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Botany · Species and varieties

Eugenioides, arabica’s other parent

A wild coffee species of the East African highlands and one of the two parents of arabica, the one that passed on its plastids. In one study its seeds held about a fifth of the caffeine of canephora.

Across the chain: Science

Source-checkedby Coffearium verification pass· Last source-checked 22 Oct 2026· Prepared with AI assistance· 11 sources (9 tier A)· 1 contested· Updated 22 Oct 2026
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Contents
  • *Coffea eugenioides* is a shrub or tree native from South Sudan to east-central and eastern tropical Africa.1
  • *C. arabica* (2n = 44) is a hybrid of *C. eugenioides* and *C. canephora*, each with 2n = 22.2,3
  • Arabica’s plastid genome derives from *C. eugenioides*; in the coffee crosses studied, chloroplast DNA passed only through the mother, which makes eugenioides the maternal parent.2,4
  • In one study of four accessions, green seeds held on average 0.51% caffeine (dry matter), against 2.64% in *C. canephora*.5
  • The IUCN Red List (International Union for Conservation of Nature) lists the species as Least Concern.10

A wild coffee from East Africa#

Coffea eugenioides is one of the wild species of the coffee genus, Coffea. It is a shrub or tree of the wet tropics.1 Kew’s Plants of the World Online gives its native range as South Sudan to east-central and eastern tropical Africa.1 The countries listed are the Democratic Republic of Congo, Kenya, Rwanda, South Sudan, Tanzania and Uganda.1

It is a plant of the highlands. The Specialty Coffee Association (SCA) describes it as indigenous to the highlands of East Africa.8 A 1984 paper on wild coffees of Kenya lists it, in western Kenya, among the species of altitudes above 1,000 m.11 A coffee science textbook chapter counts it among the species with a wide altitudinal distribution and places it in humid habitats.9

Its range is smaller than that of C. canephora, the species grown as robusta. A 2024 genome study calls eugenioides more range-limited, while C. canephora has one of the widest ranges in the genus.2 The IUCN Red List (International Union for Conservation of Nature) lists C. eugenioides as Least Concern.10 How it compares with the other wild species is shown in the species index in The coffee genus.

Arabica’s maternal parent#

C. arabica arose when C. eugenioides and C. canephora crossed in the wild.2,3 Each parent is diploid: it carries two sets of 11 chromosomes, 22 in all.2 Arabica kept the sets of both parents and has 44 chromosomes.2

The two parents did not play the same part. Besides the nucleus, a plant cell holds chloroplasts, a kind of plastid with DNA of its own (chloroplast DNA).4 In the coffee crosses studied, chloroplast DNA passed only through the mother.4 Arabica’s plastid genome derives from C. eugenioides.2 Put together, the two findings make eugenioides the maternal parent of arabica and canephora the paternal one; the 2024 study itself states only where the plastid comes from.2,4

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  1. C. eugenioides nucleus. Two chromosome sets, 2n = 2x = 22.2
  2. C. canephora nucleus. Also two sets, 2n = 2x = 22.2
  3. Eugenioides plastid. Chloroplast DNA passed only through the mother in the coffee crosses studied.4
  4. Founding event. The natural hybridisation, dated by a 2024 study to 350,000–610,000 years ago.2,3
  5. Subgenome subEE. The two sets from eugenioides in arabica.2
  6. Subgenome subCC. The two sets from canephora.2
  7. Arabica plastid. Derived from eugenioides; with item 3, this makes eugenioides the maternal parent.2,4
Where the chromosomes and plastids of arabica come from. Each bar stands for one set of 11 chromosomes.2,3,4 Schematic, not to scale.

The parents were not today’s plants but their ancestors.2,9 A textbook chapter describes them as two ecotypes related to C. eugenioides and C. canephora.9 The 2024 study compares arabica with modern representatives of these diploid progenitors.2 How old the hybrid is and how its genome works is the subject of Polyploidy and the arabica genome.

