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An integrated analysis of mRNA and sRNA transcriptional profiles in Coffea arabica L. roots: insights on nitrogen starvation responses

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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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Acknowledgments

This study received grants from Brazilian Coffee Research Consortium, Fundação Araucária, CAPES (Ciência sem Fronteiras PVE 084/2013) and CNPq. TBS, JDMS, JCS, VYB, and STI acknowledge CAPES, CNPq, and FAPESP for the student fellowships. DSD, LGEV, and LFPP are CNPq research productivity fellows.

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Authors and Affiliations

  1. Laboratório de Biotecnologia Vegetal, Instituto Agronômico do Paraná, Londrina, 86047-902, Brazil

    Tiago Benedito dos Santos, João D. M. Soares, Juliana C. Silva, Suzana T. Ivamoto, Viviane Y. Baba, Anderson R. Meda, Luiz F. P. Pereira & Douglas S. Domingues

  2. Universidade do Oeste Paulista, Rodovia Raposo Tavares Km 572, Presidente Prudente, 19067-175, Brazil

    Tiago Benedito dos Santos & Luiz G. E. Vieira

  3. Centro de Energia Nuclear na Agricultura, Universidade de São Paulo, Piracicaba, 13400-970, Brazil

    Joni E. Lima & Antônio V. O. Figueira

  4. Departamento de Botânica, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, 31270-901, Brazil

    Joni E. Lima

  5. Programa de pós-graduação em Bioinformática, Universidade Tecnológica Federal do Paraná, Cornélio Procópio, 86300-000, Brazil

    Juliana C. Silva & Alexandre R. Paschoal

  6. Departamento de Botânica, Instituto de Biociências de Rio Claro, Universidade Estadual Paulista, Rio Claro, 13506-900, Brazil

    Suzana T. Ivamoto & Douglas S. Domingues

  7. Laboratório de Biologia Molecular, Universidade Paranaense, Umuarama, 87502-210, Brazil

    Silvia G. H. Souza

  8. Programa de Pós-graduação em Genética e Biologia Molecular, Universidade Estadual de Londrina, Londrina, 86057-970, Brazil

    Alan P. R. Lorenzetti

  9. Laboratório Especial de Toxinologia Aplicada, Instituto Butantan, São Paulo, 05503-900, Brazil

    Milton Y. Nishiyama Júnior, Úrsula C. de Oliveira & Inácio L. M. Junqueira-de-Azevedo

  10. Departamento de Biologia Vegetal, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, 13083-970, Brazil

    João B. Mokochinski & Paulo Mazzafera

  11. IRD, UMR IPME, COFFEEADAPT, BP 64501, 34394, Montpellier Cedex 5, France

    Romain Guyot

  12. Life Sciences Core Facility (LaCTAD), Universidade Estadual de Campinas, Campinas, 13083-886, Brazil

    Osvaldo R. Júnior

  13. Embrapa Café, Brasília, 70770-901, Brazil

    Luiz F. P. Pereira

Authors
  1. Tiago Benedito dos Santos
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  2. João D. M. Soares
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  3. Joni E. Lima
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  4. Juliana C. Silva
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  5. Suzana T. Ivamoto
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  6. Viviane Y. Baba
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  7. Silvia G. H. Souza
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  8. Alan P. R. Lorenzetti
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  9. Alexandre R. Paschoal
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  10. Anderson R. Meda
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  12. Úrsula C. de Oliveira
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  13. João B. Mokochinski
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  14. Romain Guyot
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  15. Inácio L. M. Junqueira-de-Azevedo
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  16. Antônio V. O. Figueira
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  17. Paulo Mazzafera
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  18. Osvaldo R. Júnior
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  19. Luiz G. E. Vieira
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  20. Luiz F. P. Pereira
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  21. Douglas S. Domingues
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Contributions

TBS, LGEV, and LFPP conceived and designed the research, performed transcriptional experiments, wrote and revised the final manuscript; ARM assisted in designing the experiment; JEL performed experiments using 15N and wrote the manuscript; STI RT-qPCR statistical analysis, revised the final manuscript; JDMS and VYB RT-qPCR and statistical analyses; SGHS performed GS and NR analyses; JBM and PM performed the amino acid analysis; MYNJ, JCS, ORJ, APRL, and ARP bioinformatic analysis; ILMJA and UCO library construction and mRNAseq sequencing; RG and DSD transposable element analysis, coordinated the research, and revised the final manuscript. All authors read and approved the manuscript.

Corresponding author

Correspondence to Tiago Benedito dos Santos.

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The authors declare that they have no conflict of interest.

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Fig. S1

N starvation experiment scheme. a Initially, seeds were germinated in sand boxes and transfered to pots with continuous N supply. Three-month-old plants were transferred to a nutrient solution based on Clark’s (1975). After acclimation, plants were harvested (experimental control, day 0) and then transferred to N-starvation solution for 10 days. b Lateral roots were collected for analysis at different sampling times (day 0, day 1, and day 10). (JPG 63 kb)

Fig. S2

Quantification of total N and related-enzymes in coffee root. a Total concentration of N in coffee roots. b Nitrate reductase (NR) enzyme activity in coffee roots. c Glutamine synthetase (GS) enzyme activity in coffee roots under N starvation. Different letters above the bars indicate statistically significant differences (Student’s t test; p < 0.05). FW fresh weight (JPG 50 kb)

Fig. S3

Number of assembled sequences with hits in the Coffea canephora reference transposable elements (TE) database (806), RepBase Plants transposable elements database (35), and both databases (21). (JPG 63 kb)

Fig. S4

miRNA hairpin sequences of conserved families and precursors found in the Coffea canephora genome. Expected miRNA and miRNA* sequences are represented in red and blue, respectively. (DOC 541 kb)

Fig. S5

miRNA hairpin sequences of conserved families and precursors found in Coffea arabica root transcriptome. Expected miRNA and miRNA* sequences are represented in red and blue, respectively. (DOC 40 kb)

Fig. S6

New miRNA families and precursors identified in Coffea canephora genome. Expected miRNA and miRNA* sequences are represented in red and blue, respectively. (DOC 903 kb)

Fig. S7

Eight new miRNA families and precursors identified in Coffea arabica root transcriptome. Expected miRNA and miRNA* sequences are represented in red and blue, respectively. (DOC 40 kb)

Fig. S8

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.” (JPG 102 kb)

Fig. S9

Proposed model for the representation of ammonium and nitrate transporters in coffee roots under N starvation. (JPG 81 kb)

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dos Santos, T.B., Soares, J.D.M., Lima, J.E. et al. An integrated analysis of mRNA and sRNA transcriptional profiles in Coffea arabica L. roots: insights on nitrogen starvation responses. Funct Integr Genomics 19, 151–169 (2019). https://doi.org/10.1007/s10142-018-0634-8

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  • DOI: https://doi.org/10.1007/s10142-018-0634-8

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