An EST-based analysis identifies new genes and reveals distinctive gene expression features of Coffea arabica and Coffea canephora

Jorge, Érika Cristina; Vidal, Ramon O.; Carazzolle, Marcelo Falsarella; Tokuda, Eric K.; Parizzi, Lucas Pedersen; Costa, Gustavo G.L.; Pereira, Luiz Filipe Protásio; Andrade, Alan Carvalho; Colombo, Carlos Augusto; Vieira, Luiz Gonzaga Esteves; Pereira, Gonçalo Amarante Guimarães

doi:10.1186/1471-2229-11-30

Cited by 78 publications

(90 citation statements)

References 131 publications

(159 reference statements)

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“…unicamp.br/coffea) that comprises 187,142 expressed sequence tags (ESTs) of C. arabica produced by the Brazilian Coffee Genome (CafESTs) and resulted in 32,007 contigs (Mondego et al, 2011). Arabidopsis P450 sequences already described in the literature (Nelson, 2009) were used for a local similarity search on the CafESTs database.…”

Section: Methodsmentioning

confidence: 99%

“…We observed high gene expression in leaves and low levels in flowers and in fruits collected at different DAF, corroborating the in silico approach (Figure 4). (Vieira et al, 2006;Mondego et al, 2011): seedlings and leaves treated with arachidonic acid (AR1); suspension cells treated with acibenzolar-S-methyl (BP1); non-embryogenic calli with and without 2,4 dichlorophenoxyacetic acid (CA1, IC, and PC); suspension cells treated with acibenzolar-S-methyl and brassinosteroids (CB1); hypocotyls treated with acibenzolar-S-methyl (CL2); suspension cells treated with NaCl (CS1); embryogenic calli (EA1 and IAc); flower buds in different developmental stages (FB); flower buds + pinhead fruits + fruits at different stages (FR); seedlings and leaves treated with arachidonic acid (LP1); young leaves from the orthotropic branch (LV1); mature leaves from plagiotropic branches (LV2); primary embryogenic calli (PA1); leaves infected with leaf miner and coffee leaf rust (RM1); roots with acibenzolar-S-methyl (RT5); suspension cells stressed with aluminum (RT8); stems infected with Xylella spp (RX1); water deficit-stressed field plants (pool of tissues) (SH2); and germinating seeds (whole seeds and zygotic embryos) (SI3).…”

Section: Cacyp81d8_1 Transcriptional Profile Validationmentioning

confidence: 99%

“…Despite their importance for establishing the chemical diversity of coffee beans associated with good cup qualities, there are no reports in the literature about putative functions of P450s and transcriptional activity patterns between different tissues in Coffea arabica. In this study, we used a public transcriptome database (Mondego et al, 2011) to identify, annotate, and study the transcriptional pattern of the available P450 coffee genes that are still unexplored.…”

Section: Introductionmentioning

confidence: 99%

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Identification of the transcriptionally active cytochrome P450 repertoire in Coffea arabica

Ivamoto¹,

Domingues²,

Vieira³

et al. 2015

Genet. Mol. Res.

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Section: Methodsmentioning

confidence: 99%

Section: Cacyp81d8_1 Transcriptional Profile Validationmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Identification of the transcriptionally active cytochrome P450 repertoire in Coffea arabica

Ivamoto¹,

Domingues²,

Vieira³

et al. 2015

Genet. Mol. Res.

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“…This EST database contains 130,792 ESTs of C. arabica, 12,381 ESTs of C. canephora, and 10,566 ESTs of C. racemosa. They are distributed into 37 cDNA libraries sequenced from the 5'-end Mondego et al, 2011). After BLAST searches in the coffee EST database, all singlets and contigs of candidate PME unigenes were re-assembled using Sequencher 4.2 (Gene Codes Corporation, Ann Arbor, MI, USA).…”

Section: Search For C Arabica Pme Sequencesmentioning

confidence: 99%

Gene expression and enzymatic activity of pectin methylesterase during fruit development and ripening in Coffea arabica L.

Cação

Leite

Budzinski³

et al. 2012

Genet. Mol. Res.

