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

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.

Identification and distribution of a single nucleotide polymorphism responsible for the catechin content in tea plants

Catechins are the predominant products in tea plants and have essential functions for both plants and humans.Several genes encoding the enzymes regulating catechin biosynthesis have been identified,and the identification of single nucleotide polymorphisms(SNPs)resulting in nonsynonymous mutations within these genes can be used to establish a functional link to catechin content.Therefore,the transcriptomes of two parents and four filial offspring were sequenced using next-generation sequencing technology and aligned to the reference genome to enable SNP mining.Subsequently,176 tea plant accessions were genotyped based on candidate SNPs using kompetitive allelespecific polymerase chain reaction(KASP).The catechin contents of these samples were characterized by highperformance liquid chromatography(HPLC),and analysis of variance(ANOVA)was subsequently performed to determine the relationship between genotypes and catechin content.As a result of these efforts,a SNP within the chalcone synthase(CHS)gene was shown to be functionally associated with catechin content.Furthermore,the geographical and interspecific distribution of this SNP was investigated.Collectively,these results will contribute to the early evaluation of tea plants and serve as a rapid tool for accelerating targeted efforts in tea breeding.

METABOLIC AND TRANSCRIPTOME ANALYSIS REVEALS METABOLITE VARIATION AND FLAVONOID REGULATORY NETWORKS IN FRESH SHOOTS OF TEA(CAMELLIA SINENSIS)OVER THREE SEASONS

Metabolites,especially secondary metabolites,are very important in the adaption of tea plants and the quality of tea products.Here,we focus on the seasonal variation in metabolites of fresh tea shoots and their regulatory mechanism at the transcriptional level.The metabolic profiles of fresh tea shoots of 10 tea accessions collected in spring,summer,and autumn were analyzed using ultra-performance liquid chromatography coupled with quadrupole-obitrap mass spectrometry.We focused on the metabolites and key genes in the phenylpropanoid/flavonoid pathway integrated with transcriptome analysis.Multivariate statistical analysis indicates that metabolites were distinctly different with seasonal alternation.Flavonoids,amino acids,organic acids and alkaloids were the predominant metabolites.Levels of most key genes and downstream compounds in the flavonoid pathway were lowest in spring but the catechin quality index was highest in spring.The regulatory pathway was explored by constructing a metabolite correlation network and a weighted gene co-expression network.