Tea is the world's oldest and most popular caffeine-containing beverage with immense economic, medicinal, and cultural importance. Here, we present the first high-quality nucleotide sequence of the repeat-rich (80.9%), 3.02-Gb genome of the cultivated tea tree Camellia sinensis. We show that an extraordinarily large genome size of tea tree is resulted from the slow, steady, and long-term amplification of a few LTR retrotransposon families. In addition to a recent whole-genome duplication event, lineage-specific expansions of genes associated with flavonoid metabolic biosynthesis were discovered, which enhance catechin production, terpene enzyme activation, and stress tolerance, important features for tea flavor and adaptation. We demonstrate an independent and rapid evolution of the tea caffeine synthesis pathway relative to cacao and coffee. A comparative study among 25 Camellia species revealed that higher expression levels of most flavonoid- and caffeine- but not theanine-related genes contribute to the increased production of catechins and caffeine and thus enhance tea-processing suitability and tea quality. These novel findings pave the way for further metabolomic and functional genomic refinement of characteristic biosynthesis pathways and will help develop a more diversified set of tea flavors that would eventually satisfy and attract more tea drinkers worldwide.

High-repetition rate femtosecond lasers are shown to drive heat accumulation processes that are attractive for rapid writing of low-loss optical waveguides in transparent glasses. A novel femtosecond fiber laser system (IMRA America, FCPA muJewel) providing variable repetition rate between 0.1 and 5 MHz was used to study the relationship between heat accumulation and resulting waveguide properties in fused silica and various borosilicate glasses. Increasing repetition rate was seen to increase the waveguide diameter and decrease the waveguide loss, with waveguides written with 1-MHz repetition rate yielding ~0.2-dB/cm propagation loss in Schott AF45 glass. A finite-difference thermal diffusion model accurately tracks the waveguide diameter as cumulative heating expands the modification zone above 200-kHz repetition rate.

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A variable (0.2 to 5 MHz) repetition rate femtosecond laser was applied to delineate the role of thermal diffusion and heat accumulation effects in forming low-loss optical waveguides in borosilicate glass across a broad range of laser exposure conditions. For the first time, a smooth transition from diffusion-only transport at 200 kHz repetition rate to strong heat accumulation effects at 0.5 to 2 MHz was observed and shown to drive significant variations in waveguide morphology, with rapidly increasing waveguide diameter that accurately followed a simple thermal diffusion model over all exposure variables tested. Amongst these strong thermal trends, a common exposure window of 200 mW average power and approximately 15-mm/s scan speed was discovered across the range of 200 kHz to 2 MHz repetition rates for minimizing insertion loss despite a 10-fold drop in laser pulse energy. Waveguide morphology and thermal modeling indicate that strong thermal diffusion effects at 200 kHz give way to a weak heat accumulation effect at approximately 1 microJ pulse energy for generating low loss waveguides, while stronger heat accumulation effects above 1-MHz repetition rate offered overall superior guiding. A comprehensive characterization of waveguide properties is presented for laser writing in the thermal diffusion and heat accumulation regimes. The waveguides are shown to be thermally stable up to 800 degrees C and can be written in a convenient 520 microm depth range with low spherical aberration.