Abstract
Phytophthora capsici is an oomycete pathogen responsible for damping off, root rot, fruit rot, and foliar blight in popular vegetable and legume crops. The existence of distinct aggressiveness levels and physiological races among the P. capsici population is a major constraint to developing resistant varieties of host crops. In the present study, we compared the genomes of three P. capsici isolates with different aggressiveness levels to reveal their genomic differences. We obtained genome sequences using short-read and long-read technologies, which yielded an average genome size of 76 Mbp comprising 514 contigs and 15,076 predicted genes. A comparative genomic analysis uncovered the signatures of accelerated evolution, gene family expansions in the pathogenicity-related genes among the three isolates. Resequencing two additional P. capsici isolates enabled the identification of average 1,023,437 SNPs, revealing the frequent accumulation of non-synonymous substitutions in pathogenicity-related gene families. Furthermore, pathogenicity-related gene families, cytoplasmic effectors and ATP binding cassette (ABC) transporters, showed expansion signals in the more aggressive isolates, with a greater number of non-synonymous SNPs. This genomic information explains the plasticity, difference in aggressiveness levels, and genome structural variation among the P. capsici isolates, providing insight into the genomic features related to the evolution and pathogenicity of this oomycete pathogen.
Highlights
Phytophthora capsici is a major limiting factor in the production of several economically important cultivated species, causing losses in plants grown in both covered and open-field conditions (Foster and Hausbeck, 2010)
Host-dependent aggressiveness has been observed in this pathogen; for example, no substantial aggressiveness differences were observed among isolates when inoculated into cucumber (Cucumis sativus), while the same isolates showed varied aggressiveness levels when inoculated into tomato (Solanum lycopersicum) and pepper (Capsicum annuum) (Granke et al, 2012)
The high incidence of genetic diversity identified in P. capsici has been ascribed to sexual reproduction, mutation, and a loss of heterozygosity (Lamour et al, 2012; Jiang et al, 2015; Barchenger et al, 2018); no genomic studies have yet explored these variations in P. capsici isolates
Summary
Phytophthora capsici is a major limiting factor in the production of several economically important cultivated species, causing losses in plants grown in both covered and open-field conditions (Foster and Hausbeck, 2010). The diverse geographical range of P. capsici isolates greatly affects the development of resistant varieties of crop plants. Earlier studies reported differences in the virulence and aggressiveness levels of P. capsici isolates targeting vegetable hosts (Foster and Hausbeck, 2010). The existence of several races of P. capsici in different geographical regions infecting different plant organ is a major challenge to breed resistant cultivars. At least 45 physiological races of P. capsici have been reported to cause root rot and foliar blight in pepper (Barchenger et al, 2018). The high incidence of genetic diversity identified in P. capsici has been ascribed to sexual reproduction, mutation, and a loss of heterozygosity (Lamour et al, 2012; Jiang et al, 2015; Barchenger et al, 2018); no genomic studies have yet explored these variations in P. capsici isolates
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Free) 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call
