1
|
Mondego JMC, Vidal RO, Carazzolle MF, Tokuda EK, Parizzi LP, Costa GGL, Pereira LFP, Andrade AC, Colombo CA, Vieira LGE, Pereira GAG. An EST-based analysis identifies new genes and reveals distinctive gene expression features of Coffea arabica and Coffea canephora. BMC PLANT BIOLOGY 2011; 11:30. [PMID: 21303543 PMCID: PMC3045888 DOI: 10.1186/1471-2229-11-30] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2010] [Accepted: 02/08/2011] [Indexed: 05/10/2023]
Abstract
BACKGROUND Coffee is one of the world's most important crops; it is consumed worldwide and plays a significant role in the economy of producing countries. Coffea arabica and C. canephora are responsible for 70 and 30% of commercial production, respectively. C. arabica is an allotetraploid from a recent hybridization of the diploid species, C. canephora and C. eugenioides. C. arabica has lower genetic diversity and results in a higher quality beverage than C. canephora. Research initiatives have been launched to produce genomic and transcriptomic data about Coffea spp. as a strategy to improve breeding efficiency. RESULTS Assembling the expressed sequence tags (ESTs) of C. arabica and C. canephora produced by the Brazilian Coffee Genome Project and the Nestlé-Cornell Consortium revealed 32,007 clusters of C. arabica and 16,665 clusters of C. canephora. We detected different GC3 profiles between these species that are related to their genome structure and mating system. BLAST analysis revealed similarities between coffee and grape (Vitis vinifera) genes. Using KA/KS analysis, we identified coffee genes under purifying and positive selection. Protein domain and gene ontology analyses suggested differences between Coffea spp. data, mainly in relation to complex sugar synthases and nucleotide binding proteins. OrthoMCL was used to identify specific and prevalent coffee protein families when compared to five other plant species. Among the interesting families annotated are new cystatins, glycine-rich proteins and RALF-like peptides. Hierarchical clustering was used to independently group C. arabica and C. canephora expression clusters according to expression data extracted from EST libraries, resulting in the identification of differentially expressed genes. Based on these results, we emphasize gene annotation and discuss plant defenses, abiotic stress and cup quality-related functional categories. CONCLUSION We present the first comprehensive genome-wide transcript profile study of C. arabica and C. canephora, which can be freely assessed by the scientific community at http://www.lge.ibi.unicamp.br/coffea. Our data reveal the presence of species-specific/prevalent genes in coffee that may help to explain particular characteristics of these two crops. The identification of differentially expressed transcripts offers a starting point for the correlation between gene expression profiles and Coffea spp. developmental traits, providing valuable insights for coffee breeding and biotechnology, especially concerning sugar metabolism and stress tolerance.
Collapse
Affiliation(s)
- Jorge MC Mondego
- Centro de Recursos Genéticos Vegetais, Instituto Agronômico de Campinas, CP 28, 13001-970, Campinas-SP, Brazil
| | - Ramon O Vidal
- Laboratório de Genômica e Expressão, Departamento de Genética, Evolução e Bioagentes, Instituto de Biologia, Universidade Estadual de Campinas, CP 6109, 13083-970, Campinas-SP, Brazil
- Laboratório Nacional de Biociências (LNBio), CP 6192, 13083-970, Campinas-SP, Brazil
| | - Marcelo F Carazzolle
- Laboratório de Genômica e Expressão, Departamento de Genética, Evolução e Bioagentes, Instituto de Biologia, Universidade Estadual de Campinas, CP 6109, 13083-970, Campinas-SP, Brazil
- Centro Nacional de Processamento de Alto Desempenho em São Paulo, Universidade Estadual de Campinas, CP 6141, 13083-970, Campinas, SP, Brazil
| | - Eric K Tokuda
- Laboratório de Genômica e Expressão, Departamento de Genética, Evolução e Bioagentes, Instituto de Biologia, Universidade Estadual de Campinas, CP 6109, 13083-970, Campinas-SP, Brazil
| | - Lucas P Parizzi
- Laboratório de Genômica e Expressão, Departamento de Genética, Evolução e Bioagentes, Instituto de Biologia, Universidade Estadual de Campinas, CP 6109, 13083-970, Campinas-SP, Brazil
| | - Gustavo GL Costa
- Laboratório de Genômica e Expressão, Departamento de Genética, Evolução e Bioagentes, Instituto de Biologia, Universidade Estadual de Campinas, CP 6109, 13083-970, Campinas-SP, Brazil
| | - Luiz FP Pereira
- Embrapa Café - Instituto Agronômico do Paraná, Laboratório de Biotecnologia Vegetal, CP 481, 86001-970, Londrina-PR, Brazil
