A High-Throughput Data Mining of Single Nucleotide Polymorphisms in Coffea Species Expressed Sequence Tags Suggests Differential Homeologous Gene Expression in the Allotetraploid Coffea arabica

Author(s)

Vidal, Ramon Oliveira ^[1] ; Costa Mondego, Jorge Mauricio ^[2] ; Pot, David ^[3] ; Ambrosio, Alinne Batista ^[1] ; Andrade, Alan Carvalho ^[4] ; Protasio Pereira, Luiz Filipe ^[5] ; Colombo, Carlos Augusto ^[2] ; Esteves Vieira, Luiz Gonzaga ^[6] ; Carazzolle, Marcelo Falsarella ^{[1, 7]} ; Guimaraes Pereira, Goncalo Amarante ^[1]

Affiliation

^[1] Univ Estadual Campinas, Dept Genet Evolucao & Bioagentes, Inst Biol, Lab Genom & Expressao, BR-13083970 Campinas, SP - Brazil

^[2] Inst Agron Campinas, Ctr Recursos Genet Vegetais, BR-13001970 Campinas, SP - Brazil

^[3] Ctr Cooperat Int Rech Agron Dev, UMR Dev & Ameliorat Plantes, F-34398 Montpellier 5 - France

^[4] Embrapa Recursos Genet & Biotecnol, Genet Mol Lab, Lab Genet Mol Nucleo Temat Biotecnol, BR-70770917 Brasilia, DF - Brazil

^[5] Embrapa Cafe, Inst Agron Parana, BR-86001970 Londrina, PR - Brazil

^[6] Inst Agron Parana, Lab Biotecnol Vegetal, BR-86001970 Londrina, PR - Brazil

^[7] Univ Estadual Campinas, CENAPAD SP, Ctr Nacl Processamento Alto Desempenho Sao Paulo, BR-13083970 Campinas, SP - Brazil

• Document type: Journal article
• Source: Plant Physiology; v. 154, n. 3, p. 1053-1066, NOV 2010.
• Web of Science Citations: 47

Abstract

Polyploidization constitutes a common mode of evolution in flowering plants. This event provides the raw material for the divergence of function in homeologous genes, leading to phenotypic novelty that can contribute to the success of polyploids in nature or their selection for use in agriculture. Mounting evidence underlined the existence of homeologous expression biases in polyploid genomes; however, strategies to analyze such transcriptome regulation remained scarce. Important factors regarding homeologous expression biases remain to be explored, such as whether this phenomenon influences specific genes, how paralogs are affected by genome doubling, and what is the importance of the variability of homeologous expression bias to genotype differences. This study reports the expressed sequence tag assembly of the allopolyploid Coffea arabica and one of its direct ancestors, Coffea canephora. The assembly was used for the discovery of single nucleotide polymorphisms through the identification of high-quality discrepancies in overlapped expressed sequence tags and for gene expression information indirectly estimated by the transcript redundancy. Sequence diversity profiles were evaluated within C. arabica (Ca) and C. canephora (Cc) and used to deduce the transcript contribution of the Coffea eugenioides (Ce) ancestor. The assignment of the C. arabica haplotypes to the C. canephora (CaCc) or C. eugenioides (CaCe) ancestral genomes allowed us to analyze gene expression contributions of each subgenome in C. arabica. In silico data were validated by the quantitative polymerase chain reaction and allele-specific combination TaqMAMA-based method. The presence of differential expression of C. arabica homeologous genes and its implications in coffee gene expression, ontology, and physiology are discussed. (AU)