THE PROCESS IN MOTION

What does the canephora genome say?

Start the scene or choose a stage. The animation simplifies the mechanism; what follows gives the details and the available references.

▶ Play the process01Two sets of eleven02The flower refuses its own pollen03A parent of arabica04The caffeine genes05Slower, more productive

Two sets of eleven

Canephora is diploid: 2n = 22 chromosomes, with a base number x = 11. It carries two sets of eleven, one from each parent. The first genome of the genus, published in 2014, was read on a doubled haploid, a plant whose two sets are identical: 568.6 megabases assembled out of an estimated 710.

Read the stages without animation

1. Two sets of elevenCanephora is diploid: 2n = 22 chromosomes, with a base number x = 11. It carries two sets of eleven, one from each parent. The first genome of the genus, published in 2014, was read on a doubled haploid, a plant whose two sets are identical: 568.6 megabases assembled out of an estimated 710.
2. The flower refuses its own pollenCanephora is allogamous: the flower does not fertilize with its own pollen, and an isolated tree bears nothing. All clonal programs, from the Javanese BP 534 to the Brazilian Emcapa, therefore require planting several compatible clones together. Arabica, for its part, fertilizes itself at over 90%.
3. A parent of arabicaArabica was born between 610,000 and 350,000 years before us from a hybridization between the ancestors of canephora and eugenioides, followed by a doubling of the chromosomes. Hence its four sets, and this result: half the genome of every arabica is canephora.
4. The caffeine genesCaffeine is made by three methyltransferases, enzymes that graft a methyl group onto the starting molecule: XMT, MXMT and DXMT. Canephora has three copies, highly expressed; arabica six, but less active. Result: 2.7% caffeine against 1.5%, and 3 to 7% sugars against 6 to 9%.
5. Slower, more productiveCoste gave the planter's figures: nine to eleven months from flower to ripe cherry, against six to eight for arabica; five kilos of cherries for one kilo of marketable coffee; 700 to 1,000 kg/ha in full production, against 400 to 600.

To remember: A tree alone gives nothing: canephora reproduces by crossing, hence its diversity and its plots of mixed clones.

In history: Coste had noted the 22 chromosomes in 1955 without being able, he wrote, to “draw any conclusion” from them; the conclusion came in 2014 and 2024.

Read the full article and its sources ↓

Canephora is diploid, with 2n = 22 chromosomes and a base number x = 11. It therefore carries two sets of eleven chromosomes, one from each parent, like most plants. Coste records the fact in 1955 and stops there: one cannot, he notes, “draw any conclusion from it.”

The conclusion came later, in two stages.

First stage, 2014. Denoeud and his coauthors publish in Science the first genome of the genus. They sequenced it on a doubled haploid of canephora, the accession DH200-94, that is, a plant whose two sets of chromosomes are identical: there is only one version of each gene to read, and the assembly is simplified.

The result comes down to two numbers: 568.6 megabases assembled on a genome estimated at 710. Gene order is conserved there among the asterids, the large group of flowering plants to which the coffee tree belongs: in all these neighbors, genes follow one another in the same order.

Other gene families, on the other hand, are amplified, that is, present in multiple copies: the N-methyltransferases of caffeine, defense genes, the enzymes of alkaloids and flavonoids. These are exactly the functions that make the character of the plant.

Second stage, 2024. Salojärvi and his coauthors establish in Nature Genetics that arabica was born between 610,000 and 350,000 years before us. Its origin is a hybridization between the ancestors of canephora and of eugenioides, followed by a chromosome doubling. Hence this result: half the genome of every arabica is canephora.

Coste 1955, p. 331; Denoeud et al., “The coffee genome provides insight into the convergent evolution of caffeine biosynthesis,” Science, 345 (6201), 2014, p. 1181-1184; Salojärvi et al., Nature Genetics, 2024, p. 722-725 (genetics digest); level: peer-reviewed journals

Canephora is allogamous: the flower does not fertilize with its own pollen, and an isolated tree bears nothing. This is why all clonal programs, from the Javanese BP 534 to the Brazilian Emcapa, require planting several compatible clones together, and why the species is genetically far more diverse than arabica, which is more than 90% self-pollinating. World Coffee Research warns that its genealogy poster is deceptive: the arabica circle, saturated with arrows, does not reflect more diversity, only more known directed crosses; the reality is the opposite.

Denoeud et al. 2014 (“allogamous diploid”); WCR 2024, poster user guide, p. 3; WCR 2025, p. 100; Coste 1955, p. 45 (self-pollination of arabica); LC ch. 1

The chemistry of the bean can be read in this genome. The Ugandan manual gives the baseline gap: 2.7% caffeine in canephora against 1.5% for arabica, and 3 to 7% sugars against 6 to 9%.

Yang's review (2026) says by what mechanism. Caffeine is made by three methyltransferases, enzymes that graft a methyl group onto the starting molecule: XMT, MXMT and DXMT. Canephora has three copies, highly expressed; arabica has six, but less active. The number of copies therefore decides nothing; it is activity that counts.

The rest of the gaps go in the same direction. The difference in lipid content between the two species exceeds 30%. A canephora fruit contains 16.9 mg of 5-caffeoylquinic acid against 13.6 in arabica, which on the other hand accumulates 7.3 to 11.4% sucrose.

These gaps show up in the cup, and they can be followed one by one. More caffeine and more chlorogenic acids, hence more bitterness. Less fat, hence a drier body. Less sugar, hence less material to caramelize in roasting.

Coste added the planter's figures, which describe the same plant seen from the field. Nine to eleven months from flower to ripe cherry, against six to eight for arabica. Five kilos of cherries for one kilo of marketable coffee. And 700 to 1,000 kg/ha in full production, against 400 to 600: slower to ripen, but markedly more productive.

UCDA 2019, § 1.2, p. 4; Yang et al., Agriculture, 2026, p. 3-5 (digest); Coste 1955, p. 46-48 and 324-325 (table with scrambled layout, figure to be rechecked); LC ch. 17 UCDA 2019, p. 4 and 9; Coste 1955, p. 46-48, 324-325 and 331; Denoeud et al. 2014; Yang et al. 2026; Uganda country profile (pays.json)