Low in caffeine#

The seeds of C. eugenioides hold little caffeine. The SCA states that it has less caffeine than arabica.8 A 2005 study measured four accessions from Kenya and found 0.44–0.60% caffeine in the dry matter of green seeds.5 Four accessions of C. canephora in the same study held 1.51–3.33%.5 By mean, eugenioides held about a fifth of the caffeine of canephora (0.51% against 2.64%, our calculation).5

00.511.522.533.54% of dry matterC. eugenioides(4 accessions from Kenya)0.44–0.60 (mean 0.51)5 C. arabica(average range in a 2021 review)0.9–1.57 C. canephora(4 accessions)1.51–3.33 (mean 2.64)5 C. canephora(range in a 2021 review; basis notstated)1.2–2.47
Data table
Point% of dry matterSource
C. eugenioides (4 accessions from Kenya)0.44–0.60 (mean 0.51)0.44–0.65
C. arabica (average range in a 2021 review)0.9–1.50.9–1.57
C. canephora (4 accessions)1.51–3.33 (mean 2.64)1.51–3.335
C. canephora (range in a 2021 review; basis not stated)1.2–2.41.2–2.47
Caffeine in green seeds of C. eugenioides and its two relatives. The eugenioides and first canephora rows come from one 2005 study. The other two rows are ranges cited in a 2021 review, from other studies and methods.5,7

For arabica, a 2021 review gives an average of 0.9–1.5% of dry weight.7 Arabica therefore sits between its two parents, by our comparison of these figures from different studies.5,7 Caffeine across species and brews is covered in Caffeine.

As a crop#

No study or trade-body publication opened for this entry documents commercial plantings, yields or the cup quality of C. eugenioides. We leave out such claims until a source of that kind does.

Evidence for the parentage#

A 1999 study compared the DNA of arabica with that of possible diploid parents, using molecular markers (restriction fragment length polymorphism, RFLP). It concluded that C. arabica is an amphidiploid formed by hybridisation between C. eugenioides and C. canephora.3 Genomic in situ hybridisation (GISH), which labels each parent’s chromosomes, confirmed the genome organisation.3 The same study found low divergence between the two constituent genomes and the parent species, and read this as a sign of a relatively recent speciation.3

The maternal side rests on the plastid. A 1996 study of chloroplast DNA in the genus found exclusively maternal inheritance in interspecific hybrids between arabica and canephora and in a progeny within canephora.4 The 2024 genome study states that the arabica plastid genome is derived from eugenioides.2 Taken together, the two findings imply that eugenioides was the seed parent of the founding cross; neither study states this in those words.2,4

Where the cross happened is open. The 1999 study held that a precise site in Central Africa is hard to fix, because the extent of tropical forest has varied considerably.3 The 2024 study does not name a site either. Citing earlier work, it notes that the canephora-derived subgenome is most closely related to C. canephora accessions from northern Uganda.2

The eugenioides genome#

The 2024 study assembled the genome of a wild eugenioides accession, Bu-A, alongside those of canephora and arabica.2 The assemblies span 645 Mb for eugenioides, 672 Mb for canephora and 1,088 Mb for arabica, as given in the text; the study’s Table 1 lists a total length of 661 Mb and a projected genome size of 682 Mb for eugenioides.2 Transposable elements make up 59.7% of the eugenioides genome against 67.5% in canephora, and canephora holds more recent LTR (long terminal repeat) insertions.2 The two diploid genomes show high structural conservation.2

Inside arabica the two subgenomes are named subEE and subCC.2 The study found no significant global expression dominance of either subgenome.2 It did find a bias in homoeologous exchanges, where one subgenome’s segment replaces the other’s, in favour of subCC.2 The authors suggest this may be adaptive, since canephora has a far wider range than eugenioides.2 At one end of chromosome 7, rich in genes with chloroplast-associated functions, all accessions shared a fixed bias towards subEE. The authors link it to compatibility between nuclear and plastid genes, because the plastid comes from eugenioides.2

Later breeding left subEE largely untouched. Introgression from the Timor Hybrid, the natural arabica × robusta cross used for rust resistance, occurred almost exclusively within subCC; subEE has received no substantial introgression.2 That story is told in The Timor Hybrid, and the narrow diversity of arabica in The arabica bottleneck.

