Tea genome: How a single leaf can produce so many flavours

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Despite tea’s immense cultural and economic significance, relatively little is known about the shrub behind the tea leaves. Yet news of the first mapping of the tea tree genome may help explain how tea leaves are so rich in antioxidants and caffeine, and why Camellia sinensis differs genetically from its close relatives.

The genus contains over 100 species, though only two major varieties, C. sinensis var. assamica and C. sinensis var. sinensis, are grown commercially for making tea.

“There are many diverse flavours, but the mystery is what determines or what is the genetic basis of tea flavours,” says plant geneticist Lizhi Gao of Kunming Institute of Botany in China. 

Previous studies have suggested that tea owes much of its flavour to a group of flavonoids, antioxidant molecules that are thought to help plants survive in their environments. One, the bitter-tasting catechin, is particularly associated with tea flavour. Levels of catechin and other flavonoids vary among Camellia species, as does caffeine. 

Gao and his colleagues found that C. sinensis leaves not only contain high levels of catechins, caffeine and flavonoids, but also have multiple copies of the genes that produce caffeine and flavonoids. The results have been published in Molecular Plant.

Caffeine and flavonoids such as catechins are not proteins, and therefore not encoded in the genome directly, but genetically encoded proteins in the tea leaves manufacture them. 

All Camellia species have genes for the caffeine- and flavonoid-producing pathways, but each species expresses those genes at different levels. That variation may explain why C. sinensis leaves are suitable for making tea, while other Camellia species’ leaves aren’t. 

Gao and his colleagues estimate that two-thirds of the base pairs in the tea tree genome are part of retrotransposon sequences, or “jumping genes”, which have copied and pasted themselves into different spots in the genome numerous times. 

The large number of retrotransposons has resulted in a dramatic expansion in genome size of the tea tree, and possibly many duplicates of certain genes, including the disease-resistant ones. 

The researchers think that these “expanded” gene families must have helped tea trees adapt to different climates and environmental stresses, as tea trees grow well on several continents in a wide range of climate conditions. Since much of the retrotransposon copying and pasting appears to have happened relatively recently in the tea tree’s evolutionary history, the researchers theorise that at least some of the duplications are responses to cultivation. 

However, these duplicated genes and the large number of repeat sequences also turned assembling a tea tree genome into an uphill battle. “Our lab has successfully sequenced and assembled more than twenty plant genomes,” says Gao. “But this genome, the tea tree genome, was tough.” 

For one thing, the genome turned out to be much larger than initially expected. At 3.02bn base pairs in length, it is more than four times the size of the coffee plant’s genome and much larger than most sequenced plant species. 

Further complicating the picture is the fact that many of the genes are duplicates or near-duplicates. Whole genomes are too long to sequence in one piece, so instead scientists must copy many thousands of genome fragments, sequence them, and identify overlapping sequences that appear in multiple fragments. 

Those overlap sites become signposts for lining up the fragments in the correct order. Yet when the genome itself contains sequences that are repeated hundreds or thousands of times, those overlaps disappear into the crowd of repeats—rather like assembling a million-piece jigsaw puzzle where all the middle pieces look almost exactly alike. 

In the end, assembling the genome took the team over five years, even with modern sequencing.

And there is still more work to do, both in terms of double-checking the genome draft and sequencing different tea tree varieties from around the world, says Gao. 

Together with the construction of genetic maps and new sequencing technologies, we are working on an updated tea tree genome that will investigate some of the flavour

We will look at gene copy number variation to see how they affect tea properties, like flavour. We want to get a map of different tea tree variation and answer how it was domesticated, cultivated, and dispersed to different continents of the world,” Gao adds. 

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