5mC DNA methylation modification-mediated regulation in tissue functional differentiation and important flavor substance synthesis of tea plant (Camellia sinensis L.)

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 processing)and flavor substance synthesis in pre-and post-harvest processing are 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 post-harvest processing.We found that differential 5mC methylation among four key tissues is closely related to tissue functional differentiation and that genes expressed tissue-specifically,responsible for tissue-specific functions,maintain relatively low 5mC methylation levels relative to non-tissue-specifically 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,integration of 5mC DNA methylationomics,metabolomics,and transcriptomics of post-harvest leaves 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 report that some key genes during processing are regulated by 5mC methylation,which can effectively explain the content changes of important aroma metabolites,includingα-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 processing,but also provide epimutation-related gene targets for future improvement of tea quality or breeding of whole-tissue high-theanine varieties.

Evolutionary genomics of structural variation in the tea plant,Camellia sinensis

Structural variants(SVs)are a type of genetic variation that contribute substantially to phenotypic diversity and evolution.Further study of SVs will help us understand the influence of SVs associated with tea quality and stress resistance and provide new insight into tea plant breeding improvement and genetic research.However,SVs have not been thoroughly discovered in the tea plant genomes.Herein,we constructed a large-scale SV map across a population of 107 resequenced genomes,including both ancient and cultivated tea plants.A total of 44,240 highconfident SVs were identified,including 34,124 DEL(deletions),4,448 DUP(duplications),2,503 INV(inversions),544 INS(insertions)and 2,621 TRA(translocations).In total,12,400 protein-coding genes were overlapped with SVs,of which 49.5%were expressed in all five tea tissues.SVbased analysis of phylogenetic relationships and population structure in tea plants showed a consistent evolutionary history with the SNP-based results.We also identified SVs subject to artificial selection and found that genes under domestication were enriched in metabolic pathways involving theanine and purine alkaloids,biosynthesis of monoterpenoid,phenylpropanoid,fatty acid,and isoflavonoid,contributing to traits of agronomic interest in tea plants.In addition,a total of 27 terpene synthase(TPS)family genes were selected during domestication.These results indicate that these SVs could provide extensive genomic information for tea quality improvement.

Whole-genome Duplication Reshaped Adaptive Evolution in A Relict Plant Species,Cyclocarya paliurus

Cyclocarya paliurus is a relict plant species that survived the last glacial period and shows a population expansion recently.Its leaves have been traditionally used to treat obesity and diabetes with the well-known active ingredient cyclocaric acid B.Here,we presented three C.paliurus genomes from two diploids with different flower morphs and one haplotype-resolved tetraploid assembly.Comparative genomic analysis revealed two rounds of recent whole-genome duplication events and identified 691 genes with dosage effects that likely contribute to adaptive evolution through enhanced photosynthesis and increased accumulation of triterpenoids.Resequencing analysis of 45 C.paliurus individuals uncovered two bottlenecks,consistent with the known events of environmental changes,and many selectively swept genes involved in critical biological functions,including plant defense and secondary metabolite biosynthesis.We also proposed the biosynthesis pathway of cyclocaric acid B based on multi-omics data and identified key genes,in particular gibberellinrelated genes,associated with the heterodichogamy in C.paliurus species.Our study sheds light on evolutionary history of C.paliurus and provides genomic resources to study the medicinal herbs.

Recent Advances in Assembly of Complex Plant Genomes

Over the past 20 years,tremendous advances in sequencing technologies and computational algorithms have spurred plant genomic research into a thriving era with hundreds of genomes decoded already,ranging from those of nonvascular plants to those of flowering plants.However,complex plant genome assembly is still challenging and remains difficult to fully resolve with conventional sequencing and assembly methods due to high heterozygosity,highly repetitive sequences,or high ploidy characteristics of complex genomes.Herein,we summarize the challenges of and advances in complex plant genome assembly,including feasible experimental strategies,upgrades to sequencing technology,existing assembly methods,and different phasing algorithms.Moreover,we list actual cases of complex genome projects for readers to refer to and draw upon to solve future problems related to complex genomes.Finally,we expect that the accurate,gapless,telomere-totelomere,and fully phased assembly of complex plant genomes could soon become routine.