The chromosome-scale genome reveals the evolution and diversification after the recent tetraploidization event in tea plant

Abstract

Tea is one of the most popular nonalcoholic beverages due to its characteristic secondary metabolites with numerous health benefits. Although two draft genomes of tea plant (Camellia sinensis) have been published recently, the lack of chromosome-scale assembly hampers the understanding of the fundamental genomic architecture of tea plant and potential improvement. Here, we performed a genome-wide chromosome conformation capture technique (Hi-C) to obtain a chromosome-scale assembly based on the draft genome of C. sinensis var. sinensis and successfully ordered 2984.7 Mb (94.7%) scaffolds into 15 chromosomes. The scaffold N50 of the improved genome was 218.1 Mb,~157-fold higher than that of the draft genome. Collinearity comparison of genome sequences and two genetic maps validated the high contiguity and accuracy of the chromosome-scale assembly. We clarified that only one Camellia recent tetraploidization event (CRT, 58.9-61.7 million years ago (Mya)) occurred after the core-eudicot common hexaploidization event (146.6-152.7 Mya). Meanwhile, 9243 genes (28.6%) occurred in tandem duplication, and most of these expanded after the CRT event. These gene duplicates increased functionally divergent genes that play important roles in tea-specific biosynthesis or stress response. Sixty-four catechin-and caffeine-related quantitative trait loci (QTLs) were anchored to chromosome assembly. Of these, two catechin-related QTL hotspots were derived from the CRT event, which illustrated that polyploidy has played a dramatic role in the diversification of tea germplasms. The availability of a chromosome-scale genome of tea plant holds great promise for the understanding of genome evolution and the discovery of novel genes contributing to agronomically beneficial traits in future breeding programs.

Metabolite signatures of diverse Camellia sinensis tea populations

“…The rich constituents of specialized metabolites in the growing tea leaf are believed to be essential for the flavor and quality of tea products 12 , 18 , 19 , 35 , 36 , 51 . Therefore, tea plant offers a good model to study the molecular and genetic basis underpinning the abundance, diversity, and regulation of specialized metabolites in plants.…”

“…Recently, the draft genomes of CSA and CSS have been published 18 , 19 , 35 , 36 , making it feasible to conduct genome-wide large-scale omics analyses. The tea genome is large (~3.1 GB) and complex, containing at least 34,000 protein-coding genes.…”

Transcriptional analysis reveals key insights into seasonal induced anthocyanin degradation and leaf color transition in purple tea (Camellia sinensis (L.) O. Kuntze)

“…Moreover, distribution of anthocyanin biosynthesis genes in 11 of 15 chromosomes ( Fig. 5) including Chr1, Chr2, Chr3 and Chr10 successfully mapped with quality related QTLs, suggests close linkage between anthocyanin and other quality related parameters in tea 26 .…”

Biochemical characterization of specific Alanine Decarboxylase (AlaDC) and its ancestral enzyme Serine Decarboxylase (SDC) in tea plants (Camellia sinensis)

“…The phylogenetic tree of these AADs was constructed using the Minimum-Evolution method with MEGA X. To determine the exon-intron structures of CsAlaDC and CsSDC , the cDNA sequences of those two genes were aligned to the genomic sequence of C. sinensis [ 37 ]. Alignment of the protein sequences of CsAlaDC and CsSDC was conducted by MEGA X.…”