An integrated analysis of mRNA and sRNA transcriptional profiles in Coffea arabica L. roots: insights on nitrogen starvation responses.
Amino Acids
/ isolation & purification
Ammonium Compounds
/ metabolism
Coffea
/ genetics
Gene Expression Regulation, Plant
Gene Ontology
High-Throughput Nucleotide Sequencing
MicroRNAs
/ classification
Molecular Sequence Annotation
Nitrates
/ metabolism
Nitrogen
/ deficiency
Plant Leaves
/ genetics
Plant Roots
/ genetics
Poly A
/ genetics
RNA, Messenger
/ classification
RNA, Plant
/ classification
RNA, Small Untranslated
/ classification
Seeds
/ genetics
Stress, Physiological
Transcriptome
Coffee
Differential gene expression
Nitrogen transport
RNA-seq
microRNA
Journal
Functional & integrative genomics
ISSN: 1438-7948
Titre abrégé: Funct Integr Genomics
Pays: Germany
ID NLM: 100939343
Informations de publication
Date de publication:
Jan 2019
Jan 2019
Historique:
received:
22
01
2018
accepted:
28
08
2018
revised:
21
08
2018
pubmed:
10
9
2018
medline:
16
4
2019
entrez:
10
9
2018
Statut:
ppublish
Résumé
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.
Identifiants
pubmed: 30196429
doi: 10.1007/s10142-018-0634-8
pii: 10.1007/s10142-018-0634-8
doi:
Substances chimiques
Amino Acids
0
Ammonium Compounds
0
MicroRNAs
0
Nitrates
0
RNA, Messenger
0
RNA, Plant
0
RNA, Small Untranslated
0
Poly A
24937-83-5
Nitrogen
N762921K75
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
151-169Références
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