Population Genetic Analyses of the Fungal Pathogen Colletotrichum fructicola on Tea-Oil Trees in China

Abstract

The filamentous fungus Colletotrichum fructicola is found in all five continents and is capable of causing severe diseases in a number of economically important plants such as avocado, fig, cocoa, pear, and tea-oil trees. However, almost nothing is known about its patterns of genetic variation and epidemiology on any of its host plant species. Here we analyzed 167 isolates of C. fructicola obtained from the leaves of tea-oil tree Camellia oleifera at 15 plantations in seven Chinese provinces. Multilocus sequence typing was conducted for all isolates based on DNA sequences at fragments of four genes: the internal transcribed spacers of the nuclear ribosomal RNA gene cluster (539 bp), calmodulin (633 bp), glutamine synthetase (711 bp), and glyceraldehyde-3-phosphate dehydrogenase (190 bp), yielding 3.52%, 0.63%, 8.44%, and 7.89% of single nucleotide polymorphic sites and resulting in 15, 5, 12 and 11 alleles respectively at the four gene fragments in the total sample. The combined allelic information from all four loci identified 53 multilocus genotypes with the most frequent represented by 21 isolates distributed in eight tea-oil plantations in three provinces, consistent with long-distance clonal dispersal. However, despite evidence for clonal dispersal, statistically significant genetic differentiation among geographic populations was detected. In addition, while no evidence of recombination was found within any of the four gene fragments, signatures of recombination were found among the four gene fragments in most geographic populations, consistent with sexual mating of this species in nature. Our study provides the first insights into the population genetics and epidemiology of the important plant fungal pathogen C. fructicola.

When Do We Call Genetically Distinct Strains Different Species? - A Cautionary Case Study of the Colletotrichum gloesporioides Species Complex

“…Specifically, the two pairs of loci (ITS vs. GS and CL vs. GS) that showed phylogenetic compatibility (i.e., no evidence of recombination) within either species are phylogenetically incompatible in the combined dataset (Tables 1 and 3). Third, upon further genotype/allele comparisons, the five genetically novel and phylogenetically uncertain isolates (GXNN1, CQXS4, JXGS-B11, JXGS-B12 and JXGS-A28) identified in the recent study [29] could almost all be explained by recombination/hybridization among three of the four known phylogenetic species isolated from the tea-oil tree plantations (Table 2). Indeed, only one locus at each of two isolates (locus GS in isolate GXNN1 and locus GD in isolate JXGS-B12) contained unique alleles not found in other existing "species".…”

“…In the recent population genetic study of the C. gloeosporioides species complex (CGSC) from the tea-oil tree species Camellia oleifera, we analyzed 199 strains from 15 geographic populations in southern China [29] using sequences from the same four DNA fragments (except ACT1) as those analyzed by Weir et al [11]. Even though our recent study was focused on the patterns of population genetic variations within the dominant species C. fructicola (containing 167 of the 199 isolates), the availability of information from several other species and with all samples from the same host plant species in a defined geographic region enable us to further examine the species boundaries within CGSC.…”

“…Strains of CGSC can infect the fruits, buds, and leaves of C. oleifera plants, resulting in premature leaf and fruit rot and drop as well as wilting of the leaves and buds. Anthracnose can occur from early April to late October, peaking in August [18,27,29].…”

“…The remaining five isolates clustered distinctly from all 22 known species. Interestingly, these five isolates shared alleles at one or more loci with isolates belonging to three of the four known species [29][30][31]. Here we further examined the allelic relationships among the 199 strains at the four loci to determine the extent of genetic exchange and recombination in this species complex from tea-oil tree plantations in southern China.…”

“…However, after the two species were combined in the analyses, the two loci were phylogenetically incompatible (b). The allelic designations correspond to those in Supplementary Table 2 in Li et al [29]. The number of strains with each allelic combination is presented in corresponding boxes.…”