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

为了适应环境的挑战，植物表现出多种复杂的特殊代谢特征。这些代谢特征的进化涉及几种机制，包括专门代谢基因家族的扩展，先前存在的代谢途径的基因共选择，以及基因簇的形成。在开花植物石竹目中，一类特殊的代谢物，被称为甜菜素色素，最近被证明已经收敛进化了四次。至少有一个起源与基因簇的形成有关。betalain色素的趋同起源为探索复杂代谢性状的进化组装和基因簇的组装提供了一个理想的系统。因此，该项目的首要目标是利用密集采样和整合的转录组学和基因组数据集来剖析β素色素的进化，重点关注趋同现象。基因组特征和模块化基因表达结构与每个进化起源的β色素沉着将被探索。潜在的假设表明，与不同起源相关的基因组和基因表达结构将揭示共性，但也将揭示基因合作选择、遗传调控和基因组基因聚类的不同模式。我的具体目标是：1)通过使用应用于RNA-seq数据的系统发育和网络方法来分析β蛋白色素沉着的多个起源的遗传元件的整合和连通性，了解复杂性状的重复进化。这一目标将在很大程度上依赖于对支持特殊代谢的基因表达的模块化理解。2)通过组装和注释早于最早推断的β蛋白酶途径复制的两个分类群的基因组，探索β蛋白酶色素沉着的基因组前体。通过与其它石竹科植物基因组的比较分析，探索色素沉着多起源的基因组结构和重组。

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.