Extending the knowledge of Phyllosticta citricarpa population structure in USA with re-sequencing and genome wide analysis

Phyllosticta citricarpa is a fungal plant pathogen that causes citrus black spot (CBS). This study is the first to use high throughput sequencing (HTS) to study the genetic diversity within a P. citricarpa population. Seventeen isolates from the United States of America were sequenced and their genomes assembled. A pairwise mapping and variant calling analysis were performed on all isolates, and a low number of inter-isolate variants detected. Furthermore, the HTS data was also used to genotype 4029 SSRs in the isolates, and only 57 polymorphic markers were found. These results confirm the clonality of this P. citricarpa population. However, it is not a totally homogeneous group and it was shown that HTS can detect this fine-scale genetic differentiation. The two different approaches, pairwise mapping and variant calling versus SSR detection and in silico genotyping, yielded similar results, dividing the isolates into the same two groups. The results from this study demonstrate the feasibility of HTS and comparative genome analyses to study the genetic diversity and population structure of this fungus.

Automated summary

This study used high throughput sequencing to study the genetic diversity of Phyllosticta citricarpa population, confirming its clonality and revealing fine-scale genetic differentiation. Two different approaches yielded similar results, dividing the isolates into the same two groups.