Pathogen: Ash Dieback Microsatellite Analysis

Usage Rights

This data is Private.

Dataset Abstract

The ash dieback pathogen Hymenoscyphus fraxineus threatens European ash (Fraxinus excelsior) since its introduction into Europe in the early 1990s. European-wide population genetics analysis has been previously carried out and revealed that the fungus population had weak structure and was a sexually reproducing species. To date, no work has been done to understand the population dynamics at a more local scale, and in particular along a tree species diversity gradient. In this study, the population structure of H. fraxineus was investigated in plots of varying tree species mixture containing F. excelsior in Hainich National Park, Germany. Fallen previous years' ash petioles were collected in July 2012 from targeted ash trees. DNA was extracted and microsatellite markers were amplified. We aim to determine the population genetics structure and understand the infection biology of the pathogen.

Dataset Design

In addition to the collection fresh leaves within task 4.6, we collected fallen ash petioles to perform molecular analysis on population genetic structure of the specific pathogen Hymenoscyphus fraxineus from Fraxinus excelsior. Trees from three plots that were previously selected for leaf sampling, were selected for petiole sampling. There were four trees from the monoculture plot (GER04), three trees from the 2 species mixture (GER03), and three trees from the 4 species mixture (GER37), and two trees from the 4 species mixture (GER31). Approximately 45 petioles were collected within 1 m around each stem of targeted trees.

Spatial Extent

Exploratory Region: Germany

Temporal Extent

Between July 9, 2012 and July 16, 2012

Taxonomic Extent

Fallen previous year's ash petioles collected within 1 m around the stem of targeted Fraxinus excelsior

Measurement Circumstances

Additional petiole samples were collected from other ash trees within the plots with Fraxinus excelsior, but were not processed in the above described methods as a result of cost constraints. Thus data for these are not presented here.

Data Analysis

Each petiole was separated into petiole sections at each leaf node, and each sample is a one such petiole section. After confirmation of the presence of the fungus within ash petiole sections with species-specific primers, 14 previously published microsatellite markers will be amplified to determine the genotype of the fungus within each petiole section. Genotypic diversity will be calculated from the given fragment lengths. Principal Coordinates Analysis will be conducted to determine the spatial distribution of the genotypes. Analysis of molecular variance will determine the degree of genetic differentiation. Structure analysis will aid in the investigation of the existence of population structure. The index of association will be calculated to determine the reproductive mode of the fungus.

Data columns available in the raw data part of this dataset

ID_Plot
Plot Id
Data group: Exploratory plot id
Values
GER03
GER04
GER37
GER31
ID_Tree
Tree number
Data group: Tree number
Values
13
1
14
11
12
ID_Petiole
Petiole number
Data group: Petiole number
Values
12
1
10
2
11
ID_PetioleSection
Petiole section ID
Data group: Petiole section
Values
11a
10a
10d
10b
10c
Richness
Tree species richness
Data group: Plot descriptor
Values
4
1
2
mHp067022
DNA marker with associated DNA fragment length
Unit: bp
Data group: Pathogen assessment
Keywords: pathogen, ash dieback
Values
251
249
247
mHp077098
DNA marker with associated DNA fragment length
Unit: bp
Data group: Pathogen assessment
Keywords: pathogen, ash dieback
Values
166
mHp108810
DNA marker with associated DNA fragment length
Unit: bp
Data group: Pathogen assessment
Keywords: pathogen, ash dieback
Values
0
268
277
264
mHp060142
DNA marker with associated DNA fragment length
Unit: bp
Data group: Pathogen assessment
Keywords: pathogen, ash dieback
Values
164
170
Chafra03
DNA marker with associated DNA fragment length
Unit: bp
Data group: Pathogen assessment
Keywords: pathogen, ash dieback
Values
191
189
208
Chafra04
DNA marker with associated DNA fragment length
Unit: bp
Data group: Pathogen assessment
Keywords: pathogen, ash dieback
Values
0
101
111
Chafra13
DNA marker with associated DNA fragment length
Unit: bp
Data group: Pathogen assessment
Keywords: pathogen, ash dieback
Values
178
176
0
180
SSR114
DNA marker with associated DNA fragment length
Unit: bp
Data group: Pathogen assessment
Keywords: pathogen, ash dieback
Values
246
0
242
mHp080497
DNA marker with associated DNA fragment length
Unit: bp
Data group: Pathogen assessment
Keywords: pathogen, ash dieback
Values
245
0
254
mHp095481
DNA marker with associated DNA fragment length
Unit: bp
Data group: Pathogen assessment
Keywords: pathogen, ash dieback
Values
139
146
137
mHp080495
DNA marker with associated DNA fragment length
Unit: bp
Data group: Pathogen assessment
Keywords: pathogen, ash dieback
Values
150
143
mHp079915
DNA marker with associated DNA fragment length
Unit: bp
Data group: Pathogen assessment
Keywords: pathogen, ash dieback
Values
184
201
SSR198
DNA marker with associated DNA fragment length
Unit: bp
Data group: Pathogen assessment
Keywords: pathogen, ash dieback
Values
224
SSR211
DNA marker with associated DNA fragment length
Unit: bp
Data group: Pathogen assessment
Keywords: pathogen, ash dieback
Values
298
0
294
296