10.5061/DRYAD.TTDZ08KXX
Skrede, Inger
0000-0002-1113-7403
University of Oslo
Murat, Claude
University of Lorraine
Hess, Jaqueline
University of Oslo
Maurice, Sundy
University of Oslo
Sønstebø, Jørn Henrik
University of Oslo
Kohler, Annegret
University of Lorraine
Barry-Etienne, Dominique
Société MYCEA
Eastwood, Dan
Swansea University
Högberg, Nils
Swedish University of Agricultural Sciences
Martin, Francis
University of Lorraine
Kauserud, Håvard
University of Oslo
Contrasting demographic histories revealed in two invasive populations of
the dry rot fungus Serpula lacrymans
Dryad
dataset
2021
Illumina full genome sequencing
GATK
2021-04-30T00:00:00Z
2021-04-30T00:00:00Z
en
https://doi.org/10.22541/au.161363779.98341786/v1
https://doi.org/10.22541/au.161363779.98341786/v1
85747630 bytes
2
CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
Globalization and international trade have impacted organisms around the
world leading to a considerable number of species establishing in new
geographic areas. Many organisms have taken advantage of human-made
environments, including buildings. One such species is the dry rot fungus
Serpula lacrymans, which is the most aggressive wood-decay fungus in
indoor environments in temperate regions. Using population genomic
analyses of 36 full genome sequenced isolates, we demonstrated that
European and Japanese isolates are highly divergent and the populations
split 3,000 - 19,000 generations ago, probably predating human influence.
Approximately 250 generations ago, the European population went through a
tight bottleneck, likely corresponding to the fungus colonization of the
built environment in Europe. The demographic history of these populations,
probably lead to low adaptive potential. Only two loci under selection
were identified using a Fst outlier approach, and selective sweep analyses
identified three loci with extended haplotype homozygosity. The selective
sweep analyses found signals in genes possibly related to decay of various
substrates in Japan and in genes involved DNA replication and protein
modification in Europe. Our results suggest that the dry rot fungus
independently established in indoor environments in Europe and Japan and
that invasive species can potentially establish large populations in new
habitats based on a few colonizing individuals.
Full genome sequences from Illumina from 36 isolates of Serpula lacrymans
were analyzed in parallel using two pipelines: (1) the first pipeline
trimmed the data using TrimGalore version 0.3.3, aligned using Bowtie2
(Langmead & Salzberg), and SAMtools (Li et al. 2009) to include
only reads that mapped concordantly and only once to remove PCR
duplicates. Variants were called for each alignment using HaplotypeCaller,
combined into a common variant file with GenotypeGVCFs and further quality
filtered with VariantFiltration
(QD<2.0||FS>60.0||MQ<40.0||MQRankSum<
-12.5||ReadPosRankSum< -8.0) in Genome Analysis Tool Kit (GATK)
(McKenna et al. 2010; Van der Auwera et al. 2013). (2) The second pipeline
trimmed the sequences using Trimmomatic (Bolger et al. 2014), mapped the
reads using BWAmem (Li 2013), filtered using SAMtools, called variants
using BCFtools call and filtered with BCFtools view. For both pipelines,
the sequence data were mapped to the monokaryotic S. lacrymans isolate
S7.3, version 2 (Eastwood et al. 2011). Repetitive regions of the S.
lacrymans v. 2 genome were annotated using the REPET package v.2.5 (Flutre
et al. 2011), following the procedure outlined in (Sipos et al. 2017).
Regions annotated as transposable element-derived were filtered from the
SNP data set using BEDtools (Quinlan & Hall 2010). A combined data
set using only SNPs called by both pipelines resulted in 419,196 high
quality SNPs for the 36 isolates included in this analysis.
The file is in vcf format, and gziped.