Functional Annotation of Novel Heat Stress-responsive Genes in Rice Utilizing Public Transcriptomes and Structurome
Discuss this preprint
Start a discussion What are Sciety discussions?Listed in
This article is not in any list yet, why not save it to one of your lists.Abstract
Motivation
Life science databases include large collections of public transcriptome and large-scale structural data. The reuse and integration of these datasets may facilitate the identification of understudied genes and enable functional annotation across distantly related species, including plants and humans.
Results
In this study, we used heat stress-responsive genes in rice as a model to functionally annotate previously understudied genes by integrating publicly available transcriptome data with structural information from the AlphaFold Protein Structure Database. Initially, we conducted a meta-analysis of public heat stress-related transcriptome datasets, identified gene groups, and verified stress-related terms through enrichment analysis. Subsequently, we performed structural alignment and sequence alignment between rice and human proteins, focusing on candidates exhibiting low sequence similarity but high structural similarity (LS–HS conditions). We further incorporated supplemental data from public databases, including shared domain information between rice and human. This approach yielded a unique set of LS–HS candidates, notably those associated with metal homeostasis, such as iron and copper metabolism. Overall, our integrative method provided insights into these genes by leveraging diverse, publicly available datasets.
Availability and implementation
The “plant2human workflow” for this analysis is available at https://doi.org/10.48546/WORKFLOWHUB.WORKFLOW.1206.8 .