| | - Alan C Andrade
- Núcleo de Biotecnologia-NTBio, Embrapa Recursos Genéticos e Biotecnologia, Parque Estação Biológica, CP 02372, 70770-900, Brasília-DF, Brazil
| | - Carlos A Colombo
- Centro de Recursos Genéticos Vegetais, Instituto Agronômico de Campinas, CP 28, 13001-970, Campinas-SP, Brazil
| | - Luiz GE Vieira
- Instituto Agronômico do Paraná, Laboratório de Biotecnologia Vegetal, CP 481, CEP 86001-970, Londrina-PR, Brazil
| | - Gonçalo AG Pereira
- Laboratório de Genômica e Expressão, Departamento de Genética, Evolução e Bioagentes, Instituto de Biologia, Universidade Estadual de Campinas, CP 6109, 13083-970, Campinas-SP, Brazil
| |
Collapse
|
2
|
Yang X, Zhang X. Regulation of Somatic Embryogenesis in Higher Plants. CRITICAL REVIEWS IN PLANT SCIENCES 2010; 29:36-57. [PMID: 0 DOI: 10.1080/07352680903436291] [Citation(s) in RCA: 128] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Affiliation(s)
- Xiyan Yang
- a National Key Laboratory of Crop Genetic Improvement , Huazhong Agricultural University , Wuhan, Hubei, 430070, P. R. China
| | - Xianlong Zhang
- a National Key Laboratory of Crop Genetic Improvement , Huazhong Agricultural University , Wuhan, Hubei, 430070, P. R. China
| |
Collapse
|
5
|
Thakur JK, Malik MR, Bhatt V, Reddy MK, Sopory SK, Tyagi AK, Khurana JP. A POLYCOMB group gene of rice (Oryza sativa L. subspecies indica), OsiEZ1, codes for a nuclear-localized protein expressed preferentially in young seedlings and during reproductive development. Gene 2003; 314:1-13. [PMID: 14527713 DOI: 10.1016/s0378-1119(03)00723-6] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The SET domains are conserved amino acid sequences present in chromosomal proteins that contribute to the epigenetic control of gene expression by altering regional organization of the chromatin structure. The SET domain proteins are divided into four subgroups as categorized by their Drosophila members; enhancer of zeste (E(Z)), trithorax (TRX), absent small or homeotic 1 (ASH1) and supressor of variegation (SU(VAR)3-9). Homologs of all four classes have been characterized in yeast, mammals and plants. We report here the isolation and characterization of rice (Oryza sativa L. subspecies indica) cDNA, OsiEZ1, as a monocot member of this family. The OsiEZ1 cDNA is 3133 bp long with an ORF of 2799 bp, and the predicted amino acid sequence (895 residues) corresponds to a protein of ca. 98 kDa. All the characteristic domains known to be conserved in E(Z) homologs (subgroup I) of SET domain containing proteins are present in OsiEZ1. In the rice genome, a 7499 bp long OsiEZ1 sequence is split into 17 exons interrupted by 16 introns. Southern analysis indicates that OsiEZ1 is represented as single copy in the rice genome. Expression studies revealed that the OsiEZ1 transcript level was highest in rice flowers, almost undetectable in developing seeds of 1-2 days post-fertilization but increased significantly in young seeds of 3-5 days post-fertilization. The OsiEZ1 transcript was barely detectable in mature zygotic embryos, but its levels were significantly higher in callus derived from rice scutellum, somatic embryos and young seedlings. The OsiEZ1/GUS recombinant protein was confined to the nucleus in living cells of particle-bombarded onion peels. The expression of OsiEZ1 complemented a set1Delta Saccharomyces cerevisiae mutant that is impaired in telomeric silencing. We suggest that the nuclear-localized OsiEZ1 has a role in regulating various aspects of plant development, and this control is most likely brought about by repressing the activity of downstream regulatory genes.
Collapse
MESH Headings
- Amino Acid Sequence
- Base Sequence
- Blotting, Northern
- Chromosome Mapping
- Chromosomes, Plant/genetics
- DNA, Complementary/chemistry
- DNA, Complementary/genetics
- Flowers/genetics
- Flowers/growth & development
- Gene Expression Regulation, Developmental
- Gene Expression Regulation, Plant
- Genetic Complementation Test
- Molecular Sequence Data
- Mutation
- Nuclear Proteins/genetics
- Oryza/genetics
- Oryza/growth & development
- Phylogeny
- Plant Proteins/genetics
- Polycomb-Group Proteins
- RNA, Plant/genetics
- RNA, Plant/metabolism
- Repressor Proteins/genetics
- Reproduction/genetics
- Reverse Transcriptase Polymerase Chain Reaction
- Saccharomyces cerevisiae/genetics
- Sequence Alignment
- Sequence Analysis, DNA
- Sequence Homology, Amino Acid
- Telomere/genetics
Collapse
Affiliation(s)
- Jitendra K Thakur
- Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, 110021, New Delhi, India
| | | | | | | | | | | | | |
Collapse
|