Transcriptome sequencing and digital expression analyses of flower morphogenesis genes in Clivia.

Naidoo, P.*, Maleka, M. F.

University of the Free State, Genetics Department.

The developmental process of flower formation has been used to study the regulatory gene networks involved in floral initiation and morphogenesis in flowering plants. Flower morphology is an important aspect in horticulture as it can be used to create new varieties and influences the visual appeal of a plant. Clivia is a genus of angiosperms belonging to the family Amaryllidaceae and is endemic to southern Africa. This genus is important in horticulture due to the plant’s ornamental value, adaptability, low maintenance requirements, easy propagation, and showy flowers. The genus comprises plants exhibiting two distinct flower morphologies: the pendulous (drooping) and non-pendulous (upright) forms. The study aimed to sequence the transcriptome of the two Clivia flower shapes, to identify flower morphogenesis genes and the differentially expressed transcripts between the pendulous and non-pendulous Clivia flowers. A total of nine flower buds were used for RNA extraction and sequencing, including three small pendulous independent buds (SPB), three medium pendulous buds (MPB), and three medium non-pendulous buds (MNP). Illumina sequencing and analyses generated 150 million reads that were quality filtered and assembled into a 200 Mbp flower transcriptome of Clivia. The transcriptome showed 97.23% read representation. The assembly had a GC content of 39.6% and an N50 value of 1176. Transcript sequences representing 36 flower development-related genes were identified based on the Flower Interactive database (FLOR-ID). Differential Expression (DE) analysis of transcripts from the pairwise comparisons of the flower samples led to the identification of 3,026, 14,928, and 7,411 DEGs for MPB/MNB, SPB/MNP, and SPB/MPB, respectively. Several transcription factors were found to be distinctive to each flower form, including a MADS-box gene likely to be responsible for the different morphologies. Our results have contributed to understanding the molecular mechanisms that occur during flowering, flower development, and morphogenesis in Clivia. Future studies should focus on the functional validation of the identified transcription factors and their roles in determining flower morphogenesis in Clivia.

Keywords: Clivia, differential expression, flower morphogenesis, horticulture, MADS-box, next-generation sequencing, transcriptome analysis