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Floral color plays a key role as visual signaling and is therefore of great importance in shaping plant-pollinator interactions. Iris ( Iridaceae ), a genus comprising over 300 species and named after the Greek goddess of the colorful rainbow, is famous for its dazzling palette of flower colors and patterns, which vary considerably both within and among species. Despite the large variation of flower color in Iris , little is known about the phylogenetic and ecological contexts of floral color. Here, we seek to resolve the evolution of flower color in the genus Iris in a macroevolutionary framework. We used a phylogenetic analysis to reconstruct the ancestral state of flower color and other pollination-related traits (e.g., the presence of nectar and mating system), and also tracked the evolution of color variation. We further explored weather floral trait transitions are better explained by environmental or pollinator-mediated selection. Our study revealed that the most recent common ancestor likely had monomorphic, purple flowers, with a crest and a spot on the fall. The flowers were likely insect-pollinated, nectar-rewarding, and self-compatible. The diversity of floral traits we see in modern irises, likely represents a trade-off between conflicting selection pressures. Whether shifts in these flower traits result from abiotic or biotic selective agents or are maintained by neutral processes without any selection remains an open question. Our analysis serves as a starting point for future work exploring the genetic and physiological mechanisms controlling flower coloration in the most color-diverse genus Iris .

The Royal Irises (section Oncocyclus) are a Middle-Eastern group of irises, characterized by extremely large flowers with a huge range of flower colors and a unique pollination system. The Royal Irises are considered to be in the course of speciation and serve as a model for evolutionary processes of speciation and pollination ecology. However, no transcriptomic and genomic data are available for these plants. Transcriptome sequencing is a valuable resource for determining the genetic basis of ecological-meaningful traits, especially in non-model organisms. Here we describe the de novo transcriptome assembly of Iris atropurpurea, an endangered species endemic to Israel’s coastal plain. We sequenced and analyzed the transcriptomes of roots, leaves, and three stages of developing flower buds. To identify genes involved in developmental processes we generated phylogenetic gene trees for two major gene families, the MADS-box and MYB transcription factors, which play an important role in plant development. In addition, we identified 1503 short sequence repeats that can be developed for molecular markers for population genetics in irises. This first reported transcriptome for the Royal Irises, and the data generated, provide a valuable resource for this non-model plant that will facilitate gene discovery, functional genomic studies, and development of molecular markers in irises, to complete the intensive eco-evolutionary studies of this group.

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Transcriptome sequencing of non-model organisms is valuable resource for the genetic basis of ecologicalmeaningful traits. The Royal Irises, Iris section Oncocyclus, are a Middle-East group of species in the course of speciation. The species are characterized with extremely large flowers, a huge range of flower colors and a unique pollination system. The Royal Irises serve as a model for evolutionary processes of speciation and plant ecology. However, there are no transcriptomic and genomic data for molecular characterization.Here we describe the de novo transcriptome sequencing and assembly of Iris atropurpurea of the Royal Irises. We employed RNA-seq to analyze the transcriptomes of root, leaf and three stages of flower development. We generated over 195 million paired-end sequencing reads. De novo assembly yielded 184,341 transcripts with an average length of 535 bp. At the protein level, a total of 28,709 Iris transcripts showed significant similarity with known proteins from UniProt database. Orthologues of key flowering genes and genes related to pigment synthesis were identified, showing differential expression in different tissues. In addition, we identified 1,503 short sequence repeats that can be developed for molecular markers for population genetics in irises.In the era of large genetic datasets, the Iris transcriptome sequencing provides valuable resource for studying adaptation-associated traits in this non-model plant. Although intensive eco-evolutionary studies, this is the first reported transcriptome for the Royal Irises. The data available from this study will facilitate gene discovery, functional genomic studies and development of molecular markers in irises, and will provide genetic tools for their conservation.