A library where books copy themselves and squeeze duplicates between the shelves quickly descends into chaos. That is roughly what the sapote genome looks like. This tropical tree bears sweet fruit that many know as chiku. Scientists have now assembled the full sequence of its DNA for the first time, and it turned out that the genome is inflated to 1.63 billion base pairs, twice as large as those of its closest relatives, even though the number of genes has barely changed.
The culprits turned out to be mobile elements, stretches of DNA capable of moving and multiplying within the genome. The Gypsy retrotransposons were especially active, inserting themselves into DNA like self-replicating books. By comparing sapote with four other species in the Sapotaceae family, the researchers reconstructed the history of these invasions. The peak of Gypsy activity came around 0.09 million years ago, which by evolutionary standards is yesterday. These insertions did not add new genes; they inflated the spaces between them, as if thousands of blank pages had been slipped between the real books in a library.
The cell did not remain passive. Chemical marks on DNA, a kind of "do not touch" label, are more common in sapote than in its relative M. longifolia, especially on old Gypsy insertions. This is like librarians working overtime to keep the proliferating books under lock and key. Such enhanced methylation helps stabilize the genome, preventing mobile elements from stirring again.
But the chaos also brought an unexpected benefit. Among the duplicated genes of sapote, 5736 turned out to have been carried by transposons, and these genes are especially often involved in the production of flavonoids and phenylpropanoids, the compounds responsible for taste, aroma and medicinal properties. In other words, the parasitic books accidentally brought along recipes for new dishes.
Now that sapote has a reference genome, breeders can search for the genes responsible for sweetness and aroma and develop improved varieties without genetic engineering. And sapote itself is becoming a model for understanding how plants survive "genomic obesity" and turn it into new opportunities.
The sapodilla genome is only 1.6 times larger than the human genome, yet it contains just about 35 thousand genes versus 20 thousand in humans: the difference in size is almost entirely due to repeats, not gene number.
Not published on arXiv. Here are its page, the PDF and the formalization: you can check it yourself, not only read our account.