Comparative genomics approaches to understanding and manipulating plant metabolism

Over 3000 genomes, including numerous plant genomes, are now sequenced. However, their annotation remains problematic as illustrated by the many conserved genes with no assigned function, vague annotations such as ‘kinase’, or even wrong ones. Around 40% of genes of unknown function that are conserved between plants and microbes are probably metabolic enzymes or transporters; finding functions for these genes is a major challenge. Comparative genomics has correctly predicted functions for many such genes by analyzing genomic context, and gene fusions, distributions and co-expression. Comparative genomics complements genetic and biochemical approaches to dissect metabolism, continues to increase in power and decrease in cost, and has a pivotal role in modeling and engineering by helping identify functions for all metabolic genes.

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► Comparative genomics can help predict the function of unknown plant metabolic genes.
► Functional gene annotations are foundational to the construction of metabolic models.
► Models can simulate effects of genetic changes and thus guide metabolic engineering.
► Examples of comparative genomics facilitating gene discovery in plants are presented.