Genome-wide and expression analyses of MADS-box genes in the tetraploid Coffea arabica L. and its diploid parental subgenomes

Abstract

MADS-box is a family of transcription factors widely found in different kingdoms and essential for plant development. Understanding the evolution and functioning of such genes in developmental processes is essential to develop more adapted crops and guarantee food production. However, genome-wide analyses of MADS-box genes are poorly explored in tropical perennial species with complex phenological cycles and floral synapomorphic characters, such as Coffea sp. Moreover, Coffea arabica L. is unique in its genre being the only autogamous and tetraploid species, formed from the hybridization of the parental diploid genomes C. canephora and C. eugenioides, offering an opportunity to study recent ploidization and functionalization events. Here, we identified a total of 102 MADS-box unigenes in Coffea sp., being 81 unpublished. They were classified into Type I and II proteins (MIKC* and MIKCC), 42 and 60 respectively, and categorized in the currently described subgroups. A chromosomal map revealed an irregular distribution and low positional variation of genes between homologous parental chromosomes. Gene structure analysis showed higher similarity for genes closely related, but a variable number of introns and its lengths between distant ones. Next, in order to provide functional insights, we determined the expression profiles of these genes in RNA-Seq libraries of different coffee tissues. Transcripts relative to Type II proteins presented a broader expression pattern than Type I, with low expression values and restricted to specific libraries. Thus, our work contributed to elucidating the evolutionary history of MADS-box genes in Rubiaceae, providing perspectives to functional studies and useful to direct breeding programs.