Camellia oleifera Abel. is a critical oil tree species. Camellia oil, which is extracted from the seeds, is widely regarded as a premium cooking oil, with the content of oleic acid being over 80%. Light is thought to be one of the largest essential natural components in the regulation of plant developmental processes, and different light qualities can considerably influence plant physiological and phenotypic traits. In this research, we examined the growth and physiological responses of C. oleifera “MIN 43” cultivar plantlets to three different wavelengths of light, containing white, red, and blue light, and we utilized the combination of the PacBio single-molecule real-time (SMRT) and Illumina HiSeq RNA sequencing to obtain the mRNA expression profiles. The results showed that plantlets growing under blue light conditions displayed superior growth performance, including stimulated enhancement of the leaf area, increased leaf number, increased chlorophyll synthesis, and improved photosynthesis. Furthermore, SMAT sequencing created 429,955 reads of inserts, where 406,722 of them were full-length non-chimeric reads, and 131,357 non-redundant isoforms were produced. Abundant differentially expressed genes were found in leaves under different light qualities by RNA-sequencing. Gene expression profiles of actin, dynein, tubulin, defectively organized tributaries 3 (DOT3), and ADP ribosylation factor 5 (ARF5) were associated with the greatest leaf performance occurring under blue light conditions. Moreover, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis identified hundreds of pathways involved in different light conditions. The pathways of the plant circadian rhythm and hormone signal transduction were associated with different light quality responses in C. oleifera. Phytochrome B (PHYB), constitutively photomorphogenic 1 (COP1), long hypocotyl 5 (HY5), auxin/indole-3-acetic acid (AUX/IAA), Gretchen Hagen 3 (GH3), and small auxin-up RNA (SAUR), which were differentially expressed genes involved in these two pathways, play a vital role in responses to different wavelengths of light in C. oleifera. In addition, blue light significantly promotes flavonoid biosynthesis via changing expression of related genes.
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