance of evaluating the different dimensions of the gender gap separately within each field and context. We obtained a census of 2104 female and 3721 male tenured and tenure-eligible faculty members affiliated with Biology Departments at the 146 United States R1 universities. We show that women represent 46.94% of Assistant Professors, 38.51% of Associate Professors and 30.09% of Professors in our dataset. Compared with their male peers, female faculty members tend to produce fewer publications per year (even after controlling for career stage and university ranking), to publish in lower-impact factor journals, and to be less cited (even after controlling for career length, career stage, number of publications, average impact factor of the journals in which they publish, and university ranking). Despite their lower publication and citation rates, female faculty members in our dataset require the same amount of time to attain the rank of Professor as their male peers.

scientific communication and education↗

bioRxiv2022

The Codon Statistics Database: a Database of Codon Usage Bias

MotivationMost amino acids can be encoded by a set of synonymous codons. Often, for any given amino acid, certain codons are significantly more used than others, a phenomenon known as codon usage bias. The genomes of different species differ in the frequencies at which they use each codon (e.g., a codon that is highly used in one species may be lowly used in another species). In addition, within any given genome, genes differ in their degree of codon bias, with highly expressed genes being more likely to use preferred codons. Knowing the codons that are preferred by a certain genome, and the amount of codon bias exhibited by each gene, has multiple applications (e.g., in heterologous expression, gene prediction, or phylogenetic inference). ResultsWe have developed the Codon Statistics Database, an online database that contains codon usage statistics for all the species with reference or representative genomes in RefSeq. The user can search for any species and access two sets of tables. One set lists, for each codon, the frequency, the Relative Synonymous Codon Usage (RSCU), and whether the codon is preferred. Another set of tables lists, for each gene, its GC content, Effective Number of Codons (ENC), Codon Adaptation Index (CAI), and frequency of optimal codons (Fop). Equivalent tables can be accessed for 1) all nuclear genes, 2) nuclear genes encoding ribosomal proteins, 3) mitochondrial genes and 4) chloroplastic genes (if available in the relevant assembly). The user can also search for any taxonomic group (e.g., "primates") and obtain a table comparing all the species in the group. AvailabilityThe database is free to access without registration at http://codonstatsdb.unr.edu.

bioinformatics↗

bioRxiv2022

The last missing piece of the Triangle of U: the evolution of the tetraploid Brassica carinata genome

Ethiopian mustard (Brassica carinata) is an ancient crop with significant potential for expanded cultivation as a biodiesel feedstock. The remarkable stress resilience of B. carinata and desirable seed fatty acid profile addresses the ongoing food vs. fuel debate as the crop is productive on marginal lands otherwise not suitable for even closely related species. B. carinata is one of six key Brassica spp. that share three major genomes: three diploid species (AA, BB, CC) that spontaneously hybridized in a pairwise manner, forming three allotetraploid species (AABB, AACC, and BBCC). Each of these genomes has been researched extensively, except for that of B. carinata. In the present study, we report a high-quality, 1.31 Gbp genome with 156.9-fold sequencing coverage for B. carinata var. Gomenzer, completing and confirming the classic Triangle of U, a theory of the evolutionary relationships among these six species that arose almost a century ago. Our assembly provides insights into the genomic features that give rise to B. carinatas superior agronomic traits for developing more climate-resilient Brassica crops with excellent oil production. Notably, we identified an expansion of transcription factor networks and agronomically-important gene families. Completing the Triangle of U comparative genomics platform allowed us to examine the dynamics of polyploid evolution and the role of subgenome dominance in domestication and agronomical improvement.

genetics↗

bioRxiv2020

Divergent DNA methylation signatures underlying X chromosome regulation in marsupials and eutherians

