Systems Biology as a Tool to Uncover Interdisciplinary Links within the Complex Forest Tree System

Abstract

Individual or multi-omics analyses (i.e. genomics, transcriptomics, proteomics, and metabolomics) have gained popularity among plant researchers due to the possibility of analyzing different molecular levels. Over the last decade, the technological improvement in high-throughput sequencing and identification of different molecules has contributed significantly to reducing the costs of omics analysis, leading to a scenario in which researchers are combining multiple omics datasets in comprehensive multi-omics experiments. The integration of omics experiments is the premise of system biology, which allows a holistic understanding of cellular mechanisms and regulatory processes and uncovers hidden associations at the different levels of cell organization. However, due to their inherent data differences, the integration of data obtained from multiple omics platforms remains an ongoing challenge. In this chapter, we thoroughly examine the main methods currently in use to integrate metabolomics with other omics datasets as well as examples of integrated analyses of metabolomics with genomics, transcriptomics, and proteomics data. In addition, we discuss the use of systems biology in metabolite annotation and the main challenges regarding multi-omics integrative approaches in forestry research.