ArticlePloS one2017
Transcriptome Analysis of Leaves, Flowers and Fruits Perisperm of Coffea arabica L. Reveals the Differential Expression of Genes Involved in Raffinose Biosynthesis.
Article in PloS one, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers, 1 of them a synthesis that pooled it.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
23 citing papers in PubMed, 1 synthesis or guideline pooled it, 60 citations in OpenAlex.
- Pooled it
- Scion genotype dominates drought tolerance in graftedFrontiers in plant science · 2026Article
- Unveiling the Microbial Signatures of Arabica Coffee Cherries: Insights into Ripeness Specific Diversity, Functional Traits, and Implications for Quality and Safety.Foods (Basel, Switzerland) · 2025Article
- The Identification and Characterization of WOX Family Genes inInternational journal of molecular sciences · 2024Article
- Transcriptomic Data Analysis Using the Galaxy Platform: Coffee (Coffea arabica L.) Flowers as Example.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Small RNAs: Promising Molecules to Tackle Climate Change Impacts in Coffee Production.Plants (Basel, Switzerland) · 2023Review
- Comparative transcriptome analysis in peaberry and regular bean coffee to identify bean quality associated genes.BMC genomic data · 2023Article
- Transcriptome and carotenoid profiling of different varieties ofPlant diversity · 2022Article
- Endosperm Evolution by Duplicated and Neofunctionalized Type I MADS-Box Transcription Factors.Molecular biology and evolution · 2022Article
- Comparative transcriptome analysis of wheat in response to corn leaf aphid,Frontiers in plant science · 2022Article
- CsAGA1 and CsAGA2 Mediate RFO Hydrolysis in Partially Distinct Manner in Cucumber Fruits.International journal of molecular sciences · 2021Article
- Transcriptomic Leaf Profiling Reveals Differential Responses of the Two Most Traded Coffee Species to Elevated [COInternational journal of molecular sciences · 2020Article
- Low-Copy Genes in Terpenoid Metabolism: The Evolution and Expression ofPlants (Basel, Switzerland) · 2020Article
- An innovative automated active compound screening system allows high-throughput optimization of somatic embryogenesis in Coffea arabica.Scientific reports · 2020Article
- Full moonlight-induced circadian clock entrainment in Coffea arabica.BMC plant biology · 2020Article
- Gene Expression Maps in Plants: Current State and Prospects.Plants (Basel, Switzerland) · 2019Review
- Transcriptome analysis reveals the effects of grafting on sweetpotato scions during the full blooming stages.Genes & genomics · 2019Article
- Transcriptome sequencing of Himalayan Raspberry (3 Biotech · 2019Article
- Article
- An integrated analysis of mRNA and sRNA transcriptional profiles in Coffea arabica L. roots: insights on nitrogen starvation responses.Functional & integrative genomics · 2019Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
11 authors at 7 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Coffea arabica L. is an important crop in several developing countries. Despite its economic importance, minimal transcriptome data are available for fruit tissues, especially during fruit development where several compounds related to coffee quality are produced. To understand the molecular aspects related to coffee fruit and grain development, we report a large-scale transcriptome analysis of leaf, flower and perisperm fruit tissue development. Illumina sequencing yielded 41,881,572 high-quality filtered reads. De novo assembly generated 65,364 unigenes with an average length of 1,264 bp. A total of 24,548 unigenes were annotated as protein coding genes, including 12,560 full-length sequences. In the annotation process, we identified nine candidate genes related to the biosynthesis of raffinose family oligossacarides (RFOs). These sugars confer osmoprotection and are accumulated during initial fruit development. Four genes from this pathway had their transcriptional pattern validated by quantitative reverse transcription polymerase chain reaction (qRT-PCR). Furthermore, we identified ~24,000 putative target sites for microRNAs (miRNAs) and 134 putative transcriptionally active transposable elements (TE) sequences in our dataset. This C. arabica transcriptomic atlas provides an important step for identifying candidate genes related to several coffee metabolic pathways, especially those related to fruit chemical composition and therefore beverage quality. Our results are the starting point for enhancing our knowledge about the coffee genes that are transcribed during the flowering and initial fruit development stages.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.