Comparative genomics analysis reveals gene family expansion and changes of expression patterns associated with natural adaptations of flowering time and secondary metabolism in yellow Camellia

Identification of flowering genes in Camellia perpetua by comparative transcriptome analysis

Camellia perpetua has the excellent characteristic of flowering multiple times throughout the year, which is of great importance to solve the problem of "short flowering period" and "low fresh flower yield" in the yellow Camellia industry at present. Observations of flowering phenology have demonstrated that most floral buds of C. perpetua were formed by the differentiation of axillary buds in the scales at the base of the terminal buds of annual branches. However, the molecular mechanism of flowering in C. perpetua is still unclear. In this study, we conducted a comparative transcriptomic study of the terminal buds and their basal flower buds in March (spring) and September (autumn) using RNA-seq and found that a total of 11,067 genes were significantly differentially expressed in these two periods. We identified 27 genes related to gibberellin acid (GA) synthesis, catabolism, and signal transduction during floral bud differentiation. However, treatment of the terminal buds and axillary buds of C. perpetua on annual branch with GA3 did not induce floral buds at the reproductive growth season (in August) but promoted shoot sprouting. Moreover, 203 flowering genes were identified from the C. perpetua transcriptome library through homology alignment, including flowering integrators LEAFY (LFY) and UNUSUAL FLORAL ORGANS (UFO), as well as MADS-box, SQUAMOSA PROMOTER BINDING PROTEIN-box (SBP-box), and TEOSINTE BRANCHED1/CYCLOIDEA/PROLIFERATING CELL FACTOR (TCP) genes, which were specifically upregulated in floral buds and were likely involved in flowering in C. perpetua. The floral inhibitor CperTFL1b was identified and cloned from C. perpetua, and its expression level was specifically regulated in terminal buds in autumn. Ectopic overexpression of CperTFL1b delayed flowering time and produced abnormal inflorescence and floral organs in Arabidopsis, suggesting that CperTFL1b inhibits flowering. In conclusion, this study deepens our understanding of the molecular mechanism of blooms throughout the year in C. perpetua and provides a helpful reference for cultivating new varieties of yellow Camellia with improved flowering traits.

Genome-wide identification and analysis of the evolution and expression pattern of the SBP gene family in two Chimonanthus species

BACKGROUND

Chimonanthus praecox and Chimonanthus salicifolius are closely related species that diverged approximately six million years ago. While both C. praecox and C. salicifolius could withstand brief periods of low temperatures of - 15 °C. Their flowering times are different, C. praecox blooms in early spring, whereas C. salicifolius blooms in autumn. The SBP-box (SQUAMOSA promoter-binding protein) is a plant-specific gene family that plays a crucial vital role in regulating plant flowering. Although extensively studied in various plants, the SBP gene family remains uncharacterized in Calycanthaceae.

METHODS AND RESULTS

We conducted genome-wide identification of SBP genes in both C. praecox and C. salicifolius and comprehensively characterized the chromosomal localization, gene structure, conserved motifs, and domains of the identified SBP genes. In total, 15 and 18 SBP genes were identified in C. praecox and C. salicifolius, respectively. According to phylogenetic analysis, the SBP genes from Arabidopsis, C. praecox, and C. salicifolius were clustered into eight groups. Analysis of the gene structure and conserved protein motifs showed that SBP proteins of the same subfamily have similar motif structures. The expression patterns of SBP genes were analyzed using transcriptome data. The results revealed that more than half of the genes exhibited lower expression levels in leaves than in flowers, suggesting their potential involvement in the flower development process and may be linked to the winter and autumn flowering of C. praecox and C. salicifolius.

CONCLUSION

Thirty-three SBPs were identified in C. praecox and C. salicifolius. The evolutionary characteristics and expression patterns were examined in this study. These results provide valuable information to elucidate the evolutionary relationships of the SBP family and help determine the functional characteristics of the SBP genes in subsequent studies.

