# WCSdb: a database of wild Coffea species

Romain Guyot, Perla Hamon, Emmanuel Couturon, Nathalie Raharimalala, Jean-Jacques Rakotomalala, Sreenath Lakkanna, Sylvie-Annabel Sabatier, Antoine Affouard, Pierre Bonnet

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Romain Guyot, Perla Hamon, Emmanuel Couturon, Nathalie Raharimalala, Jean-Jacques Rakotomalala, et al.. WCSdb: a database of wild Coffea species. Database - The journal of Biological Databases and Curation, 2020, 2020, 10.1093/database/baaa069. hal-04182535

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Distributed under a Creative Commons Attribution 4.0 International License
Original article

# WCSdb: a database of wild *Coffea* species

Romain Guyot¹,⁵,*, Perla Hamon¹, Emmanuel Couturon¹, Nathalie Raharimalala², Jean-Jacques Rakotomalala², Sreenath Lakkanna³, Sylvie Sabatier⁴, Antoine Affouard⁶ and Pierre Bonnet⁴

¹Institut de Recherche pour le Développement, UMR DIADE, Université de Montpellier, 911 Avenue Agropolis, 34394 Montpellier, France, ²FOFIFA, BP 1444, Ambatobe, Antananarivo 101, Madagascar, ³Plant Biotechnology Division, Unit of Central Coffee Research Institute, Coffee Board, Manasagangothri, Mysore 570 006, India, ⁴AMAP, Univ Montpellier, CIRAD, CNRS, INRA, IRD Avenue Agropolis, 34398 Montpellier Cedex 5, France, ⁵Department of Electronics and Automatization, Universidad Autónoma de Manizales, Antigua Estacion del Ferrocarril, 170001 Manizales, Colombia and ⁶INRIA Sophia-Antipolis—ZENITH team, LIRMM—UMR 5506—CC 477, 161 rue Ada, 34095 Montpellier Cedex 5, France

*Corresponding author: Email: romain.guyot@ird.fr Tel: +33467416229; Fax: +33467416330

Citation details: Guyot,R., Hamon,P., Couturon,E., et al. WCSdb: a database of wild *Coffea* species *Database* (2020) Vol. 00: article ID baaa069; doi:10.1093/database/baaa069

Received 28 January 2020; Revised 22 June 2020; Accepted 30 July 2020

## Abstract

Coffee is a beverage enjoyed by millions of people worldwide and an important commodity for millions of people. Beside the two cultivated species (*Coffea arabica* and *Coffea canephora*), the 139 wild coffee species/taxa belonging to the *Coffea* genus are largely unknown to coffee scientists and breeders although these species may be crucial for future coffee crop development to face climate changes. Here we present the Wild Coffee Species database (WCSdb) hosted by PI@ntNet platform (http://publish.plantnet-project.org/project/wildcofdb_en), providing information for 141 coffee species/taxa, for which 84 contain a photo gallery and 82 contain sequencing data (genotyping-by-sequencing, chloroplast or whole genome sequences). The objective of this database is to better understand and characterize the species (identification, morphology, biochemical compounds, genetic diversity and sequence data) in order to better protect and promote them.

Database URL: http://publish.plantnet-project.org/project/wildcofdb_en

## Introduction

Coffee is a beverage enjoyed by millions of people worldwide. It is also an important commodity for millions of small coffee farmers living in tropical countries. Two species are mainly cultivated Arabica (*Coffea arabica*)

and Robusta (*Coffea canephora*). Coffee fields are deeply impacted by climate change and the emergence of diseases (1). Beside cultivated coffee trees, numerous wild coffee species are known to botanists, but largely ignored by agronomists and breeders although these species may be
crucial for future coffee crop development to face climate
changes.

Based on morphological data, the phylogenetically clos-
est genus called *Psilanthus* (2) has been recently placed
into *Coffea* (3). The genus *Coffea* (broad sense since (3))
includes woody plants belonging to the Rubiaceae family.
It comprises 124 species and 17 additional taxa, with a
natural distribution covering tropical Africa, Madagascar,
Comoros, Mauritius and the Reunion Islands extending to
Southern and Southeast Asia and Australasia. However,
the two genera mainly differ by the flower morphology
with short corolla tube and reproductive organs exerted for
*Coffea*, long corolla tube and reproductive organs inserted
for *Psilanthus*. They differ also by their natural distri-
bution. The genus *Psilanthus* is present on the African
continent, Asia (India, Sri Lanka, tropical and Southeast
Asia) and Oceania (Northern Australia) but absent from the
islands of the West Indian Ocean (Madagascar, Mascarenes
and Comoros). The merging of these two genera introduced
a possible source of name confusion as numerous works
are focused only on *Coffea sensu stricto*. Another source of
species name confusion is the presence of numerous past or
modern synonymies. For example, it is generally accepted
that *Psilanthus minor* is in fact *P. sapinii* or that *Coffea
vaughanii* is *C. myrtifolia*.