Seed chemistry#

The 2005 caffeine study sorted wild Coffea species into four groups, separated by discontinuities in caffeine content.6 Group means rose about twofold from one group to the next: 0.55%, 1.1% and 2.3% on a dry matter basis (dmb), with a fourth group holding only traces.6 A companion study placed C. eugenioides in the second group, together with one undescribed taxon, C. sp. Moloundou.5

The same companion study measured chlorogenic acids (CGA). Eugenioides held 5.17% (dmb), against 11.34% in canephora.5 Across 21 taxa, caffeine and CGA contents were qualitatively related: species low in one tended to be low in the other.5 Both compounds are treated in Caffeine and Chlorogenic acids.

Reference values#

Parameter C. eugenioides Comparison Source
Chromosomes 2n = 2x = 22 C. arabica 2n = 4x = 44 Salojärvi et al.2
Native range South Sudan to E Central and E tropical Africa – POWO1
Altitude, western Kenya above 1,000 m – Hamon et al.11
Caffeine, green seed (% dmb) 0.51 (0.44–0.60), 4 accessions C. canephora 2.64 (1.51–3.33) Campa et al.5
Caffeine, arabica (% dry weight) – 0.9–1.5 (average) Olechno et al.7
Chlorogenic acids, green seed (% dmb) 5.17 (4.55–6.08) C. canephora 11.34 (9.76–14.4) Campa et al.5
Genome assembly 645 Mb (text); 661 Mb total length, 682 Mb projected (Table 1) C. canephora 672 Mb Salojärvi et al.2
Transposable elements 59.7% C. canephora 67.5% Salojärvi et al.2
Plastid inheritance maternal – Lashermes et al. 19964
IUCN Red List Least Concern C. arabica Endangered IUCN10

Caffeine and CGA values are means with the range of four accessions in brackets, from one collection and one method.5 The arabica range is a review average, not a measurement made alongside eugenioides.7

Open questions#

Place of the founding cross. Neither the 1999 nor the 2024 study could locate where eugenioides and canephora met.3,2

Caffeine across the whole range. The caffeine figures opened for this entry rest on four accessions from Kenya.5 No study opened for this entry measured eugenioides from the other countries of its range.

Eugenioides as a crop. No study opened for this entry measured yield, agronomy or cup quality of cultivated C. eugenioides.

Key studies#

Lashermes et al., 1999 – The origin of the arabica genome. Compares arabica with candidate diploid parents using RFLP markers and confirms the result by GISH. Identifies *C. eugenioides* and *C. canephora* as the two parents and finds little divergence from them, pointing to a recent origin.

Molecular and General Genetics 261(2), 259–266 · agritrop.cirad.fr/519522

Lashermes et al., 1996 – Chloroplast DNA in Coffea. Surveys chloroplast DNA across 25 coffee taxa and follows its inheritance in crosses. Finds that it passed only through the mother in the crosses studied, including arabica × canephora hybrids.

Theoretical and Applied Genetics 93(4), 626–632 · doi:10.1007/BF00417958

Salojärvi et al., 2024 – Arabica and its parents sequenced. Assembles the genomes of arabica, canephora and a wild eugenioides accession. Shows that arabica’s plastid comes from eugenioides, that exchanges between subgenomes favour the canephora side, and that later introgression stayed almost entirely in subCC.

Nature Genetics 56(4), 721–731 · doi:10.1038/s41588-024-01695-w

Campa et al., 2005 – Caffeine and chlorogenic acids in wild coffee. Measures both compounds in 21 wild coffee taxa, four accessions each. Places eugenioides in a low-caffeine, low-CGA group, with about a fifth of the caffeine of canephora.

