title: Assessment of the geographic origins of pinewood nematode isolates via single nucleotide polymorphism in effector genes.
abstract: The pinewood nematode, Bursaphelenchus xylophilus, is native to North America but it only causes damaging pine wilt disease in those regions of the world where it has been introduced. The accurate detection of the species and its dispersal routes are thus essential to define effective control measures. The main goals of this study were to analyse the genetic diversity among B. xylophilus isolates from different geographic locations and identify single nucleotide polymorphism (SNPs) markers for geographic origin, through a comparative transcriptomic approach. The transcriptomes of seven B. xylophilus isolates, from Continental Portugal (4), China (1), Japan (1) and USA (1), were sequenced in the next generation platform Roche 454. Analysis of effector gene transcripts revealed inter-isolate nucleotide diversity that was validated by Sanger sequencing in the genomic DNA of the seven isolates and eight additional isolates from different geographic locations: Madeira Island (2), China (1), USA (1), Japan (2) and South Korea (2). The analysis identified 136 polymorphic positions in 10 effector transcripts. Pairwise comparison of the 136 SNPs through Neighbor-Joining and the Maximum Likelihood methods and 5-mer frequency analysis with the alignment-independent bilinear multivariate modelling approach correlated the SNPs with the isolates geographic origin. Furthermore, the SNP analysis indicated a closer proximity of the Portuguese isolates to the Korean and Chinese isolates than to the Japanese or American isolates. Each geographic cluster carried exclusive alleles that can be used as SNP markers for B. xylophilus isolate identification.
authors.affiliation: Department of Life Sciences, University of Coimbra, Coimbra, Portugal.
authors.forename: Joana
authors.initials: J
authors.lastname: Figueiredo
authors.affiliation: Genoinseq, Next Generation Sequencing Unit, Biocant, Cantanhede, Portugal.
authors.forename: Maria José
authors.initials: MJ
authors.lastname: Simões
authors.affiliation: Genoinseq, Next Generation Sequencing Unit, Biocant, Cantanhede, Portugal.
authors.forename: Paula
authors.initials: P
authors.lastname: Gomes
authors.affiliation: Genoinseq, Next Generation Sequencing Unit, Biocant, Cantanhede, Portugal.
authors.forename: Cristina
authors.initials: C
authors.lastname: Barroso
authors.affiliation: Genoinseq, Next Generation Sequencing Unit, Biocant, Cantanhede, Portugal.
authors.forename: Diogo
authors.initials: D
authors.lastname: Pinho
authors.affiliation: IMAR-CMA, Department of Life Sciences, University of Coimbra, Coimbra, Portugal.
authors.forename: Luci
authors.initials: L
authors.lastname: Conceição
authors.affiliation: IMAR-CMA, Department of Life Sciences, University of Coimbra, Coimbra, Portugal.
authors.forename: Luís
authors.initials: L
authors.lastname: Fonseca
authors.affiliation: IMAR-CMA, Department of Life Sciences, University of Coimbra, Coimbra, Portugal.
authors.forename: Isabel
authors.initials: I
authors.lastname: Abrantes
authors.affiliation: Genoinseq, Next Generation Sequencing Unit, Biocant, Cantanhede, Portugal.
authors.forename: Miguel
authors.initials: M
authors.lastname: Pinheiro
authors.affiliation: Genoinseq, Next Generation Sequencing Unit, Biocant, Cantanhede, Portugal.
authors.forename: Conceição
authors.initials: C
authors.lastname: Egas
mesh_terms: D000818:Animals; D016000:Cluster Analysis; D018509:DNA, Helminth / Q000235:genetics; D017238:Genes, Helminth; D014644:Genetic Variation; D010802:Phylogeny; D028223:Pinus / Q000469:parasitology*; D010935:Plant Diseases / Q000469:parasitology; D020641:Polymorphism, Single Nucleotide; D017187:Tylenchida / Q000235:genetics* / Q000302:isolation & purification / Q000472:pathogenicity
chemical_list: D018509:DNA, Helminth