RESUMEN
Arguably, the nitrogen (N) is an important and essential component for plant growth and development. Among the sources of N available, the ammonium is a major inorganic nitrogen source for plants is mobilized by ammonium transporter (AMT). In this study, data mining revealed that the Ananas comosus L. genome was identified eight genes of the AMT family. Based on this information, we conducted a comprehensive analysis using some bioinformatics tools in order to individually characterize the identified genes. The comprehensive analysis of AMT will provide an important foundation for further investigation of the regulatory mechanisms of AcoAMTs in A. comosus L.
Indiscutivelmente, o nitrogênio (N) é um componente importante e essencial para o crescimento e desenvolvimento das plantas. Dentre as fontes de N disponíveis, o amônio é a principal fonte de nitrogênio inorgânico para as plantas, sendo mobilizado pelo transportador de amônio (AMT). Neste estudo, a mineração de dados revelou que no genoma de Ananas comosus L. foram identificados oito genes da família AMT. Com base nessas informações, realizamos uma análise abrangente usando algumas ferramentas de bionformática com a finalidade de caracterizar individualmente os genes identificados. A análise abrangente do AMT fornecerá uma base importante para uma investigação mais aprofundada dos mecanismos regulatórios de AcoAMTs em A. comosus L.
Asunto(s)
Ananas/genética , Minería de Datos , NitrógenoRESUMEN
Arguably, the nitrogen (N) is an important and essential component for plant growth and development. Among the sources of N available, the ammonium is a major inorganic nitrogen source for plants is mobilized by ammonium transporter (AMT). In this study, data mining revealed that the Ananas comosus L. genome was identified eight genes of the AMT family. Based on this information, we conducted a comprehensive analysis using some bioinformatics tools in order to individually characterize the identified genes. The comprehensive analysis of AMT will provide an important foundation for further investigation of the regulatory mechanisms of AcoAMTs in A. comosus L.(AU)
Indiscutivelmente, o nitrogênio (N) é um componente importante e essencial para o crescimento e desenvolvimento das plantas. Dentre as fontes de N disponíveis, o amônio é a principal fonte de nitrogênio inorgânico para as plantas, sendo mobilizado pelo transportador de amônio (AMT). Neste estudo, a mineração de dados revelou que no genoma de Ananas comosus L. foram identificados oito genes da família AMT. Com base nessas informações, realizamos uma análise abrangente usando algumas ferramentas de bionformática com a finalidade de caracterizar individualmente os genes identificados. A análise abrangente do AMT fornecerá uma base importante para uma investigação mais aprofundada dos mecanismos regulatórios de AcoAMTs em A. comosus L.(AU)
Asunto(s)
Ananas/genética , Minería de Datos , NitrógenoRESUMEN
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.
Asunto(s)
Coffea/genética , MicroARNs/genética , Nitrógeno/deficiencia , ARN Mensajero/genética , ARN de Planta/genética , ARN Pequeño no Traducido/genética , Aminoácidos/aislamiento & purificación , Aminoácidos/metabolismo , Compuestos de Amonio/metabolismo , Coffea/metabolismo , Regulación de la Expresión Génica de las Plantas , Ontología de Genes , Secuenciación de Nucleótidos de Alto Rendimiento , MicroARNs/clasificación , MicroARNs/metabolismo , Anotación de Secuencia Molecular , Nitratos/metabolismo , Hojas de la Planta/genética , Hojas de la Planta/metabolismo , Raíces de Plantas/genética , Raíces de Plantas/metabolismo , Poli A/genética , Poli A/metabolismo , ARN Mensajero/clasificación , ARN Mensajero/metabolismo , ARN de Planta/clasificación , ARN de Planta/metabolismo , ARN Pequeño no Traducido/clasificación , ARN Pequeño no Traducido/metabolismo , Semillas/genética , Semillas/metabolismo , Estrés Fisiológico , TranscriptomaRESUMEN
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.
RESUMEN
Abstract Nitrogen (N) is quantitatively the main nutrient required by coffee plants, with acquisition mainly by the roots and mostly exported to coffee beans. Nitrate (NO3-) and ammonium (NH4+) are the most important inorganic sources for N uptake. Several N transporters encoded by different gene families mediate the uptake of these compounds. They have an important role in source preference for N uptake in the root system. In this study, we performed a genome-wide analysis, including in silico expression and phylogenetic analyses of AMT1, AMT2, NRT1/PTR, and NRT2 transporters in the recently sequenced Coffea canephora genome. We analyzed the expression of six selected transporters in Coffea arabica roots submitted to N deficiency. N source preference was also analyzed in C. arabica using isotopes. C. canephora N transporters follow the patterns observed for most eudicots, where each member of the AMT and NRT families has a particular role in N mobilization, and where some of these are modulated by N deficiency. Despite the prevalence of putative nitrate transporters in the Coffea genome, ammonium was the preferential inorganic N source for N-starved C. arabica roots. This data provides an important basis for fundamental and applied studies to depict molecular mechanisms involved in N uptake in coffee trees.