Biology subjects

Rocha, V. D. d.

Publications and source records attributed to Rocha, V. D. d..

3 recordsLinked to original sources

bioRxiv2026

COMPARATIVE GENOMIC ANALYSIS OF CORE AND ACCESSORY GENES IN RUST FUNGI REVEALS PATHOGENICITY-ASSOCIATED GENE FAMILIES IN Phakopsora pachyrhizi

Accessory genes are thought to contribute to fungal adaptation and pathogenicity by modulating host immunity, while core genes play crucial roles in maintaining fundamental biological processes. Rust fungi (order Pucciniales) are obligate biotrophic plant-pathogens and infect economically relevant crops. Here, we characterize core and accessory gene repertoires across rust fungi, with a particular focus on Phakopsora pachyrhizi, the causal agent of Asian soybean rust. Across Pucciniales genomes, accessory genes represented the largest fraction of gene content ([~]44.6% on average), whereas core genes accounted for a smaller proportion ([~]18-35%). Notably, variations in accessory gene content among rust fungi are perhaps attributed to lineage-specific gene expansions and losses. Core gene content was positively correlated with total gene number across Pucciniales genomes, suggesting retention after gene duplication events, consistent with their essential biological functions. Among P. pachyrhizi genes expressed during soybean infection, core effectors were associated with cysteine-rich proteins, pectin-degrading enzymes, and SPFH/Band 7 family, while accessory effectors included phosphatidylethanolamine-binding proteins, trehalose phosphatases, and CFEM domain-containing proteins. The in-plant induced core and accessory genes in P. pachyrhizi also comprised multiple families of CAZymes (GH5/GH7 cellulases, CE5 cutinases, CE8 pectinesterases, CE4/GH18 chitin-modifying enzymes); proteases (aspartyl proteases, serine carboxypeptidases, alpha/beta hydrolases); transporters (amino acid permeases, ferric reductase-like transmembrane proteins, and OPT oligopeptide transporter), and transcription factors (bZIP, GATA zinc finger, STE-like, and homeobox KN). Our study highlights that core and accessory gene families have shaped P. pachyrhizi-soybean interactions, identifying promising targets for functional studies aimed at elucidating host-adaptation mechanisms in rust fungi.

genomics↗

bioRxiv2024

The genetic diversity of the soybean rust pathogen Phakopsora pachyrhizi has been driven by two major evolutionary lineages

Phakopsora pachyrhizi, an obligate biotrophic rust fungus, is the causal agent of Asian Soybean Rust (ASR) disease. Here, we utilized whole-genome data to explore the evolutionary patterns and population structure across 45 P. pachyrhizi isolates collected from 1972 to 2017 from diverse geographic regions worldwide. We also characterized in-silico mating-type (MAT) genes of P. pachyrhizi, in the predicted proteome of three isolates, to investigate the sexual compatibility system. Our molecular phylogenetic analysis in P. pachyrhizi inferred two distinct evolutionary lineages structured on a temporal scale, with lineage Pp1 grouping isolates obtained from 1972 to 1994, while more recently collected isolates formed a second lineage, Pp2. We found high levels of genetic diversity in lineage Pp1, whereas lineage Pp2 exhibited a strong clonal genetic structure, with a significant lower diversity. The widespread propagation of P. pachyrhizi clonal spores across soybean-growing regions likely explains the absence of a large-scale spatial genetic structure within each lineage. Two independent isolates (TW72-1 and AU79-1) showed moderate levels of genetic admixture, suggesting potential somatic hybridization between the two P. pachyrhizi lineages. We observed no clear congruence between virulence levels of P. pachyrhizi isolates and their phylogenetic patterns. Our findings support a probable tetrapolar mating system in P. pachyrhizi. Taken together, our study offers new insights into the evolutionary history of P. pachyrhizi and demonstrates that multiple MAT genes are highly expressed during the later stages of soybean infection, suggesting their potential role in the formation of urediniospores within the life cycle of P. pachyrhizi. AUTHOR SUMMARYThe Asian Soybean Rust (ASR) disease, caused by basidiomycetes fungus P. pachyrhizi, represents a critical threat to soybean crops worldwide. With the recent availability of high-quality genome assemblies for P. pachyrhizi, we are committed to exploring the genetic diversity of this destructive pathogen. This study analyzed whole-genome resequencing data from P. pachyrhizi isolates collected over several decades in various geographic regions. We identified recent diversification patterns in P. pachyrhizi, with two major lineages. The origin of the two lineages is likely due to temporal shifts in the genetic structure of P. pachyrhizi. Additionally, we investigated the genes responsible for sexual compatibility, known as mating-type (MAT) genes. Transcriptome data indicated that MAT genes are actively expressed during the later stages of the P. pachyrhizi-soybean infection. We conclude that the evolutionary dynamic of P. pachyrhizi is shaped by divergent lineages, which exhibit varying levels of virulence on differential soybean lines containing ASR resistance genes.

evolutionary biology↗

bioRxiv2023

FROM FOREST TO SAVANNA AND BACK TO FOREST: EVOLUTIONARY HISTORY OF THE GENUS Dimorphandra (LEGUMINOSAE)

The tree genus Dimorphandra comprises 26 species, which are circumscribed into three subgenera. The subgenus Dimorphandra is associated with both rainforests (Amazon and Atlantic Forest) and savanna-like vegetation (Cerrado); whereas the subgenera Pocillum and Phaneropsia are restricted to the Amazon. We obtained DNA sequence data from six gene regions of the chloroplast genome (cpDNA) and the nuclear internal transcribed spacer (ITS) from 17 species of Dimorphandra and 12 closely related species. Bayesian phylogeny and haplotype network analyses together with both ancestral area reconstructions and ecological niche modeling allowed for exploring the late evolutionary history of the genus Dimorphandra. Species within the subgenus Phaneropsia were more closely related to species of the genus Mora than to the remaining congeners in the plastid tree (but not in the ITS tree), casting doubts on the monophyly of Dimorphandra. Such incongruence may be the result of incomplete lineage sorting of ancient polymorphisms. Amazonian lineages (subgenera Pocillum and Phaneropsia) were highly polymorphic and divergent; whereas lineages from either the Cerrado or the Atlantic Forest were genetically depauperate. The Amazon seems to be the likely source of the lineage that gave rise to the extant species of Dimorphandra of the Cerrado. In turn, a lineage that occupied the Cerrado likely gave rise to the extant species that occur in the Atlantic Forest. Habitat shifts may have been a key driving force that shaped the late evolutionary history of Dimorphandra.

evolutionary biology↗