De novo transcriptome assembly of the cotyledon of Camellia oleifera for discovery of genes regulating seed germination

Abstract

Background: Camellia oleifera (C. oleifera) is one of the most important wood oil species in the world. It was propagated by nurse seedling graft in C.oleifera. Since morphology of rootstock has a significant impact on grafting efficiency and seedling quality, it is necessary to have a clear understanding molecular mechanism of morphogenesis for cultivating high quality and controllable rootstocks,. However, the genomic resource for this species is relatively limited, thus hampering our understanding of the molecular mechanisms of seed germination in C.oleifera. Results: In this paper, we measured the gene expression in the C.oleifera cotyledon in different development stages and the global gene expression profiles through transcriptome sequencing. Approximately 45.4 gigabases (GB) paired-end clean reads were obtained and assembled into 113,582 unigenes with an average length of 396 bp. 61.5% (68,217) of the unigenes were annotated in six public protein databases. We identified 11,391 differentially expressed genes (DEGs) between the different stages in the germination process. Enrichment analysis revealed that the DEGs were mainly involved in hormone signal transduction and starch sucrose metabolism pathways. The gravitropism regulator UNE10, the meristem regulator STM, KNAT1, PLT2, and root-specific transcription factor WOX11 has higher expression level in the CAM2 stage (seed soaking), indicating the cotyledon-regulated program upon seed germination has been initiated to establish in early imbibition. Our data showed that multiple hormone-related genes in cotyledons were differentially reprogrammed during C. oleifera seed germination.Conclusion: The cotyledons play key roles, both as the main nutrient provider and as one of the main instructors for seed germination and seedling growth. Together, our study will remarkably enrich the genomic resources of Camellia and contribute to our understanding of the molecular mechanisms of the development in the seed germination and seedling growth of C.oleifera. It is helpful to culture in standardizing and superior quality rootstock for C. oleifera breeding.