ArticleFunctional & integrative genomics2019
An integrated analysis of mRNA and sRNA transcriptional profiles in Coffea arabica L. roots: insights on nitrogen starvation responses.
Article in Functional & integrative genomics, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- MicroRNA and target gene dynamics in potato under nitrogen deficiency.Scientific reports · 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
- Identification of Low-Nitrogen-Related miRNAs and Their Target Genes in Sugarcane and the Role ofInternational journal of molecular sciences · 2022Article
- Genome-Wide Identification and Characterization of Long Noncoding RNAs inFrontiers in plant science · 2022Article
- Identification of Nitrogen Starvation-Responsive miRNAs to Reveal the miRNA-Mediated Regulatory Network inFrontiers in genetics · 2022Article
- Physiological characteristics and miRNA sequencing of two root zones with contrasting ammonium assimilation patterns in Populus.Genes & genomics · 2022Article
- Identification of Genes Associated with Nitrogen Stress Responses in Apple Leaves.Plants (Basel, Switzerland) · 2021Article
- The urea transporter DUR3 is differentially regulated by abiotic and biotic stresses in coffee plants.Physiology and molecular biology of plants : an international journal of functional plant biology · 2021Article
- MicroRNAs in Woody Plants.Frontiers in plant science · 2021Review
- miRNAomic Approach to Plant Nitrogen Starvation.International journal of genomics · 2021Review
- Genome-Wide Screening and Characterization of Non-Coding RNAs inNon-coding RNA · 2020Article
- Transcriptional patterns ofPeerJ · 2020Article
- A Small RNA-Mediated Regulatory Network inFrontiers in plant science · 2019Article
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Authors and funding
21 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Coffea arabica L. is an important agricultural commodity, accounting for 60% of traded coffee worldwide. Nitrogen (N) is a macronutrient that is usually limiting to plant yield; however, molecular mechanisms of plant acclimation to N limitation remain largely unknown in tropical woody crops. In this study, we investigated the transcriptome of coffee roots under N starvation, analyzing poly-A+ libraries and small RNAs. We also evaluated the concentration of selected amino acids and N-source preferences in roots. Ammonium was preferentially taken up over nitrate, and asparagine and glutamate were the most abundant amino acids observed in coffee roots. We obtained 34,654 assembled contigs by mRNA sequencing, and validated the transcriptional profile of 12 genes by RT-qPCR. Illumina small RNA sequencing yielded 8,524,332 non-redundant reads, resulting in the identification of 86 microRNA families targeting 253 genes. The transcriptional pattern of eight miRNA families was also validated. To our knowledge, this is the first catalog of differentially regulated amino acids, N sources, mRNAs, and sRNAs in Arabica coffee roots.
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