Anyway, these 141 identified and classified species/taxa
are currently considered for further phylogenetic and
molecular analyses (4).

Fourteen years ago, Davis and co-workers (5) revealed
that numerous wild coffee species are vulnerable (23
species), endangered (30 species) or seriously threatened
(19 species). A recent reassessment (1) confirmed that 60%
of them are now threatened with extinction, suggesting a
bad prospect for wild coffee species all over the tropical
world. Wild coffee species living collections were initiated
in the years 1960 in Africa and Madagascar. Today only
55% of them are in such collections: at the research sta-
tion of the Centre National de Recherche en Agronomie,
Divo, Côte d'Ivoire (for African species), at the Centre
de Ressources Biologiques (CRB) Bassin-Martin, Reunion
island (http://florilege.arcad-project.org/fr/crb/coffea; for
African, Comorian and Mascarene species; Supplemental
data 1) and at the research station of the National Cen-
tre for Applied Research for Rural Development (FOFIFA)
in Kianjavato, Madagascar (for Madagascan species; Sup-
plemental data 2). The analysis of wild coffee species
conserved in living collection revealed large morphologi-
cal variation such as flower morphology, size and color
of fruits, plant height and leaf morphologies, days to
fruit maturation and growth habitats and adaptation. In
addition to morphology, large variations were observed
in terms of seed biochemical compounds involved in the
quality of coffee such as caffeine (6), trigonelline, sucrose
and mangiferin contents into others (7-9). However, this

diversity is not comprehensively reported so far in any
publication or any publicly available database.

The first *Coffea* genome has been published in 2014 and concerned *Coffea canephora* (10). Since this first release, several sequencing data have been published such as the genotyping-by-sequencing data to provide the first resolved phylogeny of the *Coffea* genus (11), the partial sequencing of 16 *Coffea* species (12) and the chloroplast reconstructions and nuclear SNP mining (13). Now the Genus is subjected to intensive genome sequencing (*C. arabica*, *C. eugenioides* and *C. canephora* (14); 82 wild coffee species, unpublished results; Supplemental data 3), allowing research of genes of agronomical interest and genome composition and evolution studies.

To intensify the protection and the conservation of
wild coffee species and to promote their use in the search
of agronomic genes of interest, more shared information
is needed. So far, few databases are dedicated to wild
coffee species. The Global Biodiversity Information Facil-
ity (GBIF, https://www gbif org/species/2895315) includes
8462 occurrences with images for 176 species. How-
ever, the reported samples include those collected in their
natural area and also, those introduced by humans out-
side their natural distribution and those collected from
ex situ living collections. The Reunion_Coffea database
hosted in GBIF database was published by INRA Antilles-
Guyane (15, https://www gbif org/dataset/510b8030-6293
-4bd9-812d-c195a9915a74). This database provides the
taxonomic distribution of occurrences (number of acces-
sions per species), date of setting up in Reunion but
does not include pictures or associated Supplementary
data. Other databases are only focused on genomic data,
such as the coffee Genome hub (http://coffee-genome.
org; Robusta genome only), the TropGeneDB (http:
//tropgenedb cirad fr/tropgene/JSP/interface.jsp?module=
COFFEE, mainly genetic markers) and the SOL Genomics
Network https://sgn.cornell.edu/search/organisms).

In this study, we developed a wild coffee species
database (WCSdb), hosted by Pl@ntNet (http://publish.
plantnet-project.org/project/wildcofdb_en). The general
objective of this database is to better understand the
species (identification, morphology, biochemical com-
pounds, genetic diversity and sequence data) in order to
better protect and promote them. More specifically, the
database presents: (i) each species held in collection on
the sites of Bassin-Martin, Reunion Island and Kianjavato,
Madagascar with a photo gallery of the tree morphology
with a total of 597 images; (ii) different detailed infor-
mation such as synonymy, natural distributions, habitats,
architectural, morphological, phenological, biochemistry
traits, genetic/genomic data, trait of interest retrieved from
the literature and personal observations on living collec-
tion and (iii) a general geographical map of the species
distribution.
# Database construction and content

