Transcriptome Profiling of Ornithogalum dubium Leaves and Flowers to Identify Key Carotenoid Genes for CRISPR Gene Editing
Open Access
- 21 April 2020
- Vol. 9 (4), 540
- https://doi.org/10.3390/plants9040540
Abstract
Ornithogalum dubium is a popular ornamental monocot native to South Africa with flower colors ranging from pure white to deep orange. Gene editing based on the CRISPR/Cas9 system has recently been shown to hold potential for color improvement in ornamental flower crops. To apply this approach to Ornithogalum color manipulation, genomic or transcriptomic data must first be collected. Here, cDNA libraries of O. dubium leaves and flowers were constructed and sequenced using the Illumina HiSeq 2500. Over 155 million 100-bp paired-end reads were assembled into a transcriptome database of 360,689 contigs, of which 18,660 contigs were differentially expressed between leaves and flowers. Carotenoids are the main pigment imparting spectrum of orange hues to O. dubium flowers. By querying our database, we identified a total of 16 unique transcripts (unigenes) predicted to be involved in the carotenoid biosynthesis pathway of Ornithogalum. Combining carotenoid profiles, we further inferred several key unigenes responsible for floral coloration and accumulation in O. dubium, of which the gene LCYB/comp146645_c0 was found as a suitable target to generate potentially red flower varieties of O. dubium. Our research thus provides a framework for the application of CRISPR/Cas9 technology to improve this ornamental crop.Keywords
This publication has 51 references indexed in Scilit:
- A novel carotenoid cleavage activity involved in the biosynthesis of Citrus fruit-specific apocarotenoid pigmentsJournal of Experimental Botany, 2013
- RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genomeBMC Bioinformatics, 2011
- Full-length transcriptome assembly from RNA-Seq data without a reference genomeNature Biotechnology, 2011
- Cloning of the Papaya Chromoplast-Specific Lycopene β-Cyclase, CpCYC-b, Controlling Fruit Flesh Color Reveals Conserved Microsynteny and a Recombination Hot SpotPlant Physiology, 2010
- Jasmonate and ppHsystemin Regulate Key Malonylation Steps in the Biosynthesis of 17-Hydroxygeranyllinalool Diterpene Glycosides, an Abundant and Effective Direct Defense against Herbivores inNicotiana attenuataPlant Cell, 2010
- edgeR: a Bioconductor package for differential expression analysis of digital gene expression dataBioinformatics, 2009
- Ultrafast and memory-efficient alignment of short DNA sequences to the human genomeGenome Biology, 2009
- A Chromoplast-Specific Carotenoid Biosynthesis Pathway Is Revealed by Cloning of the Tomato white-flower LocusPlant Cell, 2006
- Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics researchBioinformatics, 2005
- Analysis of Relative Gene Expression Data Using Real-Time Quantitative PCR and the 2−ΔΔCT MethodMethods, 2001