Plant Co-expression Annotation Resource: a web server for identifying targets for genetically modified crop breeding...

Area of Science:

• Genomics
• Bioinformatics
• Plant Science

Background:

• Genetically modified (GM) crops require novel genes for development.
• Proteins of unknown function (PUFs) are valuable targets for GM crop innovation.
• Inferring PUF function is crucial for crop improvement.

Purpose of the Study:

• To identify and functionally annotate Proteins of Unknown Function (PUFs) in 53 angiosperm species.
• To associate PUFs with abiotic stress responses using bioinformatics approaches.
• To develop a publicly accessible resource for plant gene discovery.

Main Methods:

• Downloaded and processed genomics data from 53 angiosperms (1,862,010 genes, 2,332,974 RNA).
• Identified 72,266 PUFs using Diamond and InterproScan.
• Constructed co-expression networks using LSTrAP with RNA-seq data related to abiotic stresses.
• Associated PUFs with abiotic stress-related clusters via orthology (OrthoMCL) and guilt-by-association.

Main Results:

• Discovered 72,266 PUFs across 53 plant species.
• Generated co-expression networks revealing gene clusters associated with abiotic stresses.
• Successfully linked numerous PUFs to abiotic stress response pathways.
• Developed the Plantannot web resource (https://www.machado.cnptia.embrapa.br/plantannot) for querying PUF-stress associations.

Conclusions:

• The study provides a method for inferring the function of PUFs in plants.
• Plantannot facilitates the discovery of novel genes for developing climate-resilient GM crops.
• This resource aids researchers in breeding crops for improved stress tolerance.