Pomegranate (Punica granatum L.) is a perennial fruit crop grown since ancient times that has been planted worldwide and is known for its functional metabolites, particularly punicalagins. We have sequenced and assembled the pomegranate genome with 328 Mb anchored into nine pseudo-chromosomes and annotated 29 229 gene models. A Myrtales lineage-specific whole-genome duplication event was detected that occurred in the common ancestor before the divergence of pomegranate and Eucalyptus. Repetitive sequences accounted for 46.1% of the assembled genome. We found that the integument development gene INNER NO OUTER (INO) was under positive selection and potentially contributed to the development of the fleshy outer layer of the seed coat, an edible part of pomegranate fruit. The genes encoding the enzymes for synthesis and degradation of lignin, hemicelluloses and cellulose were also differentially expressed between soft- and hard-seeded varieties, reflecting differences in their accumulation in cultivars differing in seed hardness. Candidate genes for punicalagin biosynthesis were identified and their expression patterns indicated that gallic acid synthesis in tissues could follow different biochemical pathways. The genome sequence of pomegranate provides a valuable resource for the dissection of many biological and biochemical traits and also provides important insights for the acceleration of breeding. Elucidation of the biochemical pathway(s) involved in punicalagin biosynthesis could assist breeding efforts to increase production of this bioactive compound.

For a better understanding terpenoid volatile production in Camellia sinensis, global terpenoid synthase gene (TPS) transcription analysis was conducted based on transcriptomic data combined with terpenoid metabolic profiling under different abiotic stress conditions. Totally 80 TPS-like genes were identified. twenty-three CsTPS genes possessed a complete coding sequence and most likely were functional. The remaining 57 in the currently available database lack essential gene structure or full-length transcripts. Distinct tempo-spatial expression patterns of CsTPS genes were found in tea plants. 17 genes were substantially expressed in all the tested organs with a few exceptions. The other 17 were predominantly expressed in leaves whereas additional eight were primarily expressed in flowers. Under the treatments of cold acclimation, salt and polyethylene glycol, CsTPS67,-69 and-71 were all suppressed and the inhibited expression of many others were found in multiple stress treatments. However, methyl jasmonate resulted in the enhanced expression of the majority of CsTPS genes. These transcription data were largely validated using qPCR. Moreover, volatile terpenoid profiling with leaves, flowers and stress-treated plants revealed a general association between the abundances of mono-and sesqui-terpenoids and some CsTPS genes. These results provide vital information for future studies on CsTPS regulation of terpenoid biosynthesis. Plant terpenoids (isoprene-C5, monoterpenes-C10, sesquiterpenes-C15, diterpenes-C20, and polyterpenoids-C5xn) possess diverse functions in plant growth and development 1-7. They play significant ecological roles in the interactions between plants and stress conditions. Generally, terpenoid molecules smaller than diterpenoids are volatile and well known for their airborne signaling function, particularly against herbivore attack 8,9. High volatility of monoterpenes and sesquiterpenes enhances the flavor and aroma of crop products 10 such as tea, which is a popular beverage well known for its fragrance and aroma 11. Tea volatile terpenoids not only are defense components against insects 12 or high solar radiation 13 , but are also essential odorants of tea products with a direct influence on flavor and quality 14-16. Aroma from volatile terpenoids is one of the main sensory properties affecting tea flavor quality 17. For instance, monoterpene alcohols such as linalool and geraniol, two of the most abundant and odor active terpenoids in tea 15 , impart pleasant floral scent to green tea and black tea 17. Terpene synthases possess a characteristic catalytic function that generates multiple terpenoid products with one substrate 18 , thus collectively contributing to numerous and different structures of plant terpenoids in addition to other modifying enzymes such as uridine diphosphate (UDP)-glucosyl transferases 19,20 and P450s 21. TPSs are responsible for converting the precursors of geranyl diphosphate (GPP), isoprenyl diphosphate (IPP), farnesyl diphosphate (FPP) and geranylgeranyl diphosphat...

The expanded outer seed coat and the rigid inner seed coat of pomegranate seeds, both affect the sensory qualities of the fruit and its acceptability to consumers. Pomegranate seeds are also an appealing model for the study of seed coat differentiation and development. We conducted nontarget metabolic profiling to detect metabolites that contribute to the morphological differentiation of the seed coats along with transcriptomic profiling to unravel the genetic mechanisms underlying this process. Comparisons of metabolites in the lignin biosynthetic pathway accumulating in seed coat layers at different developmental stages revealed that monolignols, including coniferyl alcohol and sinapyl alcohol, greatly accumulated in inner seed coats and monolignol glucosides greatly accumulated in outer seed coats. Strong expression of genes involved in monolignol biosynthesis and transport might explain the spatial patterns of biosynthesis and accumulation of these metabolites. Hemicellulose constituents and flavonoids in particular accumulated in the inner seed coat, and candidate genes that might be involved in their accumulation were also identified. Genes encoding transcription factors regulating monolignol, cellulose, and hemicellulose metabolism were chosen by coexpression analysis. These results provide insights into metabolic factors influencing seed coat differentiation and a reference for studying seed coat developmental biology and pomegranate genetic improvement.

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