X chromosome inactivation (XCI) mediated by differential DNA methylation between sexes is well characterized in eutherian mammals. Although XCI is shared between eutherians and marsupials, the role of DNA methylation in marsupial XCI remains contested. Here we examine genome-wide signatures of DNA methylation from methylation maps across fives tissues from a male and female koala (Phascolarctos cinereus) and present the first whole genome, multi-tissue marsupial "methylome atlas." Using these novel data, we elucidate divergent versus common features of marsupial and eutherian DNA methylation. First, tissue-specific differential DNA methylation in marsupials primarily occurs in gene bodies. Second, females show significant global reduction (hypomethylation) of X chromosome DNA methylation compared to males. We show that this pattern is also observed in eutherians. Third, on average, promoter DNA methylation shows little difference between male and female koala X chromosomes, a pattern distinct from that of eutherians. Fourth, the sex-specific DNA methylation landscape upstream of Rsx, the primary lncRNA associated with marsupial XCI, is consistent with the epigenetic regulation of female-(and presumably inactive X chromosome-) specific expression. Finally, we utilize the prominent female X chromosome hypomethylation and classify 98 previously unplaced scaffolds as X-linked, contributing an additional 14.6 Mb (21.5 %) to genomic data annotated as the koala X chromosome. Our work demonstrates evolutionarily divergent pathways leading to functionally conserved patterns of XCI in two deep branches of mammals.

evolutionary biology↗

bioRxiv2019

Molecular chaperones accelerate the evolution of their protein clients in yeast

Protein stability is a major constraint on protein evolution. Molecular chaperones, also known as heat-shock proteins, can relax this constraint and promote protein evolution by diminishing the deleterious effect of mutations on protein stability and folding. This effect, however, has only been stablished for a few chaperones. Here, we use a comprehensive chaperone-protein interaction network to study the effect of all yeast chaperones on the evolution of their protein substrates, that is, their clients. In particular, we analyze how yeast chaperones affect the evolutionary rates of their clients at two very different evolutionary time scales. We first study the effect of chaperone-mediated folding on protein evolution over the evolutionary divergence of Saccharomyces cerevisiae and S. paradoxus. We then test whether yeast chaperones have left a similar signature on the patterns of standing genetic variation found in modern wild and domesticated strains of S. cerevisiae. We find that genes encoding chaperone clients have diverged faster than genes encoding nonclient proteins when controlling for their number of protein-protein interactions. We also find that genes encoding client proteins have accumulated more intra-specific genetic diversity than those encoding nonclient proteins. In a number of multivariate analyses, controlling by other well-known factors that affect protein evolution, we find that chaperone dependence explains the largest fraction of the observed variance in the rate of evolution at both evolutionary time scales. Chaperones affecting rates of protein evolution mostly belong to two major chaperone families: Hsp70s and Hsp90s. Our analyses show that protein chaperones, by virtue of their ability to buffer destabilizing mutations and their role in modulating protein genotype-phenotype maps, have a considerable accelerating effect on protein evolution.

evolutionary biology↗

bioRxiv2018

Molecular evolution of DNMT1 in vertebrates: duplications in marsupials followed by positive selection

DNA methylation is mediated by a conserved family of DNA methyltransferases (Dnmts). The human genome encodes five Dnmts: Dnmt1, Dnmt2, Dnmt3a, Dnmt3b and Dnmt3L. Despite their high degree of conservation among different species, genes encoding Dnmts have been duplicated and/or lost in multiple lineages throughout evolution, indicating that the DNA methylation machinery has some potential to undergo evolutionary change. However, little is known about the extent to which this machinery, or the methylome, varies among vertebrates. Here, we study the molecular evolution of Dnmt1, the enzyme responsible for maintenance of DNA methylation patterns after replication, in 79 vertebrate species. Our analyses show that all studied species exhibit a single copy of DNMT1, with the exception of tilapia and marsupials (tammar wallaby, koala, Tasmanian devil and opossum), each of which exhibits two apparently functional DNMT1 copies. Our phylogenetic analyses indicate that DNMT1 duplicated before the divergence of marsupials (i.e., at least ~75 million years ago), thus giving rise to two DNMT1 copies in marsupials (copy 1 and copy 2). In the opossum lineage, copy 2 was lost, and copy 1 recently duplicated again, generating three DNMT1 copies: two putatively functional genes (copy 1a and 1b) and one pseudogene (copy 1{psi}). Both marsupial copies (DNMT1 copies 1 and 2) are under purifying selection, and copy 2 exhibits elevated rates of evolution and signatures of positive selection, suggesting a scenario of neofunctionalization. This gene duplication might have resulted in modifications in marsupial methylomes and their dynamics.

evolutionary biology↗