Food Chemistry 93(1), 135–139 · doi:10.1016/j.foodchem.2004.10.015

Contested
  • Range in South Sudan: Plants of the World Online includes South Sudan in the native range1; the Specialty Coffee Association’s species list names the Democratic Republic of Congo, Rwanda, Uganda, Kenya and western Tanzania (“including”), without South Sudan; it does not say the list is complete.8
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Change log

  • – Maternal-parent statements reworded as an inference from two sources, with the 1996 result limited to the crosses studied. Reason: Salojärvi et al. 2024 state only that the arabica plastid derives from eugenioides; Lashermes et al. 1996 found exclusively maternal cpDNA inheritance in arabica × canephora hybrids and a canephora progeny. Neither names eugenioides the maternal parent.
  • – The 1984 Hamon et al. paper is no longer called a survey that placed eugenioides above 1,000 m. Reason: The paper lists the species in western Kenya among high-altitude species in its introduction; its own survey covered south-eastern Kenya.
  • – Summary compares caffeine with canephora in one study instead of robusta. Reason: The study measured four wild C. canephora accessions, not commercial robusta.

Sources

  1. ARoyal Botanic Gardens, Kew (2026). Coffea eugenioides S.Moore. Plants of the World Online (World Checklist of Vascular Plants).
  2. ASalojärvi, J.; Rambani, A.; Yu, Z.; Guyot, R.; et al. (2024). The genome and population genomics of allopolyploid Coffea arabica reveal the diversification history of modern coffee cultivars. Nature Genetics 56(4), 721–731. doi:10.1038/s41588-024-01695-w · other copies
  3. ALashermes, P.; Combes, M. C.; Robert, J.; Trouslot, P.; D’Hont, A.; Anthony, F.; Charrier, A. (1999). Molecular characterisation and origin of the Coffea arabica L. genome. Molecular and General Genetics 261(2), 259–266.
  4. ALashermes, P.; Cros, J.; Combes, M.-C.; Trouslot, P.; Anthony, F.; Hamon, S.; Charrier, A. (1996). Inheritance and restriction fragment length polymorphism of chloroplast DNA in the genus Coffea L.. Theoretical and Applied Genetics 93(4), 626–632. doi:10.1007/BF00417958 · other copies
  5. ACampa, C.; Doulbeau, S.; Dussert, S.; Hamon, S.; Noirot, M. (2005). Qualitative relationship between caffeine and chlorogenic acid contents among wild Coffea species. Food Chemistry 93(1), 135–139. doi:10.1016/j.foodchem.2004.10.015 · other copies
  6. ACampa, C.; Doulbeau, S.; Dussert, S.; Hamon, S.; Noirot, M. (2005). Diversity in bean caffeine content among wild Coffea species: evidence of a discontinuous distribution. Food Chemistry 91(4), 633–637.
  7. AOlechno, E.; Puścion-Jakubik, A.; Zujko, M. E.; Socha, K. (2021). Influence of Various Factors on Caffeine Content in Coffee Brews. Foods 10(6), 1208. doi:10.3390/foods10061208 · other copies
  8. BSpecialty Coffee Association (2026). Coffee Plants of the World. Specialty Coffee Association (SCA), research pages.
  9. BHerrera, J. C.; Lambot, C. (2017). The Coffee Tree – Genetic Diversity and Origin. In: Folmer, B. (ed.), The Craft and Science of Coffee, Academic Press, ch. 1, pp. 1–16. doi:10.1016/B978-0-12-803520-7.00001-3 · other copies
  10. AIUCN (2026). The IUCN Red List of Threatened Species, version 2026-1 (via GBIF.org). International Union for Conservation of Nature; GBIF, licence CC BY 4.0. doi:10.15468/0qnb58 · other copies
  11. AHamon, S.; Anthony, F.; Le Pierres, D. (1984). La variabilité génétique des caféiers spontanés de la section Mozambicoffea A. Chev. I. Précisions sur deux espèces affines: Coffea pseudozanguebariae Bridson et C. sp. A Bridson. Bulletin du Muséum national d’Histoire naturelle, Paris, 4e sér., 6, section B, Adansonia 2, 207–223.

Tier A · authoritative · B · trade and expert · C · general. Supporting quotes for every source are in the data version of this entry. If a publisher’s site refuses access, try the doi link or “other copies”.

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