Abstract
Aquaporins (APQs) belong to the major intrinsic protein superfamily and play a key role in the transport of water and other solutes across cell membranes. Coffea canephora is an evergreen shrub used for making instant coffees. Genome analysis of C. canephora identified 33 putative aquaporin genes assigned to five subfamilies including seven plasma membrane intrinsic proteins (PIP), 9 tonoplast intrinsic proteins (TIP), 11 NOD26-like intrinsic proteins (NIP), 3 small basic intrinsic proteins (SIP), and 3 X intrinsic proteins (XIP). Generally, the AQPs gene structure was conserved within each subfamily, with exon numbers ranging from one to five. The prediction of the aromatic/arginine selectivity filter (ar/R) and Froger’s positions indicated a noticeable difference in substrate specificity between subfamilies. Synteny analysis revealed high conservation of aquaporin genes in coffee. In silico expression analysis of the CcAQPs genes indicated that they were differentially expressed in various tissues. Members of CcPIPs and CcTIPs subfamilies were validated by real-time quantitative analysis in leaves of two genotypes of C. canephora with contrasting responses to water deficit (clone 14: drought-tolerant and clone 109A: drought-susceptible). Under severe water deficit, the relative expression of isoforms of both genes decreased in clone 14 compared with that under the irrigated condition, while clone 109A showed comparatively higher mRNA levels, with the exception of CcPIP1;2 in the stress condition. This study was the first to characterize and validate aquaporin genes in C. canephora in response to water deficit, and the findings may provide insights for biotechnological approaches to increase tolerance to drought.
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The author Diliane Harumi Yaguinuma received a grant from the Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (Grant Number 001).
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Key Message
•Aquaporin gene family conservation maintained in coffee plants. PIPs and TIPs isoforms expressed differentially in the contrasting genotypes of Coffea canephora in response to water deficit.
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Fig. S1
Phylogenetic tree of AQPs of C. canephora and A. thaliana using the standard ClustalW alignment parameter. The phylogenetic dendrogram generated by MEGAX using the ML method. Bootstrap analysis was performed with 1000 replicates; only bootstrap values higher than 50% are indicated above the branches. (PNG 157 kb)
Fig. S2
Partial alignment of putative XIP sequences of three Coffea species (C. arabica (Ca), C. eugenioides (Ce) and C. canephora (Cc) using the ClustalW tool through the MEGAX platform. Highlighted in red is the NPARC motif. (PNG 49 kb)
Fig. S3
Multiple alignment of deduced amino acid sequences of CcAQP using the ClustalW tool available in the MEGAX. NPA motifs (bold); ar / R selectivity filters (H2, H5, LE1 and LE2) are highlighted in red; Froger’s 5 positions (P1 - P5) highlighted in green. Underlined transmembrane helix positions. (DOCX 125 kb)
Fig. S4
Prediction of transmembrane domains in the deduced amino acid sequences of CcAQP through the TMHMM Server v. 2.0. (DOCX 716 kb)
Fig. S5
Phylogenetic tree of C. arabica and A. thailana using the CLUSTALW standard alignment parameter. The phylogenetic dendrogram generated by MEGA X using the Maximum Likelihood method with 1000 bootstrap replicates (PNG 117 kb)
Fig. S6
Phylogenetic tree of C. eugenioides and A. thailana using the standard CLUSTALW alignment parameters. The phylogenetic dendrogram generated by MEGA X using the Maximum Likelihood method with 1000 bootstrap replicates. (PNG 106 kb)
Table S1
Date of duplication of the pairs of paralogous genes of the C. canephora aquaporin gene family. Ka represents the non-synonymous substitution number per non-synonymous site, Ks is the number of the synonymous substitution site; Ka/Ks represents the ratio of non-synonymous (Ka) to synonymous (Ks) substitutions. (DOCX 16 kb)
Table S2
Aquaporin genes synteny among three Coffea species (C. arabica (Ca), C. eugenioides (Ce) and C. canephora (Cc). (DOCX 19 kb)
Table S3
Aquaporin genes synteny between Coffea arabica (Ca) and Coffea canephora (Cc). (DOCX 19 kb)
Table S4
Aquaporin genes synteny between C. eugenioides (Ce) and C. canephora (Cc). (DOCX 17 kb)
Table S5
Primers, amplicon size and amplification efficiency for RT-qPCR analysis of CcAQPs. (DOCX 15 kb)
Table S6
List of accession numbers of from all aquaporin genes used for phylogenetic analysis (DOCX 40 kb)
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Yaguinuma, D.H., dos Santos, T.B., de Souza, S.G.H. et al. Genome-Wide Identification, Evolution, and Expression Profile of Aquaporin Genes in Coffea canephora in Response to Water Deficit. Plant Mol Biol Rep 39, 146–162 (2021). https://doi.org/10.1007/s11105-020-01235-w
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DOI: https://doi.org/10.1007/s11105-020-01235-w