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A pipeline for metatranscriptome analysis of gene expression at the community level of insect microbial symbionts

Grant number: 17/03415-8
Support Opportunities:Scholarships abroad - Research Internship - Post-doctor
Effective date (Start): April 01, 2017
Effective date (End): March 31, 2018
Field of knowledge:Agronomical Sciences - Agronomy - Plant Health
Principal Investigator:Wesley Augusto Conde Godoy
Grantee:Pedro Augusto da Pos Rodrigues
Supervisor: Thomas Girke
Host Institution: Escola Superior de Agricultura Luiz de Queiroz (ESALQ). Universidade de São Paulo (USP). Piracicaba , SP, Brazil
Research place: University of California, Riverside (UCR), United States  
Associated to the scholarship:16/11127-0 - A multi- and interdisciplinary approach to understand spatio-temporal patterns of insect pests and design landscapes for sustainable pest management in tropical agricultural systems, BP.PD


In microbe-host associations, the outcome of interactions within a microbial community helps explain their roles in host fitness, as well as the stability and resilience of these associations over evolutionary time. One approach to gain further insight on how the microbiota responds to environmental changes is by studying gene expression of their components (transcriptome). In general, transcriptomic data analysis relies on reference genomes, which aid in identifying transcripts. However, a major challenge to investigating gene expression of a whole community (metatranscriptome) is dealing with the complexity of working with transcripts from a mixture of organisms, and from which genomes are mostly unavailable. Here we propose a pipeline for community-level metatranscriptome analysis, which adopts network analysis for identifying re-arrangements of gene expression. Specifically, with the use of this pipeline it will be possible to identify emergent patterns of expression in diverse systems of microbe-insect associations, in addition to identification of candidate genes for use in biological control and biotechnology.

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