Analyses of the Population Structure in a Global Collection of Phytophthora nicotianae Isolates Inferred from Mitochondrial and Nuclear DNA Sequences

Abstract

Genetic variation within the heterothallic cosmopolitan plant pathogen Phytophthora nicotianae was determined in 96 isolates from a wide range of hosts and geographic locations by characterizing four mitochondrial (10% of the genome) and three nuclear loci. In all, 52 single-nucleotide polymorphisms (SNPs) (an average of 1 every 58 bp) and 313 sites with gaps representing 5,450 bases enabled the identification of 50 different multilocus mitochondrial haplotypes. Similarly, 24 SNPs (an average of 1 every 69 bp), with heterozygosity observed at each locus, were observed in three nuclear regions (hyp, scp, and β-tub) differentiating 40 multilocus nuclear genotypes. Both mitochondrial and nuclear markers revealed a high level of dispersal of isolates and an inconsistent geographic structuring of populations. However, a specific association was observed for host of origin and genetic grouping with both nuclear and mitochondrial sequences. In particular, the majority of citrus isolates from Italy, California, Florida, Syria, Albania, and the Philippines clustered in the same mitochondrial group and shared at least one nuclear allele. A similar association was also observed for isolates recovered from Nicotiana and Solanum spp. The present study suggests an important role of nursery populations in increasing genetic recombination within the species and the existence of extensive phenomena of migration of isolates that have been likely spread worldwide with infected plant material.

The Top 10 oomycete pathogens in molecular plant pathology

“…Frequent cases of differential virulence on a range of hosts have been revealed (Colas et al ., ; Matheron and Matejka, ), pointing out the need to decipher the genetic structure of P. parasitica on a global scale. In agreement with pathogenicity tests, recent single nucleotide polymorphism analyses conducted with mitochondrial and nuclear genes have revealed a specific association between the host of origin and genetic grouping which was particularly evident for tobacco and citrus isolates (Mammella et al ., , ). In contrast, no clear genetic structure was revealed for isolates from other hosts, especially potted ornamentals in nurseries.…”

“…In contrast, no clear genetic structure was revealed for isolates from other hosts, especially potted ornamentals in nurseries. A significant geographical structuring was revealed for tobacco, but not for citrus, isolates (Bonnet et al ., ; Colas et al ., ; Mammella et al ., ). Further studies relying on whole‐genome sequencing programmes (see below) are necessary to determine whether these molecular groups represent evidence of physiological races, pathotypes or even subspecies within P. parasitica .…”

Diversity of citrus gummosis in São Paulo State, Brazil

“…and pinpointed P. nicotianae as the most important species in citrus orchards of other states (4,18). There are conflicting findings concerning intraspecific variability of P. nicotianae from citrus in the literature since 24 citrusinfecting P. nicotianae from India were distributed in different clusters (20), whereas one single clade grouped isolates from Philippines, Italy, Syria, California and Florida (15). The genetic diversity verified in this study contrasting with the high similarity observed by Rosa et al (23) is another case of discrepancy of P. nicotianae (from São Paulo State, this time) and can be credited to different pathogen isolates and a larger number of isolates examined in our study.…”

Pineapple heart rot isolates from Ecuador reveal a new genotype of Phytophthora nicotianae

“…Moreover, nucleotide sequence variation in nuclear and mitochondrial markers revealed an association between crops and genetic groups, suggesting the possibility of host specialization driven by propagation or cultivation practices (Biasi et al ., ). For example, isolates from Citrus were genetically similar, regardless of the country of origin, and genetically differentiated from populations recovered from other hosts (Mammella et al ., , ; Biasi et al ., ). Phytophthora nicotianae from tobacco exhibited clonality within populations (Zhang et al ., ; Parkunan et al ., ), but genetic differentiation among regions (Mammella et al ., , ; Biasi et al ., ).…”

“…For example, isolates from Citrus were genetically similar, regardless of the country of origin, and genetically differentiated from populations recovered from other hosts (Mammella et al ., , ; Biasi et al ., ). Phytophthora nicotianae from tobacco exhibited clonality within populations (Zhang et al ., ; Parkunan et al ., ), but genetic differentiation among regions (Mammella et al ., , ; Biasi et al ., ). Conversely, isolates from ornamental potted plants presented more genetic variation within populations and less differentiation among host genera and regions (Biasi et al ., ).…”