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 a recent study, researchers from the Agronomic Institute of Paraná investigated the transcriptome of coffee roots under N starvation, analyzing poly-A+ libraries and small RNAs. They 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. They 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.

This is the first catalog of differentially regulated amino acids, N sources, mRNAs, and sRNAs in Arabica coffee roots.

 

Annotation of the 253 putative miRNAs target genes identified in our coffee root trancriptome database. The most represented classes were divided into three main categories: “cellular component,” “molecular function,” and “biological process.”

 

Reference
TB dos Santos, JDM Soares, JE Lima, JC Silva et al. (2018) An integrated analysis of mRNA and sRNA transcriptional profiles in Coffea arabica L. roots: insights on nitrogen starvation responses Functional & Integrative Genomics [Epub ahead of print]. doi: 10.1007/s10142-018-0634-8 [abstract]

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