Coffee

Background

Coffee is the world's leading agricultural resource in value terms. It is a major source of revenue for more than 40 tropical countries, and generates more than 120 million jobs. Coffee is grown on more than 10 million hectares worldwide, primarily on small family farms (70% of the crop comes from farms of under 5 hectares). Two species, Coffea arabica (65%) and Coffea canephora (35%), are cultivated.

Links between South Green and Coffee TropGeneDB holds many molecular markers developed locally (CIRAD-IRD) or retrieved from other databases. It's also a repository for genetic mapⁱ / QTL analysis informations linked to coffee cup quality (Leroy et al., 2011). The South Green Bioinformatics platform supported the analyses of the Coffea canephora sequence (CoffeaSeq project). The platform hosts a dedicated crop portal, the Coffee Genome Hub, which centralizes most of the resources and information systems around the coffee genome such as GNPannot, GreenPhyl and SNiPlay. The hub gives access to chromosomes, genes, trancripts, proteins and genetic markers produced over the time.

Publication(s):

1.

Cenci A, Rouard M. 2017. Evolutionary Analyses of GRAS Transcription Factors in Angiosperms. Frontiers in Plant Science. 8:273.

2.

Sarah G, Homa F, Pointet S, Contreras S, Sabot F, Nabholz B, Santoni S, Sauné L, Ardisson M, Chantret N et al.. 2016. A large set of 26 new reference transcriptomes dedicated to comparative population genomics in crops and wild relatives.. Molecular ecology resources. Abstract

3.

Monat C, Tranchant-Dubreuil C, Kougbeadjo A, Farcy C, Ortega-Abboud E, Amanzougarene S, Ravel S, Agbessi M, Orjuela-Bouniol J, Summo M et al.. 2015. TOGGLE: Toolbox for generic NGS analyses. JOBIM.

4.

Denoeud F, Carretero-Paulet L, Dereeper A, Droc G, Guyot R, Pietrella M, Zheng C, Alberti A, Anthony F, Aprea G et al.. 2014. The coffee genome provides insight into the convergent evolution of caffeine biosynthesis.. Science (New York, N.Y.). 345(6201):1181-4. Abstract

5.

Dereeper A, Bocs S, Rouard M, Guignon V, Ravel S, Tranchant-Dubreuil C, Poncet V, Garsmeur O, Lashermes P, Droc G. 2014. The coffee genome hub: a resource for coffee genomes.. Nucleic acids research. Abstract

6.

Bocs S, Dereeper A, Gayraud T, Jamilloux V, Lashermes P, Guyot R. 2014. Transposable Elements in the Robusta Coffee Genome (Coffea canephora). PAG XXII.

7.

Dereeper A, Guyot R, Tranchant-Dubreuil C, Anthony F, Argout X, de Bellis F, Combes M-C, Gavory F, de Kochko A, Kudrna D et al.. 2013. BAC-end sequences analysis provides first insights into coffee (Coffea canephora P.) genome composition and evolution.. Plant molecular biology. 83(3):177-89. Abstract

8.

Combes M-C, Dereeper A, Severac D, Bertrand B, Lashermes P. 2013. Contribution of subgenomes to the transcriptome and their intertwined regulation in the allopolyploid Coffea arabica grown at contrasted temperatures.. The New phytologist. 200(1):251-60. Abstract

9.

Guyot R, Lefebvre-Pautigny F, Tranchant-Dubreuil C, Rigoreau M, Hamon P, Leroy T, Hamon S, Poncet V, Crouzillat D, de Kochko A. 2012. Ancestral synteny shared between distantly-related plant species from the asterid (Coffea canephora and Solanum Sp.) and rosid (Vitis vinifera) clades.. BMC genomics. 13:103.

10.

Leroy T, de Bellis F, Legnate H, Kananura E, Gonzales G, Pereira LF, Andrade AC, Charmetant P, Montagnon C, Cubry P et al.. 2011. Improving the quality of African robustas: QTLs for yield- and quality-related traits in Coffea canephora. Tree Genetics & Genomes. 7:781-798.

11.

Plechakova O, Tranchant-Dubreuil C, Benedet F, Couderc M, Tinaut A, Viader V, {De Block} P, Hamon P, Campa C, de Kochko A et al.. 2009. MoccaDB - an integrative database for functional, comparative and diversity studies in the Rubiaceae family.. BMC plant biology. 9:123.

Related database(s):

Coffee Genome Hub

Related project(s):

ARCAD

Species