Homeologous regulation of Frigida-like genes provides insights on reproductive development and somatic embryogenesis in the allotetraploid Coffea arabica

Ilse Fernanda Ferrari,Juliana Lischka Sampaio Mayer,Natalia Gomes Vieira,Juliana Costa De Rezende,Jorge Maurício Costa Mondego

doi:10.1038/s41598-019-44666-6

Ilse Fernanda Ferrari, Juliana Lischka Sampaio Mayer + Show 3 more

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https://doi.org/10.1038/s41598-019-44666-6

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Abstract

Coffea arabica is an allotetraploid of high economic importance. C. arabica transcriptome is a combination of the transcripts of two parental genomes (C. eugenioides and C. canephora) that gave rise to the homeologous genes of the species. Previous studies have reported the transcriptional dynamics of C. arabica. In these reports, the ancestry of homeologous genes was identified and the overall regulation of homeologous differential expression (HDE) was explored. One of these genes is part of the FRIGIDA-like family (FRL), which includes the Arabidopsis thaliana flowering-time regulation protein, FRIGIDA (FRI). As nonfunctional FRI proteins give rise to rapid-cycling summer annual ecotypes instead of vernalization-responsive winter-annuals, allelic variation in FRI can modulate flowering time in A. thaliana. Using bioinformatics, genomic analysis, and the evaluation of gene expression of homeologs, we characterized the FRL gene family in C. arabica. Our findings indicate that C. arabica expresses 10 FRL homeologs, and that, throughout flower and fruit development, these genes are differentially transcribed. Strikingly, in addition to confirming the expression of FRL genes during zygotic embryogenesis, we detected FRL expression during direct somatic embryogenesis, a novel finding regarding the FRL gene family. The HDE profile of FRL genes suggests an intertwined homeologous gene regulation. Furthermore, we observed that FLC gene of C. arabica has an expression profile similar to that of CaFRL genes.

Highlights

Coffea arabica and C. canephora are the species responsible for the production of all coffee beans worldwide
C. canephora FRIGIDA-like proteins (FRLs) sequences were used in the BlastP search against the C. arabica genome sequence and the C. eugenioides EST databank[25]
Genes considered as present in C. canephora subgenome were designated as x.1, and the genes considered as present in C. eugenioides subgenome were designated as x.2 (CaCe; Table 1)

Summary

Introduction

Coffea arabica and C. canephora are the species responsible for the production of all coffee beans worldwide. Several studies have found that the transcriptional set of C. arabica is a combination of the homeologous gene expression of the CaCc and CaCe subgenomes[3,6,7,8,9,10,11,12]. Homeolog loss and silencing were found to be common in the CaCc subgenome, which suggested CaCe dominance, neither of the two subgenomes were preferentially expressed in C. arabica[8]. It appears that each gene has its own homeologous expression coordination, providing global intertwined homeolog regulation in C. arabica. Vernalization has no effect on FRI expression, and instead promotes flowering by causing the epigenetic repression of FLC expression[19]

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