Phylogenomic analysis clarifies the evolutionary origin of Coffea arabica

Abstract

Interspecific hybridization events have played a major role in plant speciation, yet, the evolutionary origin of hybrid species often remains enigmatic. Here, we inferred the evolutionary origin of the allotetraploid species Coffea arabica, which is widely cultivated for Arabica coffee production.We estimated genetic distances between C. arabica and all species that are known to be closely related to C. arabica using genotyping-by-sequencing (GBS) data. In addition, we reconstructed a time-calibrated multilabeled phylogenetic tree of 24 species to infer the age of the C. arabica hybridization event. Ancestral states of self-compatibility were also reconstructed to infer the evolution of self-compatibility in Coffea.C. canephora and C. eugenioides were confirmed as the putative progenitor species of C. arabica. These species most likely hybridized between 1.08 million and 543 thousand years ago.We inferred the phylogenetic relationships between C. arabica and its closest relatives and shed new light on the evolution of self-compatibility in Coffea. Furthermore, the age of the hybridization event coincides with periods of environmental upheaval, which may have induced range shifts of the progenitor species that facilitated the emergence of C. arabica.

A Chromosome-Scale Genome Assembly of Mitragyna speciosa (Kratom) and the Assessment of Its Genetic Diversity in Thailand

“…After correcting for multiple substitutions, we observed a sharp peak in 4DTv value at 0.012 synonymous transversions per site in C. arabica . This corresponded to the period between 1.08 and 0.54 million years ago, during which the hybridization of two progenitor species ( C. canephora and Coffea eugenioides ) led to the emergence of C. arabica [ 43 ]. Comparisons between the 12,198 pairs of paralogous genes residing within 418 duplicated colinear blocks within the M. speciosa genome revealed a noticeable peak at 0.139, suggesting that M. speciosa has undergone a recent whole-genome duplication ( Figure 3 B).…”

Coffee Leaves: An Upcoming Novel Food?

“…Particularly, phylogenetic studies confirmed that CAN and C. eugenioides can be considered the ARA's progenitor species, each providing half of ARA's genome. It has been assumed that these species hybridized between 1.08 million and 543 thousand years ago and that the emergence of ARA could be related to the environmental changes in East Africa during glacial-interglacial cycles in the last 1 million years [3].…”

Genome-Wide Identification, Characterization, and Comparative Analysis of NLR Resistance Genes in Coffea spp.

“…The genus Coffea consists of more than 100 botanical species ( Davis et al, 2006 ), however, the most cultivated species are Coffea canephora and Coffea arabica . C. canephora is diploid (2 n = 2x = 22 chromosomes) ( Denoeud et al, 2014 ), while C. arabica is a allotetraploid (2 n = 4x = 44 chromosomes) ( Tran et al, 2018 ) originated from natural hybridization between C. canephora and C. eugenioides ( Lashermes et al, 1999 ; Bawin et al, 2020 ). Among the more than 50 coffee-producing countries, Brazil, Vietnam, Colombia, and Indonesia are major producers, with Brazil being the largest producer by volume.…”