Abstract
Tea plants (Camellia sinensis) are commercially cultivated in >60 countries, and their fresh leaves are processed into tea, which is the most widely consumed beverage in the world. Although several chromosome-level tea plant genomes have been published, they collapsed the two haplotypes and ignored a large number of allelic variations that may underlie important biological functions in this species. Here, we present a phased chromosome-scale assembly for an elite oolong tea cultivar, “Huangdan”, that is well known for its high levels of aroma. Based on the two sets of haplotype genome data, we identified numerous genetic variations and a substantial proportion of allelic imbalance related to important traits, including aroma- and stress-related alleles. Comparative genomics revealed extensive structural variations as well as expansion of some gene families, such as terpene synthases (TPSs), that likely contribute to the high-aroma characteristics of the backbone parent, underlying the molecular basis for the biosynthesis of aroma-related chemicals in oolong tea. Our results uncovered the genetic basis of special features of this oolong tea cultivar, providing fundamental genomic resources to study evolution and domestication for the economically important tea crop.
Highlights
The development of high-throughput sequencing has vigorously promoted research progress in plant genomics and genetics, especially single-molecule long-read sequencing and high-throughput chromatin conformation capture (Hi-C) technology, which have allowed complete plant genome sequencing and assembly at a low cost[1]
Assessment through long-terminal repeat (LTR) annotation showed that the LTR Assembly Index (LAI) score[28] of the HD monoploid assembly was 16.6 (Table 1 and Fig. 2c), indicating that more LTRs were recovered in our assembly than in other published tea genomes (Supplementary Table 5)
Aroma plays a vital role in the quality of tea, and in addition to the tea manufacturing process, tea cultivars are the basis for the formation of tea aroma
Summary
The development of high-throughput sequencing has vigorously promoted research progress in plant genomics and genetics, especially single-molecule long-read sequencing and high-throughput chromatin conformation capture (Hi-C) technology, which have allowed complete plant genome sequencing and assembly at a low cost[1]. Diploid or polyploid genomes consist of two or more homologous chromosome sets. Most plant reference genome assemblies are collapsed homologous. Wang et al Horticulture Research (2021)8:107 technology and advanced assembly algorithms will help. ALLHiC is a powerful tool for genome research on heterozygous diploid and polyploid plants. At present, >2 billion cups of tea are consumed worldwide every day. These teas are mainly manufactured by processing fresh tea leaves and are rich in characteristic secondary compounds, including theanine, caffeine, catechins, and volatiles, which are beneficial to human health[9]. The United Nations General Assembly (UNGA) designated May 21 as “International Tea Day” to praise the high value of tea to the global society, economy, and culture, especially its significant role in rural poverty reduction and development in developing countries
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