Inference and analysis of gene coexpression networks in sugarcane and sorghum

• Ano de defesa: 2025
• Autor(a) principal: Pérez, Jorge Mario Muñoz
• Tipo de documento: Tese
• Tipo de acesso: Acesso aberto
• Idioma: eng
• Instituição de defesa: Biblioteca Digitais de Teses e Dissertações da USP
• Palavras-chave em Português: Bioenergy crops; Cana-de-açúcar; Comparative genomics; Cultivos bioenergéticos; Eficiência no uso do nitrogênio; Gene coexpression networks; Genômica comparativa; Nitrogen use efficiency; Pantranscriptoma; Pantranscriptome; Redes de coexpressão gênica; Sorghum; Sorgo; Sugarcane
• Link de acesso: https://www.teses.usp.br/teses/disponiveis/64/64133/tde-25042025-121333/

This Ph.D. thesis exploits publicly available transcriptomic datasets and advanced transcriptomic analysis techniques to investigate gene coexpression networks in two key bioenergy crops: sugarcane and sorghum. By reusing and integrating existing data resources, this study demonstrates the potential to uncover novel insights into complex biological processes using relatively low additional resources. Chapter 1 focuses on gene coexpression networks to dissect nitrogen use efficiency (NUE) in sugarcane, identifying key modules and candidate genes associated with genotype-specific NUE responses. Chapter 2 explores sorghum\'s evolutionary and functional diversity through a pantranscriptome assembled from 18 genotypes, providing a transcriptomic reference for sorghum and offering insights into sorghum genetic architecture. Chapter 3 presents a comparative analysis of gene coexpression networks in sugarcane and sorghum, revealing extensive network rewiring likely driven by polyploidy in sugarcane and identifying conserved transcription-associated protein families correlated with sugar trait in both species. Together, these findings enhance our understanding of gene coexpression networks of these bioenergy crops, uncovering key modules, and candidate genes while providing evidence of the evolutionary constraints that shape the gene coexpression patterns in sugarcane and sorghum. This work underscores the importance of reusing public data as a cost-effective strategy for generating new hypotheses and advancing our understanding of complex plant systems, thereby offering insights for sustainable crop improvement in bioenergy production