P-295 - Pangenomic analyses reveal structural variation and lineage-specific genes in the rice pathogen Cercospora janseana

Cercospora janseana is a fungus that causes narrow brown leaf spot in rice. Recent population analyses reveal that C. janseana in the southern U.S. is comprised of two lineages, NA1 and NA2. To understand how these lineages have emerged and differentiated, a pangenomic approach was taken using isolates from each lineage. Three NA1 isolates and two NA2 isolates were sequenced using Nanopore sequencing and assembled with Canu and Flye. Based on the presence of telomeric repeats, N50, L50, and BUSCO scores, the Canu assemblies were the most contiguous and complete. Assembly sizes ranged from 39.9 to 42.1 Mb. Moderate variation in transposable element (TE) content was observed with overall proportions ranging from 23-26%, although little variation was observed in the abundance of specific TE families. A total of 11,434 orthogroups were identified with 9821, 1207, and 406 being core, accessory, and singleton, respectively. Additionally, 127 and 132 accessory genes, as well as 13 and 15 accessory effector genes, were exclusive to NA1 and NA2, respectively. Structural variation (SV), including translocations and TE-driven expansions, were identified, including a SV on Chr9 associated with virulence. Further analysis of lineage-specific effectors and SVs is currently underway. Taken together, these results provide novel insights into genomic plasticity and gene content variation in C. janseana which will further our understanding of factors driving lineage differentiation.