Cytogenomic characterization of Colletotrichum kahawae, the causal agent of coffee berry disease, reveals diversity in minichromosome profiles and genome size expansion

Abstract

Colletotrichum kahawae is an emerging fungal pathogen, which has recently undergone a speciation process from a generalistic 'C. gloeosporioides species complex' background by acquiring the unique capacity to infect green coffee berries, thus causing coffee berry disease. This is a severe and widespread disease in Africa and an imminent threat to Arabica coffee cultivation in Asia and America, if the pathogen enters those continents. Genetic diversity within C. kahawae is low but notorious differences in pathogen aggressiveness have been described. This work characterized two cytogenomic traits (genome size and minichromosome profiles) of a collection of C. kahawae isolates, representing the breadth of its genetic diversity and distinct aggressiveness classes, along with closely related taxa. The results obtained constitute the first flow cytometry-based genome size estimation in the genus Colletotrichum and show a c. 8 Mb genome size expansion between C. kahawae (79Á5 Mb on average) and its closest relatives (71Á3 Mb), corroborating evidence indicating that C. kahawae (i.e. the coffee berry disease pathogens) should remain as a distinct species. Results have also shown the presence of two to five minichromosomes in C. kahawae, suggesting a positive relationship between the number of minichromosomes and the level of aggressiveness of the different isolates analysed, while no correlation could be established between aggressiveness and whole genome size. Overall, these results may be the basis for the identification of pathogenicity/aggressiveness-related factors in such minichromosomes, and may provide clues to the characterization of specific markers for aggressiveness classes.

Aggressiveness profiling of the coffee pathogen Colletotrichum kahawae

“…The data collected from inoculated green berries and hypocotyls were used to calculate the index of disease intensity (IDI; Loureiro et al ., ) and disease severity (DS; Pires et al ., ) during the time course of the assays, using the following formulae: …”

“…Despite this, significant differences in the aggressiveness of different C. kahawae isolates (i.e. number of days until the appearance of first symptoms, number of days until complete necrosis of coffee tissues and index of disease severity) have previously been detected and have been referred to in the literature (Beynon et al ., ; Bella et al ., ; Várzea et al ., ; Loureiro et al ., ; Pires et al ., ; Vieira et al ., ). Beynon et al .…”

“…Moreover, Pires et al . () suggested a positive relationship between the number of minichromosomes and the level of isolate aggressiveness. However, despite all these efforts, a comprehensive characterization of the aggressiveness of C. kahawae using a large set of isolates and metrics has not yet been performed.…”

Legitimacy and Implications of Reducing Colletotrichum kahawae to Subspecies in Plant Pathology

“…Whether the C. kahawae subspecies' recognized by Weir et al (2012) are after all genetically good species, will most likely be only suitably resolved with genomic data, an endeavor that is close to be accomplished (Vieira et al, 2016). For now, it should be considered that, as shown by Silva et al (2012b) and Pires et al (2016), notwithstanding the remarkable genetic similarity, there are enough evidences to accept them as distinct species, and in this light they would be better described and viewed as cryptic species.…”

“…In addition to its biology and slow growth form, the CBD pathogen can be distinguished metabolically by its inability to use either citrate or tartrate as a sole carbon source (Waller et al, 1993 and references herein; Varzea et al, 2002; Weir et al, 2012). At the genetic level, single genes or a combination of genes, specifically glutamine synthetase ( GS ) (Weir et al, 2012), mating type 1-2-1 ( MAT1-2-1 ), and a fragment of DNA lyase Apn 2 ( Apn 25L) (Silva et al, 2012b), reliably distinguish the CBD pathogen, as well as the genome size (Pires et al, 2016). …”