Cytogenomics in Coffea L.

The genus Coffea comprises ~124 species, including C. arabica and C. canephora, which are responsible for the commercial production of coffee beans. Although most cytogenomic researches are focused on commercial species and its relatives, efforts have been made to expand the scope to wild species. However, molecular cytogenetic data are still limited to karyotype organization, especially due to low quality of the cytogenetic preparations. Considering this, the present work is focused on the cytogenomics of Coffea species. The first chapter provides an up to date review on the history of Coffea cytogenomics, initiating with the first classical cytogenetic studies, encompassing the main challenges and landmarks in cytogenetics and genomics, as well as their integration. These cytogenomic data allowed us to understand the phylogenetic relationships in Coffea, as well as their genomic origins, highlighting the relatively recent events of allopolyploidy. These events include the origin of the allotetraploid C. arabica (2n = 4x = 44, C. canephora x C. eugenioides) and the allotriploid hybrid ‘Hibrido de Timor (2n =3 x = 33, C. arabica x C. canephora). The second chapter is devoted to the study of repetitive sequences (repeatome) of the C. eugenioides genome, by integrating bioinformatic tools with cytogenetic mapping. We showed that repetitive sequences comprise ~47% of C. eugenioides genome, with mobile elements representing 45%. The Ty3/Gypsy to Ty1/Copia ratio was high (32:4), as also observed for other Coffea species. We mapped three Ty1/Copia (Bianca, TAR and Tork) and one Ty3/Gypsy (Athila) LTR-retrotransposon in metaphase chromosomes and interphase nuclei of C. eugenioides. Their distribution exhibited a clustered pattern throughout different chromosomes and regions of the chromosomes. The results obtained here are unprecedented for Coffea. Thus, we hope they lay the background for further investigations regarding Coffea cytogenomics. Keywords: Coffee. Molecular Cytogenetics. Polyploidy. Genomics. Repeatome. Mobile Elements.