Chromosome‐level genome of Camellia lanceoleosa provides a valuable resource for understanding genome evolution and self‐incompatibility

Abstract

The section Oleifera (Theaceae) has attracted attention for the high levels of unsaturated fatty acids found in its seeds. Here, we report the chromosome-scale genome of the sect. Oleifera using diploid wild Camellia lanceoleosa with a final size of 3.00 Gb and an N50 scaffold size of 186.43 Mb. Repetitive sequences accounted for 80.63% and were distributed unevenly across the genome. Camellia lanceoleosa underwent a whole-genome duplication event approximately 65 million years ago (65 Mya), prior to the divergence of C. lanceoleosa and Camellia sinensis (approx. 6-7 Mya). Syntenic comparisons of these two species elucidated the genomic rearrangement, appearing to be driven in part by the activity of transposable elements. The expanded and positively selected genes in C. lanceoleosa were significantly enriched in oil biosynthesis, and the expansion of homomeric acetyl-coenzyme A carboxylase (ACCase) genes and the seed-biased expression of genes encoding heteromeric ACCase, diacylglycerol acyltransferase, glyceraldehyde-3phosphate dehydrogenase and stearoyl-ACP desaturase could be of primary importance for the high oil and oleic acid content found in C. lanceoleosa. Theanine and catechins were present in the leaves of C. lanceoleosa. However, caffeine can not be dectected in the leaves but was abundant in the seeds and roots. The functional and transcriptional divergence of genes encoding SAM-dependent N-methyltransferases may be associated with caffeine accumulation and distribution. Gene expression profiles, structural composition and chromosomal location suggest that the late-acting self-incompatibility of C. lanceoleosa is likely to have favoured a novel mechanism co-occurring with gametophytic self-incompatibility. This study provides valuable resources for quantitative and qualitative improvements and genome assembly of polyploid plants in sect. Oleifera.

Comparative transcriptomic analysis unveils the deep phylogeny and secondary metabolite evolution of 116 Camellia plants

“…Previous studies have confirmed that cultivated tea plants ( C. sinensis ), similar to many other flowering plants, have experienced a recent WGD event 30–40 MYA (Wang et al., 2021; Xia et al., 2017b); however, it is still unclear whether this WGD event occurred in other Camellia plants, as well as how it affects the diversification and quality traits of Camellia plants. Our results offered supplemental evidence demonstrating that the most recent common ancestor of Camellia plants such as cultivated tea plants, wild tea plants, and oil tea plants shared a recent WGD event with Ericales such as kiwifruit through genomic collinearity analysis (Gong et al., 2022; Xia et al., 2020b, Zhang et al., 2020b) (Figure S1d). Functional annotation of the WGD‐derived duplicated genes of three representative Camellia plants, including cultivated tea plant ( C. sinensis ), oil‐tea plant ( C. oleifera ), and common camellia ( C. reticulata ), revealed that some of these duplicated genes derived from WGD events were associated with UDP‐glycosyltransferase activity, lipid biosynthetic process, aromatic compound biosynthetic process, and pigment metabolic process.…”

Phylogenomics Resolves the Phylogeny of Theaceae by Using Low-Copy and Multi-Copy Nuclear Gene Makers and Uncovers a Fast Radiation Event Contributing to Tea Plants Diversity

“…The tea plant is one of the most significant and traditional economic crops grown in Asia, Africa, and Latin America, whose leaves are used to produce numerous kinds of tea [ 2 , 3 , 4 ]. Camellia oleifera is a woody oil plant, whose seed kernels produce abundant edible oils with high monounsaturated fatty acid content [ 5 , 6 , 7 ]. The planting area for C. oleifera was about 4.39 million hectares in China with a total output value of 116 billion RMB [ 6 ].…”

“…Camellia oleifera is a woody oil plant, whose seed kernels produce abundant edible oils with high monounsaturated fatty acid content [ 5 , 6 , 7 ]. The planting area for C. oleifera was about 4.39 million hectares in China with a total output value of 116 billion RMB [ 6 ]. It has been utilized extensively in France, Japan, and the USA, as a source of additive for cosmetics [ 8 ].…”

“…With the development of high-throughput sequencing technologies, phylogenomics and phylotranscriptomics have become effective methods for evolutionary analyses in plants. Nuclear gene sequences can be acquired cost-effectively from non-model species, as recently applied in studies of Theaceae [ 2 , 3 , 4 , 5 , 6 , 7 , 19 , 25 , 26 , 27 , 28 , 29 , 30 , 31 ]. The relationship in Theaceae has been analyzed in 610 nuclear genes from 57 species to reconstruct the phylogeny with combined supermatrix and coalescent tree inference methods [ 19 ].…”

Applications of Chinese Camellia oleifera and its By-Products: A Review

“…Recently, an abundance of genomic information has been generated for C. oleifera . The published genome of Camellia lanceoleosa provides an important reference for analyzing the formation and regulation of important traits such as self-incompatibility and lipid synthesis ( Gong et al, 2022 ). Construction of a high-quality reference genome at the chromosome level of C. oleifera has demonstrated that the alleles regulating the synthesis of C. oleifera have been under artificial selection, and this genome resource could provide new insights with implications for the genetic improvement of C. oleifera varieties ( Lin et al, 2022 ).…”