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ABSTRACT. Coffee quality is directly related to the harvest and post harvest conditions. Non-uniform maturation of coffee fruits, combined with inadequate harvest, negatively affects the final quality of the product. Pectin methylesterase (PME) plays an important role in fruit softening due to the hydrolysis of methylester groups in cell wall pectins. In order to characterize the changes occurring during coffee fruit maturation, the enzymatic activity of PME was measured during different stages of fruit ripening. PME activity progressively increased from the beginning of the ripening process to the cherry fruit stage. In silico analysis of expressed sequence tags of the Brazilian Coffee Genome Project database identified 5 isoforms of PME. We isolated and cloned a cDNA homolog of PME for further characterization. CaPME4 transcription was analyzed in pericarp, perisperm, and endosperm tissues during fruit development and ripening as well as in other plant tissues. Northern blot analysis revealed increased transcription of CaPME4 in the pericarp 300 days after flowering. Low levels of CaPME4 mRNAs were observed in the endosperm 270 days after flowering. Expression of CaPME4 transcripts was strong in the branches and lower in root and flower tissues. We showed that CaPME4 acts specifically during the later stages of fruit ripening and possibly contributes to the softening of coffee fruit, thus playing a significant role in pectin degradation in the fruit pericarp.

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“…canephora (Mondego et al, 2011). This genomic resource will be very important for further research on coffee quality improvement.…”

Section: Bacterial Artificial Chromosome (Bac) Librarymentioning

confidence: 99%

Genomic studies of biochemical compounds determining arabica coffee (Coffea arabica L.) quality

Tran¹

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Coffee is an important crop globally. Improving coffee quality is a primary breeding target that would benefit from understanding of trait inheritance and ancestral genetic information. However, comparatively little information exists on the genetics of quality and the relationships between wild and cultivated coffee genotypes, especially arabica coffee (Coffea arabica L.) which accounts for almost 60% of coffee production globally. The complex polyploidy genome and limited genomic information for C. arabica have impeded the progress of genetic studies. Arabica coffee is among the major organisms that do not have a reference genome. This project aimed to develop and utilise genomic resources in genetic studies of arabica coffee quality. The relationship between coffee species and the position of arabica within the Coffeeae tribe were investigated using complete chloroplast genome sequences to determine the value of these genetic resources in breeding. A draft genome sequence of arabica coffee was developed. Marker-trait associations were studied for caffeine and trigonelline, the two principal compounds known to be related to coffee quality, paving the way for developing new improved varieties with preferred levels of these compounds in the coffee beans.Chloroplast genomes of 16 coffee species were sequenced and their phylogeny constructed. Results support distinct Psilanthus and Coffea clades. It is likely that C. canephora is a hybrid that has a Psilanthus maternal genome but received much of its nuclear genome from Coffea. The maternal genomes of C. arabica and C. canephora are divergent. This result is in agreement with the fact that the chloroplast genome of arabica should be that of the maternal parent i.e. C. eugenioides. There were two species (C. humblotiana and C. tetragona) close to C. arabica and one species (P. ebracteolatus) close to C. canephora containing almost no caffeine. They could serve as important materials in arabica quality breeding and research.For the association study, 232 diverse arabica coffee accessions originating from 27 countries were harvested from the germplasm collection at CATIE (Tropical Agricultural Research and Higher Education Centre), Costa Rica. Substantial variation between genotypes was observed for bean morphology attributes. Non-volatiles including caffeine and trigonelline showed larger variation in range than was previously reported. Results of targeted analysis of 18 volatiles from 35 accessions also showed significant variation. No strong correlation was found between bean morphology and the levels of non-volatile or volatile compounds, implying that it is difficult to select for low or high non-volatile and volatile compounds based on bean physical characteristics. However, it also indicates that breeding for desirable combinations of traits (i.e. large bean size, low caffeine, high trigonelline, and favourable volatiles) is possible.ii The genome of the most popular arabica variety (K7) in Australia was sequenced. Genome assembly was performed using b...

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An EST-based analysis identifies new genes and reveals distinctive gene expression features of Coffea arabica and Coffea canephora

Cited by 78 publications

References 131 publications

Identification of the transcriptionally active cytochrome P450 repertoire in Coffea arabica

Identification of the transcriptionally active cytochrome P450 repertoire in Coffea arabica

Gene expression and enzymatic activity of pectin methylesterase during fruit development and ripening in Coffea arabica L.

Genomic studies of biochemical compounds determining arabica coffee (Coffea arabica L.) quality

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