Transcriptome analysis in Coffea eugenioides, an Arabica coffee ancestor, reveals differentially expressed genes in leaves and fruits

Yuyama Priscilla Mary, Reis Júnior Osvaldo, Ivamoto Suzana Tiemi, Domingues Douglas S., Carazzolle Marcelo Falsarella, Pereira Gonçalo Amarante Guimarães, Charmetant Pierre, Leroy Thierry, Pereira Luiz Filipe P.. 2016. Transcriptome analysis in Coffea eugenioides, an Arabica coffee ancestor, reveals differentially expressed genes in leaves and fruits. Molecular Genetics and Genomics, 291 (1) : 323-336.

https://doi.org/10.1007/s00438-015-1111-x

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Résumé : Studies in diploid parental species of polyploid plants are important to understand their contributions to the formation of plant and species evolution. Coffea eugenioides is a diploid species that is considered to be an ancestor of allopolyploid Coffea arabica together with Coffea canephora. Despite its importance in the evolutionary history of the main economic species of coffee, no study has focused on C. eugenioides molecular genetics. RNA-seq creates the possibility to generate reference transcriptomes and identify coding genes and potential candidates related to important agronomic traits. Therefore, the main objectives were to obtain a global overview of transcriptionally active genes in this species using next-generation sequencing and to analyze specific genes that were highly expressed in leaves and fruits with potential exploratory characteristics for breeding and understanding the evolutionary biology of coffee. A de novo assembly generated 36,935 contigs that were annotated using eight databases. We observed a total of ~5000 differentially expressed genes between leaves and fruits. Several genes exclusively expressed in fruits did not exhibit similarities with sequences in any database. We selected ten differentially expressed unigenes in leaves and fruits to evaluate transcriptional profiles using qPCR. Our study provides the first gene catalog for C. eugenioides and enhances the knowledge concerning the mechanisms involved in the C. arabica homeologous. Furthermore, this work will open new avenues for studies into specific genes and pathways in this species, especially related to fruit, and our data have potential value in assisted breeding applications.

Mots-clés Agrovoc : Coffea eugenioides, Coffea arabica, Coffea canephora, séquence d'arn, expression des gènes, Transcription génique, feuille, fruit (botanique), phylogénie, évolution, génie génétique