Dynamics of Verticillium dahliae race 1 population under managed agricultural ecosystems

Abstract

Background: Plant pathogens and their hosts undergo adaptive changes in managed agricultural ecosystems, by overcoming host resistance, but the underlying genetic adaptations are difficult to determine in natural settings. Verticillium dahliae is a fungal pathogen that causes Verticillium wilt on many economically important crops including lettuce. We assessed the dynamics of changes in the V. dahliae genome under selection in a long-term field experiment.

Results: In this study, a field was fumigated before the Verticillium dahliae race 1 strain (VdLs.16) was introduced. A derivative 145-strain population was collected over a 6-year period from this field in which a seggregating population of lettuce derived from Vr1/vr1 parents were evaluated. We de novo sequenced the parental genome of VdLs.16 strain and resequenced the derivative strains to analyze the genetic variations that accumulate over time in the field cropped with lettuce. Population genomics analyses identified 2769 single-nucleotide polymorphisms (SNPs) and 750 insertion/deletions (In-Dels) in the 145 isolates compared with the parental genome. Sequence divergence was identified in the coding sequence regions of 378 genes and in the putative promoter regions of 604 genes. Five-hundred and nine SNPs/In-Dels were identified as fixed. The SNPs and In-Dels were significantly enriched in the transposon-rich, gene-sparse regions, and in those genes with functional roles in signaling and transcriptional regulation.

Conclusions: Under the managed ecosystem continuously cropped to lettuce, the local adaptation of V. dahliae evolves at a whole genome scale to accumulate SNPs/In-Dels nonrandomly in hypervariable regions that encode components of signal transduction and transcriptional regulation.

Keywords: Genetic selection; Local adaptation; Managed agricultural ecosystems; Signal transduction; Transcriptional regulation; Transposon enrichment; Verticillium dahliae.

Fig. 1

Accumulation of the genetic variations in a Verticillium dahliae population in a managed agricultural ecosystem. The genome of the parental race 1 strain of V. dahliae (VdLs.16) was set as the reference to call the genetic variations of single-nucleotide polymorphisms (SNPs) and insertions and deletions (In-Dels). The variations were called from the VdLs.16 population that was collected from a field planted with race 1-resistant lettuce over 6 years. a Statistics of the genetic variations from the VdLs.16 population collected in 2010, 2012, 2014, and 2015. The numbers in red and black letters represent the total amount of SNPs and In-Dels in VdLs.16 population, respectively. b Identification of SNPs in the VdLs.16 population. c Collection of the insertions and deletions (In-Dels) in the VdLs.16 population. The letters “I” and “D” represent the genetic variations of insertions and deletions, respectively

Fig. 2

Genes under selection for local adaptation in the genome of strain VdLs.16 of Verticillium dahliae. a Distribution of the intergenic SNPs and In-Dels in the gene flanking sequences of 5000 bp. The yellow line is the boundary line separating the 5′ upstream 800 bp flanking sequence from the remainder of the upstream flanking sequence. b Percentage of the intergenic genetic variations among the gene flanking sequences. c Genes under selection determined by the analysis of genetic variation in the VdLs.16 genome. The green colored blocks represent the gene divergence caused by particular genetic changes. The 5′ upstream 800 bp with genetic variation was also defined as under selection. These mutations are nonsense, multiples of 3 bp deletions or insertion, but no frame shifts

Fig. 3

Functional annotation of genes under selection for local adaptation in the genome of Verticillium dahliae strain VdLs.16. a Gene ontology (GO) annotation of the genes under selection in VdLs.16 genome. Significant GO catalogs of genes under selection pressure in the VdLs.16 population were compared to the whole genome were determined by the Pearson chi-square test (P < 0.05). GO:0016301, kinase activity; GO:0046872, metal ion binding; GO:0035639, purine ribonucleoside triphosphate binding; GO:0005524, ATP binding; GO:0005198, structural molecule activity; GO:0060255, regulation of macromolecule metabolic process; GO:0006508, proteolysis; GO:0030163, protein catabolic process; GO:0010468, regulation of gene expression. b Functional annotation of the genes in VdLs.16 genome under selection with potential roles in pathogenicity. The column designated as “ratio in genome” represents the ratio of genes under selection relative to the total number of encoded genes in the VdLs.16 genome; the other columns represent the percentage of certain annotation type compared to the genes of that type under selection. c Annotation of the genes under selection in the VdLs.16 population

Fig. 4

Regions of increased genetic variations (RIVs) and associated genes and transposons in the genome of strain VdLs.16 of Verticillium dahliae. Curves were drawn according to the density of genetic variation, in which encoded genes and transposable elements were presented in windows of in 100 kb with 20-kb steps. The window contains up to 30 genetic variations (including SNPs and In-Dels) defined as the region of genetic variation

Fig. 5

Annotation of the regions of increased genetic variation (RIVs) in Verticillium dahliae. The inverted triangle in aqua color represents the gene under selection in the RIVs designated as RIV01–RIV20

Fig. 6

Analysis of the fixation of variation within a Verticillium dahliae population. a Statistics of the fixed genetic variations in the collection of the VdLs.16 population. The genetic variation that was representative of more than two strains and less than 144 strains (assumed sequence errors in the reference genome) defined fixed variations in the VdLs.16 population. b Classification of the fixed genetic variations. c Gene ontology (GO) annotation of the genes under selection with fixed genetic variations. The significant GO catalogs of genes under selection in the VdLs.16 population compared to the whole genome was determined by the Pearson chi-square test (P < 0.05). d Information on transcription factors with the fixed genetic variations

Fig. 7

Network maps of genes under selection in mitogen-activated protein kinase (MAPK) signaling pathways. The model was drawn using genes under selection annotated using the KEGG database with the species V. dahliae. +p, phosphorylation; −p, dephosphorylation; +u, ubiquitylation