Disentangling plant response to biotic and abiotic stress using HIVE, a novel tool to perform unpaired multi-transcriptomics integration

Description

Abstract Plants live in a constantly changing environment that is often unfavorable or even hostile. Indeed, they developed high phenotypic plasticity that includes rapid responses to aggressive biotic and abiotic factors and adaptations to changing environments. Multiple stresses can occur at the same time, requiring the plants to activate appropriate signaling pathways to respond to both or by prioritising the response to one stress factor. While several studies have been conducted to individual stress factors, only very few studies focus on the simultaneous plant response to multiple stressors. Currently used methods to integrate unpaired experiments consist of performing meta-analysis or finding differentially expressed genes for each condition separately and then selecting the common ones. Although these approaches allowed to find valuable results, they cannot identify non-specific conserved mechanisms that may hold promise for a broader understanding of plant defence response mechanisms. For this purpose, we developed HIVE (Horizontal Integration analysis using Variational AutoEncoders) to analyse horizontally integrated multi-transcriptomics datasets composed of unpaired and/or longitudinal experiments. Briefly, we coupled a variational autoencoder, that captures non-linear relationships and encoded them in the latent space, with a random forest regression and the SHAP explainer to select relevant genes for the studied phenotype. We illustrate the functionality of HIVE to study the transcriptional changes of two Arachis wild species submitted to root-knot nematode Meloidogyne arenaria infection and/or drought stress from seven unpaired experiments. HIVE performed better than the meta-analysis and the state-of-the-art tool and identified novel promising candidates responsible for triggering effective defense responses to biotic and abiotic stress.

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