Population genomics of Pseudocercospora griseola reveal new groups in the Middle American clade and the presence of the endophytic bacterium Achromobacter xylosoxidans

Authors: Serrato Diaz, Luz; Cuevas, Hugo; CHILAGANE, LUSEKO - Sokoine University Of Agriculture; ROSAS, JUAN - Zamorano, Panamerican School Of Agriculture; VELEZ, JESSICA - University Of Tennessee; SCHADT, CHRISTOPHER - University Of Tennessee; RIVERA-VARGAS, LYDIA - University Of Puerto Rico; BAYMAN, PAUL - University Of Puerto Rico; Porch, Timothy

Submitted to: Phytopathology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/16/2025
Publication Date: 1/1/2026
Citation: Serrato Diaz, L.M., Cuevas, H.E., Chilagane, L.A., Rosas, J.C., Velez, J.M., Schadt, C.W., Rivera-Vargas, L.I., Bayman, P., Porch, T.G. 2026. Population genomics of Pseudocercospora griseola reveal new groups in the Middle American clade and the presence of the endophytic bacterium Achromobacter xylosoxidans. Phytopathology. 116: 17-29.

Interpretive Summary: Angular leaf spot (ALS) is an important disease of common and snap beans, caused by Pseudocercospora griseola, which is a highly variable pathogen with multiple races, that co-evolved with common bean into two main groups, Andean and Middle American. Understanding the genetic variability of P. griseola is an imperative for identifying new sources of disease resistance in bean germplasm. The genomic analysis of 48 isolates of P. griseola from Puerto Rico, Guatemala, Honduras and Tanzania revealed the existence of multiple populations. Three isolates from Tanzania were identified as members of the Andean group while isolates from Guatemala, Honduras, Puerto Rico and two from Tanzania were identified as part of the Middle American group. The Middle American group was divided in three sub-populations associated with their collection location: 1) Guatemala and Honduras; 2) Tanzania and Puerto Rico; and 3) Puerto Rico. The virulence analysis of the 28 P. griseola isolates from Puerto Rico led to the identification of 10 races. This genetic diversity and virulence analysis of ALS isolates provides valuable information regarding the host genes required for ensuring genetic resistance in plant breeding programs.

Technical Abstract: Angular leaf spot (ALS) caused by Pseudocercospora griseola is an important disease of common and snap beans causing losses up to 80% in susceptible varieties. This fungus is highly variable and has co-evolved with its host, grouping P. griseola into three populations: Andean, Middle American and Afro-Andean. Due to its high variability, different races have been reported worldwide. In this study, 48 isolates of P. griseola from Puerto Rico, Guatemala, Honduras and Tanzania were sequenced using the 3RAD-seq method that resulted in the de novo assembly of 42,214 contigs. Phylogenomic tree, population structure and principal component analyses using 1,260 SNPs divided these isolates into Andean and Middle American populations, while the Middle American population was further divided into three sub-populations. There was moderate to high levels of differentiation between P. griseola populations from different countries, with pairwise FST values ranging from 0.11 to 0.95. The Andean population was composed of isolates from Tanzania, and it was clearly separated from the Middle American population (Fst = 0.95). The genetic variation within the Middle American population was separated into 3 subpopulations including isolates from: 1) Guatemala and Honduras (Fst = 0.11), 2), 2) Tanzania (Fst = 0.68), and 3) Puerto Rico (Fst = 0.82). A total of 102 private SNPs were found within the Middle American sub-populations (43 SNPs for Puerto Rico, 52 SNPs for Guatemala and Honduras, and 7 SNPs for Tanzania) of which 28 were located in known functional genes. Virulence analysis of 28 isolates from Puerto Rico using 12 common bean differential lines identified the existence of ten P. griseola races, but these races were not associated with SNPs found in virulence genes. Nevertheless, the presence of an endophytic bacterium (Achromobacter xylosoxidans) was found in seven mildly virulent isolates suggesting a possible role of the bacterium in the observed virulence patterns. Understanding the evolution and diversity of P. griseola, the virulence genes and the interaction of the endophytic bacterium associated with the fungus require further study and can be used to direct breeding strategies for the development of resistant germplasm.