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

为了适应环境的变化，植物表现出各种各样的复杂的专门化代谢特征。共同代谢性状的进化涉及几种机制，包括专门化代谢基因家族的扩大，先前存在的代谢途径的基因共选，以及基因簇的形成。在开花植物目中，一种独特的特殊代谢物，被称为甜菜碱色素，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。甜菜碱色素的汇聚起源是探索复杂代谢途径的进化组装和基因簇组装的理想系统。因此，这个项目的首要目标是利用密集采样和整合的转录和基因组数据集来剖析甜菜碱色素的进化，重点关注收敛现象。将探索与甜菜碱色素沉着的每个进化起源相关的基因组特征和模块化基因表达结构。基本的假设表明，与不同来源相关的基因组和基因表达结构将揭示共性，但也将揭示不同的基因选择、遗传调控和基因组基因聚集的模式。我的具体目标是：1)通过应用于RNA-SEQ数据的系统发育和网络方法来了解一个复杂性状的重复进化，以分析甜菜碱色素沉积多个来源上遗传元件的整合和连通性。这一目标将在支持特殊代谢作用的基因表达的模块理解上进行2)通过组装和注释在甜菜碱途径最早的复制之前分歧的两个分类群的基因组来探索甜菜碱着色的基因组前体。进行与其他石竹目基因组的比较基因组分析，以探索甜菜色素沉着的多个来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.