An integrated analysis of mRNA and sRNA transcriptional profiles in Coffea arabica L. roots: insights on nitrogen starvation responses
Instituto Agronômico do Paraná (IAPAR)¦¦Brasil ; Universidade do Oeste Paulista (UNOESTE)¦¦Brasil ; Universidade de São Paulo (USP)¦¦Brasil ; Universidade Federal de Minas Gerais (UFMG)¦¦Brasil ; Universidade Tecnológica Federal do Paraná (UTFPR)¦¦Brasil ; Universidade Estadual Paulista Júlio de Mesquita Filho (UNESP)¦¦Brasil ; Universidade Paranaense (UNIPAR)¦¦Brasil ; Universidade Estadual de Londrina (UEL)¦¦Brasil ; Universidade Estadual de Campinas (UNICAMP)¦¦Brasil ; Institut de Recherche pour le Développement (IRD)¦¦França ; Embrapa Café¦¦Brasil
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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.
Santos TB, Soares JD.M., Lima JE., Silva JC., Ivamoto ST., Baba VY., et al. An integrated analysis of mRNA and sRNA transcriptional profiles in Coffea arabica L. roots: insights on nitrogen starvation responses. Funct Integr Genomics. 2019 Jan;19(1):151-69. doi:10.1007/s10142-018-0634-8.
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Consórcio Pesquisa Café ; Fundação Araucária de Apoio ao Desenvolvimento Científico e Tecnológico do Estado do Paraná (FA) ; Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) ; Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) ; Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)
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