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

Author(s)

Yuyama, Priscila Mary ^{[1, 2]} ; Reis Junior, Osvaldo ^[3] ; Ivamoto, Suzana Tiemi ^{[1, 2]} ; Domingues, Douglas Silva ^[4] ; Carazzolle, Marcelo Falsarella ^[3] ; Guimaraes Pereira, Goncalo Amarante ^[3] ; Charmetant, Pierre ^[5] ; Leroy, Thierry ^[5] ; Protasio Pereira, Luiz Filipe ^{[6, 2]}

Affiliation

^[1] Univ Estadual Londrina, Programa Posgrad Genet & Biol Mol, Londrina, Parana - Brazil

^[2] Inst Agron Parana IAPAR, Lab Biotecnol Vegetal, Londrina, Parana - Brazil

^[3] Univ Estadual Campinas UNICAMP, Inst Biol, Dept Genet Evolucao & Bioagentes, Lab Genom & Expressao, Campinas, SP - Brazil

^[4] Univ Estadual Paulista UNESP, Inst Biociencias Rio Claro, Dept Bot, Rio Claro, SP - Brazil

^[5] Ctr Cooperat Int Rech Agron Dev CIRAD, UMR AGAP, F-34398 Montpellier - France

^[6] EMBRAPA Cafe, Brasilia, DF - Brazil

• Document type: Journal article
• Source: Molecular Genetics and Genomics; v. 291, n. 1, p. 323-336, FEB 2016.
• Web of Science Citations: 14

Abstract

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 similar to 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. (AU)

• FAPESP's process: 13/08293-7 - CCES - Center for Computational Engineering and Sciences
• Grantee: Munir Salomao Skaf
• Support Opportunities: Research Grants - Research, Innovation and Dissemination Centers - RIDC