Biology subjects

Castelan-Sanchez, H.

Publications and source records attributed to Castelan-Sanchez, H..

3 recordsLinked to original sources

bioRxiv2025

Evolutionary fingerprinting of protein-coding genes in RNA viruses

RNA viruses evolve rapidly to adapt to changing host environments. Much of this adaptation occurs at the level of protein-coding genes. Thus, some of the most well-characterized examples of rapid adaptation have been found in virus proteins that are exposed on the surface of the viral particle, where they mediate host receptor binding and cell entry. To investigate whether surface-exposed proteins and other proteins encoded by viruses exhibit different patterns of evolution under selection, we analyzed 244 protein-coding genes from 28 species of RNA viruses representing 15 taxonomic families. First, we show that gene-wide rates of non-synonymous (dN) and synonymous (dS) substitutions do not differentiate between categories of proteins. To provide a more detailed comparison between genes, we inferred for each alignment the bivariate posterior distribution over a fixed grid of codon site-specific dN and dS values. This distribution is the genes evolutionary fingerprint. Next, we computed the Wasserstein distance for every pair of fingerprints, which is analogous to amount of work required to reshape one distribution to another. After compensating for differences in genetic variation among viruses and proteins, we found that surface-exposed proteins could not be distinguished from non-exposed proteins in the space induced by the Wasserstein distance matrix. However, surface-exposed proteins from enveloped viruses were significantly clustered apart from their counterparts in non-enveloped viruses. In contrast, there was no significant separation between these categories of viruses for proteins with polymerase activity. We show that this pattern is more consistent with relaxed purifying selection than adaptive evolution in proteins associated with viral envelopes.

evolutionary biology↗

bioRxiv2025

Phylogenetic discordance cannot identify genomic reassortment events: a case study with the avian influenza virus H5Nx

Recombination plays an important role in the evolution of RNA viruses, as it allows the exchange of genetic material between viral lineages. Reassortment, a form of recombination specific to segmented genomes, involves the exchange of entire segments and has contributed significantly to the adaptation and spread of influenza viruses through novel genomic combinations, i.e., antigenic shifts. It is usually identified by phylogenetic discordance: differences in the topologies of trees reconstructed from different genomic segments. However, phylogenetic discordance can also result from error in reconstructing trees. To characterize the impact of reconstruction error, we curated a database of n = 11, 765 complete genomes of avian H5Nx influenza A viruses from avian hosts. We found evidence of widespread reassortment as measured by inferred subtree-prune-regraft (SPR) events, consistent with previous studies. Next, we ran replicate simulations of sequence evolution along the reference tree for the segment encoding hemagglutinin (HA), adjusting simulations for the lengths and clock rates of the other segments. These simulations provided a baseline for the expected amount of phylogenetic discordance in the absence of any reassortment. When sampling HA sequences at random from the database to build reference trees, we observed that simulating other segments without reassortment still yielded about 32% as many SPRs as the real segment data on average. The average proportion of SPRs without reassortment was greatly reduced (4%) if we selected an equivalent number of HA sequences retaining the most genetic diversity, which was consistent with the accuracy of phylogenetic reconstruction being the limiting factor. This implies that measuring reassortment by SPRs may have a high false positive rate, and that previous evidence of extensive reassortment in influenza viruses should be interpreted with caution. In addition, we observed that the SPRs reconstructed on simulated trees had significantly shorter distances between the prune and regraft locations than real trees. These results suggest that down-sampling sequences to maximize evolutionary divergence and filtering out the shortest SPRs may be effective measures against false positives.

bioinformatics↗

bioRxiv2023

Inoculation with Pseudomonas fluorescens UM270 alters the maize root-associated endobiome and interacting networks in a milpa model

The traditional milpa system is a polyculture originating in Mesoamerica, whose core is maize (Zea mays L.), associated with squash (Cucurbita spp.) and beans (Phaseolus vulgaris L.). In recent years, milpa-type crops have decreased owing to climate change, rapid population growth, and the excessive use of agrochemicals; therefore, the application of plant growth-promoting rhizobacteria (PGPR) to counteract these negative effects has been little explored. In this study, a maize crop in a milpa system was fertilized with the PGPR Pseudomonas fluorescens UM270, and the endophytic root microbiome (endobiome) of maize was assessed by 16S rRNA and internal transcribed spacer regions (ITS) sequencing. The results showed that UM270 the rhizosphere inoculation of P. fluorescens UM270 did not increase alpha diversity in either monoculture or the milpa, but it did alter the endophytic microbiome of maize plant roots by stimulating the presence of bacterial operational taxonomic units (OTUs) of the genera Burkholderia and Pseudomonas (in a monoculture), whereas in the milpa system, the PGPR stimulated a greater endophytic diversity and the presence of genera such as Burkholderia, Variovorax, and N-fixing rhizobia genera, including Rhizobium, Mesorhizobium and Bradyrhizobium. No clear association was found between fungal diversity and the presence of strain UM270, but beneficial fungi such as Rizophagus irregularis and Exophiala pisciphila were detected in the milpa system. In addition, network analysis revealed unique interactions with species like Stenotrophomonas sp., Burkholderia xenovorans, and Sphingobium yanoikuyae, which would potentially be playing a beneficial role with the plant. To the best of our knowledge, this is the first study in which the root microbiome of maize growing under a milpa model was assessed by bio-inoculation with PGPRs.

plant biology↗