Full-Length Transcriptome Sequencing Provides Insights into Flavonoid Biosynthesis in Camellia nitidissima Petals

Flavonoids are the main medicinal ingredients in Camellia nitidissima, but the regulatory mechanism of flavonoid biosynthesis in flowers is unclear; therefore, the flavonoids in C. nitidissima have not been effectively used. The present study performed full-length transcriptome sequencing of C. nitidissima flower. Furthermore, the reported RNA-sequencing data of C. nitidissima petals were reanalyzed using the full-length transcriptome as a reference, and the regulatory mechanism of flavonoid synthesis in petals was elucidated. The analysis identified 43,350 isoforms annotated in non-redundant protein (Nr), Kyoto Encyclopedia of Genes and Genomes (KEGG), EuKaryotic Orthologous Groups (KOG), and Swiss-Prot databases, among which 34,602 aligned to Camellia sinensis genes. A total of 11,857 differentially expressed genes (DEGs), including 112 related to flavonoid synthesis, were identified by pairwise comparison. Subsequently, analysis of the phylogeny and the conserved motifs of R2R3-MYB using the proteins sequences identified three R2R3-MYB transcription factors that regulated flavonoid biosynthesis. Weighted gene co-expression network analysis (WGCNA) identified phenylalanine ammonia-lyase (PAL) and 4-coumarate: CoA ligase(4CL) as the hub genes and showed that bHLH79 interacted with PAL. Finally, validated the expression of seven DEGs involved in flavonoid biosynthesis using real-time quantitative PCR (qRT-PCR). Thus, the present study generated and used the full-length transcriptome as the reference to analyze the transcriptome of petals and proposed a possible regulatory mechanism of flavonoid synthesis in C. nitidissima. The study's findings unravel the genetic mechanisms underlying flavonoid synthesis and suggest candidate genes for the genetic improvement of C. nitidissima.

Comparative Transcriptome and Pigment Analyses Reveal Changes in Gene Expression Associated with Flavonol Metabolism in Yellow Camellia

The accumulation of various pigments leads to the formation of different flower colors in plants. However, the regulation mechanism of yellow flower formation and flower color differences between Camellia nitidssima C.W.Chi (CN) and its hybrids C. ‘Zhenghuangqi’ (ZHQ), C. ‘Huangxuanlv’ (HXL), and C. ‘Xinshiji’ (XSJ), remains largely unknown. Here, we showed that the content of two flavonols, quercetin-7-O-glucoside (Qu7G) and quercetin-3-O-glucoside (Qu3G), was positively correlated with the yellow degree of petals in CN and its three hybrids. Additionally, we performed a comparative transcriptomic analysis of petals of the four yellow camellia plants, which revealed 322 common upregulated and 866 common downregulated DEGs (differentially expressed genes) in the CN vs. ZHQ, CN vs. HXL, and CN vs. XSJ comparison groups. Their regulatory pathway analysis showed that flavonol biosynthesis genes (FLSs and GTs) and transcriptional regulatory genes MYBs were all expressed higher in CN than its three hybrids, which corresponded to differences in the flavonol content among the four yellow camellias. Further, two ethylene synthesis genes (ACSs, ACO) and three ethylene signaling genes (EIN2s, EIN3, ERFs) were all upregulated in the yellow petals of CN. In conclusion, the expression of flavonol-related genes and flavonols (Qu7G and Qu3G) accumulation could play a key role in the formation of yellow flowers in camellia, and the ethylene pathway might be involved in the regulation of yellow flower formation of camellias. This work describes the possible regulatory pathway of yellow camellia, thereby laying a foundation for future verification of genes linked to flower coloring and the breeding of yellow camellia.

