De novo transcriptome characterization of Iris atropurpurea (the Royal Iris) and phylogenetic analysis of MADS-box and R2R3-MYB gene families

Abstract

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.

Figure 1

Plant materials used for RNA sequencing. (a) Iris atropurpurea flower in the field site where collected (Dora). (b) Representation of three stages of bud development (1 to 3) in I. atropurpurea, as defined in the text.

Figure 2

Distribution of contig lengths (in base pairs) across the assembled contigs from the Iris transcriptome.

Figure 3

Top 10-hit species distribution of annotated transcripts. Other species represented in the transcriptome had only 1% or less of the transcripts annotated to them.

Figure 4

Clusters of orthologous group (COG) classification, showing 22,564 transcripts that were classified.

Figure 5

Clusters of orthologous group (COG) classification, showing 22,564 transcripts that were classified.

Figure 6

(a) The 10 most abundant PFAM protein families in the I. atropurpurea a transcriptome. (b) The 10 most abundant transcription factors families in the I. atropurpurea transcriptome.

Figure 7

Phylogenetic analysis of MADS-box proteins from the I. atropurpurea transcriptome, I. fulva, Arabidopsis and rice. I. atropurpurea transcripts names are in red and I. fulva in light blue. Colours are for visual separation only. Sequences that were separated from their known clade have the name of their original clade written on the branch.

Figure 8

Phylogenetic analysis of R2R3-MYB proteins from the Iris transcriptome (highlighted in red), I. fulva (If), Arabidopsis, encoded by AtMYB, and rice (Oryza sativa, Os). I. atropurpurea transcripts names are in red. Colours are for visual separation only.

Figure 9

Characterization of SSRs loci found in Iris transcriptome. (a) Distribution of SSR motif repeat numbers and relative frequency. (b) Frequency distribution of SSRs based on motif sequence types.