Transcriptomic Data Analysis Using the Galaxy Platform
An interesting book chapter presents an overview of a transcriptomics data analysis pipeline using Galaxy, specifically designed for studying gene expression in coffee flowers. This pipeline can be leveraged in genetic improvement programs, for instance, to combat climate change
Recently, Thiely Patricia Fabian Dos Santos, Elodia Sánchez-Barrantes, Luiz Filipe Pereira & Andrés Gatica-Arias published a protocol titled "Transcriptomic Data Analysis Using the Galaxy Platform: Coffee (Coffea arabica L.) Flowers as Example" in the book "Plant Functional Genomics". Maghuly, F. (eds). Methods in Molecular Biology, vol 2787. Humana, New York, NY. You can find it here.
Abstract
Coffee, an important agricultural product for tropical producing countries, is facing challenges due to climate change, including periods of drought, irregular rain distribution, and high temperatures. These changes result in plant water stress, leading to significant losses in coffee productivity and quality. Understanding the processes that affect coffee flowering is crucial for improving productivity and quality. In this chapter, we describe a protocol for transcriptome analysis using available Internet software, mainly in the Galaxy Platform, using RNA-Seq data from flowers collected from different parts of the coffee tree. The methods presented in this chapter provide a comprehensive protocol for transcriptome analysis of differentially expressed genes from flowers of coffee plant. This knowledge can be utilized in coffee genetic improvement programs, particularly in the selection of cultivars that are tolerant to water deficit.
Thanks note : We express our heartfelt gratitude to all the authors for choosing the Galaxy Platform for their analyses, highlighting its efficiency. Sincerely appreciate the opportunity to support their work.