Integrating metataxonomics and host transcriptomics data in maize

• Grant number: 23/11133-3
• Support Opportunities: Scholarships abroad - Research Internship - Post-doctor
• Start date: February 01, 2024
• End date: January 31, 2025
• Field of knowledge: Biological Sciences - Genetics - Plant Genetics
• Principal Investigator: Diego Mauricio Riano Pachon
• Grantee: Renato Augusto Corrêa dos Santos
• Supervisor: Jason Wallace
• Host Institution: Centro de Energia Nuclear na Agricultura (CENA). Universidade de São Paulo (USP). Piracicaba , SP, Brazil
• Institution abroad: University of Georgia, Athens (UGA), United States
• Associated to the scholarship: 21/11057-0 - Identifying gene co-expression modules with novel transcription factors involved in hemicellulose biosynthesis in C4 grasses, BP.PD

Abstract

CoNekT Grasses is a platform for comparative transcriptome analysis that enables researchers to have insights about gene expression based on expression profiles and co-expression networks. Approaches involving genomics, transcriptomics, and meta-taxonomics have been gaining importance for the understanding of host-microbiome interaction. Therefore, integration of such data in CoNekT Grasses would help us to better understand the host-microbiome system. The availability of paired datasets of gene expression and microbiome for the same samples enables the calculation of association metrics that potentially lead to unique and informative insights. Prof. Wallace's research group and his collaborators recently generated transcriptome and meta-taxonomic data from leaves for approximately 300 maize genotypes representing the genotypic and phenotypic diversity of modern crop varieties (Goodman Maize Association Panel), which are available for this project. Previously, associations between genotype and microbiome composition were analyzed for these samples. In this project, we have two aims, (i) to exploit associations between gene expression and microbiome composition, (ii) to extend CoNekT Grasses to incorporate meta-taxonomic data. The internship abroad comprises a valuable opportunity to study methods for exploiting the relationship between gene expression and microbiome data using maize as a model. Analyses in the platform after incorporating such functionalities will benefit important Brazilian crops in the future. (AU)

Scientific publications

(References retrieved automatically from Web of Science and SciELO through information on FAPESP grants and their corresponding numbers as mentioned in the publications by the authors)

PELLEGRINETTI, THIERRY ALEXANDRE; MONTEIRO, GABRIEL GUSTAVO TAVARES NUNES; LEMOS, LEANDRO NASCIMENTO; DOS SANTOS, RENATO AUGUSTO CORREA; BARROS, ARTUR GOMES; MENDES, LUCAS WILLIAM. PGPg finder : A comprehensive and user-friendly pipeline for identifying plant growth-promoting genes in genomic and metagenomic data. RHIZOSPHERE, v. 30, p. 9-pg., 2024-06-01. (23/07080-1, 19/16043-7, 21/11057-0, 23/11133-3)