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.

Genome-wide identification of the AcMADS-box family and functional validation of AcMADS32 involved in carotenoid biosynthesis in Actinidia

“…Therefore, a comprehensive understanding of the MADS family and the function of key members is meaningful for the modification of crop yield and quality. In recent years, the MADS family has been identified in many horticultural plants, such as pineapple ( Zhang et al., 2020 ), apple ( Tian et al., 2015 ), pear ( Wang et al., 2017 ), tomato ( Wang et al., 2019 ), iris ( Bar-Lev et al., 2021 ), banana ( Lakhwani et al., 2022 ), chrysanthemum ( Won et al., 2021 ), pomegranate ( Zhao et al., 2020 ), rhododendron ( Huo et al., 2021 ), and litchi ( Guan et al., 2021 ). A total of 74 MADS family members were identified in the kiwifruit genome in this study, which is smaller than that in Arabidopsis (106), poplar (105) and apple (147), and comparable with that of rice (75).…”

Identification of MADS-Box Transcription Factors in Iris laevigata and Functional Assessment of IlSEP3 and IlSVP during Flowering

“…Notably, transcriptomics data generated from floral and young leaf tissues were also used for the Louisiana Irises study due to the lack of genome sequencing data. Similarly, 43 MADS-box genes were identified in the de novo transcriptomics study of Iris atropurpurea , an endemic species in Israel [ 29 ]. Compared to 33 MIKC C genes identified in this study, 28 were found in the I. atropurpurea transcriptome.…”

De novo transcriptome assembly reveals characteristics of flower sex determination of Excoecaria agallocha

“…We performed the phylogenetic analysis on MADS-box protein sequences from J. curcas. The MADS-box proteins regulate floral organogenesis and are essential for flower development and sex determination (De Bodt et al 2003;Pan et al 2018;Bar-Lev et al 2021). These proteins can be subdivided into two lineages, the M-type (type I) and MIKC (type II).…”