Biology subjects

Behnken, B.

Publications and source records attributed to Behnken, B..

3 recordsLinked to original sources

bioRxiv2026

BAT: an integrated pipeline for gene tree construction, annotation, and functional inference

Gene family functional exploration often requires analyzing motifs, domains, and associated datasets (e.g. gene expression) in the phylogenetic context of a gene tree. As genomic resources become more abundant, local pipelines are needed to analyze gene families of interest with project-specific resources. Here we present BLAST-Align-Tree (BAT), a bioinformatic pipeline for automated gene family phylogeny construction and annotation to enable gene tree exploration. BAT combines a BLAST search of local genome databases with a robust and flexible gene tree construction pipeline that enables multiple modes of annotation. Output visualizations display experimental datasets, custom regex specified amino acid motifs, and protein HMM domain annotations. For flexibility, BAT runs locally and is independent of pre-existing databases, allowing the easy incorporation of custom genomes and datasets. Three primary case studies described here demonstrate the utility of BAT for inferring the function of homologs and orthologs within characterized gene families. BAT is suitable for fine scale phylogenomic analysis of gene families across the tree of life, and default genomes available on installation span model eukaryotes.

bioinformatics↗

bioRxiv2025

Natural variation in expression of a plant immune receptor mediates elicitor sensitivity

Plant immune systems rely on pattern recognition receptors (PRRs) to specifically detect diverse pathogen/pest-associated molecular patterns (PAMPs). While many distinct receptors are known to mediate PAMP recognition, the role of transcriptional regulation of PRRs remains poorly understood. In legume plants, Inceptin Receptor (INR) senses an 11-amino acid peptide, In11, to activate direct and indirect defenses against caterpillar pests. Here we investigated the genetic basis of the rare In11 insensitivity phenotype found in common bean (Phaseolus vulgaris) landraces. Natural variation in the rapid In11-induced ethylene response corresponded with genetic variation at the locus encoding INR itself. Surprisingly, phenotypic variation corresponded with expression level of the INR receptor, rather than coding sequence variation. Promoter sequence variation across 21 accessions of Andean Phaseolus vulgaris, as well as near-isogenic lines (NILs) derived from crosses between an In11-sensitive and insensitive line, corresponded with strength of In11-induced ethylene response. Promoter alleles also corresponded with strength of activation of a luciferase reporter in the heterologous expression model, Nicotiana benthamiana, indicating that cis-element variation is sufficient to drive differences in leaf expression levels. Surprisingly, NILs encoding either WT or the lower expression inr-2 allele did not show differences in resistance to herbivory by beet armyworm (Spodoptera exigua), or in In11-pretreatment protection assays, suggesting that even low INR expression can still mediate effective responses against herbivores despite insensitivity to the In11 elicitor in laboratory assays. Our results demonstrate that natural variation in PRR expression can contribute to differential PAMP responses while not necessarily affecting downstream resistance phenotypes.

plant biology↗

bioRxiv2025

A plant immune receptor mediates tritrophic interactions by linking caterpillar detection to predator recruitment

Plants deploy direct and indirect defenses in response to insect herbivory. The specific antiherbivore responses involve cell surface immune receptors that recognize herbivore associated molecular patterns (HAMPs), yet the ecological relevance of this molecular interplay remains unexplored. We demonstrate that the Inceptin Receptor (INR) encoded by common bean, upon recognition of inceptin, a HAMP in caterpillar oral secretions, orchestrates a tritrophic interaction. Laboratory and field experimentation in Mexico using a naturally occurring inceptin-insensitive mutant and its near-isogenic wild type equivalent, revealed that inceptin recognition by INR activates an herbivore-specific immune pathway, and triggers the emission of a volatile blend that recruits predatory wasps. These findings provide a novel molecular-to-ecological link, revealing how an immune receptor mediates ecologically relevant plant-insect-predator interactions in nature.

plant biology↗