Data from: Comparative transcriptomic analysis of the evolution and development of flower size in Saltugilia (Polemoniaceae)

Background: Flower size varies dramatically across angiosperms, representing innovations over the course of >130 million years of evolution and contributing substantially to relationships with pollinators. However, the genetic underpinning of flower size is not well understood. Saltugilia (Polemoniaceae) provides an excellent non-model system for extending the genetic study of flower size to interspecific differences that coincide with variation in pollinators.

Results: Using targeted gene capture methods, we infer phylogenetic relationships among all members of Saltugilia to provide a framework for investigating the genetic control of flower size differences via RNA-Seq de novo assembly. Nuclear concatenation and species tree inference methods provide congruent topologies. The inferred evolutionary trajectory of flower size is from small flowers to larger flowers. We identified 4 to 10,368 transcripts that are differentially expressed during flower development, with many unigenes associated with cell wall modification and components of the auxin and gibberellin pathways.

Conclusions: Saltugilia is an excellent model for investigating covarying floral and pollinator evolution. Four candidate genes from model systems (BIG BROTHER, BIG PETAL, GASA, and LONGIFOLIA) show differential expression during development of flowers in Saltugilia, and four other genes (FLOWERING-PROMOTING FACTOR 1, PECTINESTERASE, POLYGALACTURONASE, and SUCROSE SYNTHASE) fit into hypothesized organ size pathways. Together, these gene sets provide a strong foundation for future functional studies to determine their roles in specifying interspecific differences in flower size.

背景：被子植物（angiosperms）的花大小差异悬殊，这是其历经超1.3亿年进化历程所产生的演化创新，且对其与传粉者的互作关系具有关键贡献。然而，学界对花大小的遗传基础仍缺乏充分解析。Saltugilia属（花荵科，Polemoniaceae）为将花大小的遗传研究拓展至与传粉者变异相伴的种间差异，提供了极佳的非模式研究体系。
结果：本研究采用靶向基因捕获（targeted gene capture）技术，对Saltugilia属所有类群的系统发育关系进行推断，以此为研究框架，通过RNA测序从头组装（RNA-Seq de novo assembly）解析花大小差异的遗传调控机制。核序列串联与物种树推断（species tree inference）方法得到了一致的拓扑结构。研究推断的花大小演化轨迹为由小花向大花演化。本研究鉴定出4至10368个在花发育过程中差异表达（differentially expressed）的转录本，其中大量单基因簇（unigenes）与细胞壁修饰、生长素（auxin）及赤霉素（gibberellin）通路的组分相关。
结论：Saltugilia属是研究花与传粉者协同演化的极佳模型。来自模式系统的4个候选基因（candidate genes）：BIG BROTHER、BIG PETAL、GASA及LONGIFOLIA，在Saltugilia属植物的花发育过程中呈现差异表达；另有4个基因：FLOWERING-PROMOTING FACTOR 1、果胶甲酯酶（PECTINESTERASE）、多聚半乳糖醛酸酶（POLYGALACTURONASE）及蔗糖合酶（SUCROSE SYNTHASE），可归入已提出的器官大小通路。上述基因集为后续开展功能研究、明确其在决定花大小种间差异中的作用提供了坚实基础。