## Data source

Pictures were mainly provided by Emmanuel Couturon for CRB (BassinMartin, La réunion) hosted plants (Supplemental data 1; list of species present at BassinMartin), by Eva N Raharimalala and Perla Hamon for Madagascan species (Supplemental data 2; list of species present at Kianjavato), and Lakkanna Sreenath for *Psi*-lanthus. bengalensis, *Psilanthus*. travancorensis and *Psi*-lanthus. wightianus. Links to molecular data were introduced such as genome size (Mbp 1C) from the plant DNA C-value database (https://cvalues.science.kew.org) for 57 species, genotyping-by-sequencing (GBS) data

for 77 species (11, https://datadryad.org/resource/doi:10.5061/dryad.kk71t), the sequenced and assembled chloroplast genomes for 39 species (13; Guyeux et al. unpublished results) and whole genome deep pair-end Illumina sequencing for 82 species (R. Guyot and Perla Hamon, unpublished results, data available upon request). genotyping-by-sequencing (GBS) and sequencing data information are available on the web site in a separate table and in Supplemental data 3).

## Web interface, usage

PI@ntNet Publish is an IT platform dedicated to the dissemination of botanical data focused on taxa or specimen

<figure><img src="image_2.png" /><figcaption>**Figure 1.** Schematic representation of the PI@ntNet Publish UML class diagram.</figcaption></figure>
levels. It is based on Symfony (PHP) and MongoDB and allows its users to manage data publication spaces: descriptive texts, search forms, taxonomic data, visual data, geographic data, etc. (Figure 1). Data can be uploaded via comma-separated values (CSV) files and are then available through responsive Web pages dedicated to the portal created by users. Data exploration is also possible via a RESTful Web services (JSON). Pl@ntNet Publish was initially developed in 2014, with the support of Agropolis Fondation and has been adapted to various cases studies, such as Herbarium collections, Regional taxonomic checklists, information for Weed and Invasive species management, into others. Pl@ntNet Publish was deposited in 2015 at the Agency for the Protection of Programs (IDDN.FR.001.320007.OOO.R.C.2015.000.31235).

The main tab or species tab shows information for 124 accepted species and 17 taxa (Figure 2). Three species has duplicated entries, according to their distribution or variety: *C. mauritiana* for populations from Mauritius and Reunion islands, for *Coffea liberica* (variety liberica and variety dewevrei), and for *Psilanthus bengalensis* (variety bababudanii and variety bengalensis). In the species tab, we decide to keep the nomenclature *Coffea* and *Psilanthus* for the species to avoid any confusion. This database also shows species according to their botanical section or geographic origin: Eucoffea, Mascarocoffea, Mascarenes, Baracoffea (Madagascan species endemic to the western coast), *Psilanthus* from Africa and *Psilanthus* from Asia. The species table allows the user to select the species to examine. In total, for each species, 30 data fields were

<figure><img src="image_3.png" /><figcaption>**Figure 2.** Home page of the wild coffee species database (http://publish.plantnet-project.org/project/wildcofdb_en).</figcaption></figure>
<figure><img src="image_4.png" /><figcaption>**Figure 3.** Flowchart showing the database use and outputs.</figcaption></figure>

completed into a detailed table such as species name, section, living collection, synonymy and reference, distribution, habitat, caffeine content in bean and leaves, sucrose, mangiferin, ripening time and color of mature fruits, foliar dimension, genome sizes, sequencing data, and plastid genomes into others (Figure 3). The fields are described in the web site (section ‘How to use this site’). The detailed table contains also references and the links to access to the molecular data when available (GBS data, nuclear genome sequences, plastid genomes and raw sequencing data).

In total, 201 localization entries were linked with coffee species, representative approximate area where the species were found when collected in the wild (mainly between years 1960 and 1980). With the detailed table, a photo gallery is available for 84 species. The photographs depict the morphology of beans, leaves, mature fruits, flowers, and the overall tree, allowing a better identification. In total, 551 photographs are available.

## Conclusions and prospects

The WCS database represents the first comprehensive information about wild coffees species, largely unknown to coffee scientists and breeders. The information collected from the literature and from living collections at Kianjavato, Madagascar and Bassin-martin, La Réunion, may help researchers working in the preservation of coffee species, geneticists and breeders working with trait or genes of interest and improvement of cultivated species (tolerance to drought, resistances to diseases and pest, increase the quality of beans) or breeders motivated to re-cultivate forgotten species adapted to climate changes or adapted to specific habitats. More information will be integrated into the WCS database in the future, such as the availability of raw genomic sequences and assembled genome sequences, new characterized species, and new photo gallery.

## Supplementary Data

Supplementary data are available at *Database* Online.
## Funding

We thank the respective institutions IRD, FOFIFA, and CIRAD for support and funding.

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