The complete chloroplast genome sequence of Camellia chuongtsoensis

Camellia chuongtsoensis is an evergreen shrub with a single-petaled flower and golden yellow color. The complete chloroplast genome of C. chuongtsoensis was sequenced and analyzed in this study by Illumina sequencing. The chloroplast genome is 156,504 bp in length with a quadripartite structure containing a large single copy (LSC) region of 86,215 bp, a small single copy (SSC) region of 18,253 bp, and a pair of inverted repeat regions of 26,018 bp (IRa and IRb). The chloroplast genome of C. chuongtsoensis encodes 135 genes, comprising 87 protein-coding genes, 37 tRNA genes, 8 rRNA genes, and 3 pseudogenes.

Functional Diversification of the Dihydroflavonol 4-Reductase from Camellia nitidissima Chi. in the Control of Polyphenol Biosynthesis

Plant secondary metabolism is complex in its diverse chemical composition and dynamic regulation of biosynthesis. How the functional diversification of enzymes contributes to the diversity is largely unknown. In the flavonoids pathway, dihydroflavonol 4-reductase (DFR) is a key enzyme mediating dihydroflavanol into anthocyanins biosynthesis. Here, the DFR homolog was identified from Camellia nitidissima Chi. (CnDFR) which is a unique species of the genus Camellia with golden yellow petals. Sequence analysis showed that CnDFR possessed not only conserved catalytic domains, but also some amino acids peculiar to Camellia species. Gene expression analysis revealed that CnDFR was expressed in all tissues and the expression of CnDFR was positively correlated with polyphenols but negatively with yellow coloration. The subcellular localization of CnDFR by the tobacco infiltration assay showed a likely dual localization in the nucleus and cell membrane. Furthermore, overexpression transgenic lines were generated in tobacco to understand the molecular function of CnDFR. The analyses of metabolites suggested that ectopic expression of CnDFR enhanced the biosynthesis of polyphenols, while no accumulation of anthocyanins was detected. These results indicate a functional diversification of the reductase activities in Camellia plants and provide molecular insights into the regulation of floral color.

Identifying Conserved Functional Gene Modules Underlying the Dynamic Regulation of Tea Plant Development and Secondary Metabolism

Tea plants adjust development and metabolism by integrating environmental and endogenous signals in complex but poorly defined gene networks. Here, we present an integrative analysis framework for the identification of conserved modules controlling important agronomic traits using a comprehensive collection of RNA-seq datasets in Camellia plants including 189 samples. In total, 212 secondary metabolism-, 182 stress response-, and 182 tissue development-related coexpressed modules were revealed. Functional modules (e.g., drought response, theobromine biosynthesis, and new shoot development-related modules) and potential regulators that were highly conserved across diverse genetic backgrounds and/or environmental conditions were then identified by cross-experiment comparisons and consensus clustering. Moreover, we investigate the preservation of gene networks between Camellia sinensis and other Camellia species. This revealed that the coexpression patterns of several recently evolved modules related to secondary metabolism and environmental adaptation were rewired and showed higher connectivity in tea plants. These conserved modules are excellent candidates for modeling the core mechanism of tea plant development and secondary metabolism and should serve as a great resource for hypothesis generation and tea quality improvement.

Unraveling the Roles of Regulatory Genes during Domestication of Cultivated Camellia: Evidence and Insights from Comparative and Evolutionary Genomics

With the increasing power of DNA sequencing, the genomics-based approach is becoming a promising resolution to dissect the molecular mechanism of domestication of complex traits in trees. Genus Camellia possesses rich resources with a substantial value for producing beverage, ornaments, edible oil and more. Currently, a vast number of genetic and genomic research studies in Camellia plants have emerged and provided an unprecedented opportunity to expedite the molecular breeding program. In this paper, we summarize the recent advances of gene expression and genomic resources in Camellia species and focus on identifying genes related to key economic traits such as flower and fruit development and stress tolerances. We investigate the genetic alterations and genomic impacts under different selection programs in closely related species. We discuss future directions of integrating large-scale population and quantitative genetics and multiple omics to identify key candidates to accelerate the breeding process. We propose that future work of exploiting the genomic data can provide insights related to the targets of domestication during breeding and the evolution of natural trait adaptations in genus Camellia.