The European race of Gremmeniella abietina hosts a single species of Gammapartitivirus showing a global distribution and possible recombinant events in its history

Abstract

The population genetics of the family Partitiviridae was studied within the European race of the conifer pathogen Gremmeniella abietina. One hundred sixty-two isolates were collected from different countries, including Canada, the Czech Republic, Finland, Italy, Montenegro, Serbia, Spain, Switzerland, Turkey and the United States. A unique species of G. abietina RNA virus-MS1 (GaRV-MS1) appears to occur indistinctly in G. abietina biotypes A and B, without a particular geographical distribution pattern. Forty-six isolates were shown to host GaRV-MS1 according to direct specific RT-PCR screening, and the virus was more common in biotype A than B. Phylogenetic analysis based on 46 partial coat protein (CP) cDNA sequences divided the GaRV-MS1 population into two closely related clades, while RNA-dependent RNA polymerase (RdRp) sequences revealed only one clade. The evolution of the virus appears to mainly occur through purifying selection but also through recombination. Recombination events were detected within alignments of the three complete CP and RdRp sequences of GaRV-MS1. This is the first time that recombination events have been directly identified in fungal partitiviruses and in G. abietina in particular. The results suggest that the population dynamics of GaRV-MS1 do not have a direct impact on the genetic structure of its host, G. abietina, though they might have had an innocuous ancestral relationship.

Keywords: Biotype; Brunchorstia pinea; Conifers; Evolutio; Mycoviruses; Partitiviridae.

Fig 1

Representation of the genome organisation of GaRV-MS1-3 and recombination events occurred between strains. *The actual breakpoint position is undetermined (it was most likely overprinted by a subsequent recombination event). Minor Parent, parent contributing the smaller fraction of sequence. Major Parent, parent contributing the larger fraction of sequence. Unknown, only one parent, and a recombinant need be in the alignment for a recombination event to be detectable. The sequence listed as unknown was used to infer the existence of a missing parental sequence.

Fig 2

Optimal unrooted NJ tree based on 46 partial nucleotide CP sequences of GaRV-MS1. Branches corresponding to partitions reproduced in less than 90 % bootstrap replicates are collapsed. GaRV-MS1 strains hosted in biotype A of G. abietina are represented by ■, those hosted in Biotype B are represented by ●, ▼ represents strains in EU race isolates, and finally, ♦ represents the strains in the Spanish population.