Plant co-expression annotation resource 2.0: uma ferramenta web para a associação de proteínas de função desconhecida a estresses abióticos em plantas

Abstract

The development of genetically modified (GM) crops includes the discovery of candidate genes through bioinformatics analysis, using genomic data, gene expression, among others. Proteins of unknown function (PUF) are interesting targets for GM crop pipelines due to the novelty associated with these targets and also to avoid copyright protections. One method to infer the possible function of PUF is to relate them to factors of interest, such as abiotic stresses, using orthology and coexpression networks, applying the guilt by association approach. The objective of this work is to develop and make available version 2 of the PlantAnnot tool (PlantAnnot2) and the objective of PlantAnnot2 is the discovery of PFD involved in responses to abiotic stresses in plants. For that, genomic data from 67 plants were processed, with some important species tolerant to abiotic stresses. Diamond and InterproScan software were used to discover PUF in all plants. Gene expression data (RNA-seq) related to abiotic stresses were downloaded from NCBI / GEO and used in the LSTrAP software to build coexpression clusters whose members are most likely related to the molecular mechanisms associated with abiotic stress in plants. Groups of orthologous were created with OrthoFinder, then PUF associated with these groups of orthologous and also with coexpression clusters were searched simultaneously. As a result, 2,136,336 genes and 2,714,161 mRNA were stored in Machado, along with their translated proteins. 78,416 PUF were recovered with Diamond and Interproscan analyzes, 91,172 groups of orthologous and 1,975 coexpression clusters were created. A protocol for searching PUF annotations was developed, which retrieves PUF that belong to a group of orthologous that also contain proteins whose mRNA is part of coexpression clusters related to abiotic stresses. Thus, 4,673 PUF were recovered, in version 1 of the system it had been 1,364 PUF. A bibliographic search was carried out on proteins belonging to orthologous groups, for all PUF belonging to the species Pearl millet (Cenchrus americanus), Populus simonii, Oropethium thomaeum and Boea hygrometrica, all known to be tolerant to abiotic stresses (517 PUF). Studies related to abiotic stresses were found, on average, for 67.5% of PUF, in version 1 of the system the percentage was 35%. A web server https://www.machado.cnptia.embrapa.br/plantannot2 is available for free and provides indexed queries for PUF possibly associated with abiotic stresses. PlantAnnot2 is expected to be useful for researchers looking to obtain genes related to responses to abiotic stresses for the production of new GM crops tolerant to the risks of climate change.