Specialized metabolites not only play important roles in biotic and abiotic stress adaptation of tea plants (Camellia sinensis (L.) O. Kuntze) but also contribute to the unique flavor of tea, the most important nonalcoholic beverage. However, the molecular networks and major genes that regulate specialized metabolites in tea plants are not well understood. Here, we constructed a population-level pan-transcriptome of the tea plant leaf using second-leaf transcriptome data from 134 accessions to investigate global expression differences in the population, expression presence or absence variations (ePAVs), and differentially expressed genes (DEGs) between pure Camellia sinensis var. assamica (CSA) and pure Camellia sinensis var. sinensis (CSS) accessions. Next, we used a genome-wide association study, a quantitative trait transcript study, and a transcriptome-wide association study to integrate genotypes, accumulation levels of specialized metabolites, and expression levels of pan-transcriptome genes to identify candidate regulatory genes for flavor-related metabolites and to construct a regulatory network for specialized metabolites in tea plants. The pan-transcriptome contains 30 482 expressed genes, 4940 and 5506 of which were newly annotated from a de novo transcriptome assembly without a reference and a genome reference-based assembly, respectively. DEGs and ePAVs indicated that CSA and CSS were clearly differentiated at the population transcriptome level, and they were closely related to abiotic tolerance and secondary metabolite synthesis phenotypes of CSA and CSS based on gene annotations. The regulatory network contained 212 specialized metabolites, 3843 candidate genes, and 3407 eQTLs, highlighting many pleiotropic candidate genes, candidate gene-rich eQTLs, and potential regulators of specialized metabolites. These included important transcription factors in the AP2/ERF-ERF, MYB, WD40, and bHLH families. CsTGY14G0001296, an ortholog of AtANS, appeared to be directly related to variation in proanthocyanins in the tea plant population, and the CsTGY11G0002074 gene encoding F3′5′H was found to contribute to the biased distribution of catechins between pure CSAs and pure CSSs. Together, these results provide a new understanding of the metabolite diversity in tea plants and offer new insights for more effective breeding of better-flavored tea varieties.
The lemon (Citrus limon; family Rutaceae) is one of the most important and popular fruit worldwide. Lemon also tolerates Huanglongbing disease, which is a devastating citrus disease. Here, we produced a gap-free and haplotype-resolved chromosome-scale genome assembly of the lemon by combining Pacific Biosciences circular consensus sequencing, Oxford Nanopore 50-kb ultra-long, and high-throughput chromatin conformation capture technologies. The assembly contained nine-pair chromosomes with a contig N50 of 35.6 Mb and zero gaps. While a total of 633.0 Mb genomic sequences were generated. The origination analysis identified 338.5 Mb genomic sequences originating from citron (53.5 %), 147.4 Mb from mandarin (23.3 %), and 147.1 Mb from pummelo (23.2 %). The genome included 30,528 protein-coding genes, and most of the assembled sequences were found to be repetitive sequences. Several significantly expanded gene families were associated with plant-pathogen interactions, plant hormone signal transduction, and the biosynthesis of major active components, such as terpenoids and flavor. Most HLB-tolerant genes were expanded in the lemon genome, such as 2-oxoglutarate (2OG) / Fe(II)-dependent oxygenase and constitutive disease resistance 1, cell wall-related genes, and lignin synthesis genes. Comparative transcriptomic analysis showed that the phloem regeneration and lower levels of phloem plugging are the elements that contribute to HLB tolerance in lemon. Our results provide insight into lemon genome evolution, active component biosynthesis, and genes associated with HLB tolerance.
In plants, 5mC DNA methylation is an important and conserved epistatic mark involving genomic stability, gene transcriptional regulation, developmental regulation, abiotic stress response, metabolite synthesis, etc. However, the roles of 5mC DNA methylation modification (5mC methylation) in tea plant growth and development (in pre-harvest) and flavor substance synthesis in pre- and post-harvest is unknown. We therefore conducted a comprehensive methylation analysis of four key pre-harvest tissues (root, leaf, flower, and fruit) and two processed leaves during oolong tea postharvest processing. We found that differential 5mC methylation among four key tissues are closely related to tissue functional differentiation and that tissue-specific expressed genes responsible for tissue-specific functions maintain relatively low 5mC methylation levels relative to non-tissue-specific expressed genes. Importantly, hypomethylation modifications of CsAlaDC and TS/GS genes in roots provided the molecular basis for the dominant synthesis of theanine in roots. In addition, integrating of 5mC DNA methylationomics, metabolomics, and transcriptomics of postharvest leaf revealed that content changes in flavor metabolites during oolong tea processing were closely associated with transcription level changes in corresponding metabolite synthesis genes, and changes in transcript levels of these important synthesis genes were strictly regulated by 5mC methylation. We further reported that some key genes during processing are regulated by 5mC methylation, which can effectively explain the content changes of important aroma metabolites, including α-farnesene, nerolidol, lipids, and taste substances such as catechins. Our results not only highlight the key roles of 5mC methylation in important flavor substance synthesis in pre- and post-harvest, but also provide epimutation-related gene targets for future improvement of tea quality or breeding of whole-tissue high theanine varieties.
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