Understanding the convergent evolution of a complex metabolic trait, the Betalains, through comparative genomics and co-expression networks

点击翻译按钮获取中文摘要

Plants display a vast diversity of complex specialized metabolic traits in order to adapt to thechallenges of their environment. Several mechanisms are involved in the evolution of thesemetabolic traits including expansion of specialised metabolic gene families, gene co-option frompreviously existing metabolic pathways, and the formation of gene clusters. In the floweringplant order Caryophyllales, a unique class of specialised metabolites, termed betalain pigments,have recently been shown to have convergently evolved four times. At least one origin isassociated with the formation of a gene cluster. The convergent origins of betalain pigmentsoffer an ideal system in which to explore the evolutionary assembly of complex metabolic traitsand the assembly of gene clusters. Therefore, the overarching goal of this project is to employdensely sampled and integrated transcriptomic and genomic datasets to dissect the evolution ofbetalain pigments, focussing on phenomena of convergence. Genomic characteristics andmodular gene expression structure associated with each evolutionary origin of betalainpigmentation will be explored. The underlying hypotheses suggest that the genomic and geneexpression structure associated with the different origins will reveal commonalities, but will also reveal distinct patterns of gene co-option, genetic regulation, and genomic gene clustering.My specific objectives are:1) To understand the repeated evolution of a complex trait by using phylogenetic andnetwork methods applied to RNA-seq data to analyze the integration and connectivity ofgenetic elements over multiple origins of betalain pigmentation. This objective will drawheavily on a modular understanding of gene expression underpinning specialisedmetabolism.2) To explore the genomic precursors of betalain pigmentation by assembling andannotating the genomes of two taxa diverging prior to the earliest inferred duplications ofbetalain pathway. To conduct comparative genomic analyses against otherCaryophyllales genomes to explore genomic structure and re-organisation acrossmultiple origins of betalain pigmentation.