10.5061/DRYAD.VF5FK
Jueterbock, Alexander
Nord University
Franssen, Susanne U.
University of Münster
Bergmann, Nina
Kiel University
Gu, Jenny
University of Münster
Coyer, James A.
University of Groningen
Reusch, Thorsten B. H.
GEOMAR Helmholtz Centre for Ocean Research Kiel
Bornberg-Bauer, Erich
University of Münster
Olsen, Jeanine L.
University of Groningen
Data from: Phylogeographic differentiation versus transcriptomic
adaptation to warm temperatures in Zostera marina, a globally important
seagrass
Dryad
dataset
2016
Zostera marina
Common-garden experiment
differential expression
RNAseq
2016-08-29T14:25:37Z
2016-08-29T14:25:37Z
en
https://doi.org/10.1111/mec.13829
357902780 bytes
1
CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
Populations distributed across a broad thermal cline are instrumental in
addressing adaptation to increasing temperatures under global warming.
Using a space-for-time substitution design, we tested for parallel
adaptation to warm temperatures along two independent thermal clines in
Zostera marina, the most widely distributed seagrass in the temperate
Northern Hemisphere. A North–South pair of populations was sampled along
the European and North American coasts and exposed to a simulated heatwave
in a common-garden mesocosm. Transcriptomic responses under control, heat
stress and recovery were recorded in 99 RNAseq libraries with ~13 000
uniquely annotated, expressed genes. We corrected for phylogenetic
differentiation among populations to discriminate neutral from adaptive
differentiation. The two southern populations recovered faster from heat
stress and showed parallel transcriptomic differentiation, as compared
with northern populations. Among 2389 differentially expressed genes, 21
exceeded neutral expectations and were likely involved in parallel
adaptation to warm temperatures. However, the strongest differentiation
following phylogenetic correction was between the three Atlantic
populations and the Mediterranean population with 128 of 4711
differentially expressed genes exceeding neutral expectations. Although
adaptation to warm temperatures is expected to reduce sensitivity to
heatwaves, the continued resistance of seagrass to further anthropogenic
stresses may be impaired by heat-induced downregulation of genes related
to photosynthesis, pathogen defence and stress tolerance.
Table S1 (Excel): cDNA library characteristics of all 108 cDNA
libraries.Sample preparation failed for eight libraries (indicated in the
second column).stab1.xlsxTable S2 (Excel): Numbers of mapped reads.Number
of reads that mapped to each of 20554 exons (rows), listed separately for
each library (columns E-CX); ZosmaID (column A): gene ID based on the
Zostera marina genome annotation v2.1 (GenBank Accession: LFYR00000000);
mRNAID (column B): the mapped sequence ID; Source (column C): the source
of annotation (inference from homology or top BLAST hit); Description
(column D): the gene description.stab2.xlsxTable S3 (Excel): Regularized
log-transformed expression values.Regularized log-transformed expression
values of 12948 exons (rows), listed separately for each library (column
E-CY). Exons of low expression (library average <5) or highly
variable expression (standard deviation over all libraries >
library average) are not listed; ZosmaID (column A): gene ID based on the
Zostera marina genome annotation v2.1 (GenBank Accession: LFYR00000000);
mRNAID (column B): the mapped sequence ID; Source (column C): the source
of annotation (inference from homology or top BLAST hit); Description
(columnD): the gene description; baseMean (column CZ): the mean of
normalized counts for all samples; sdcol (column DA): the standard
deviation of expression counts that were normalized by size factors for
all samples.stab3.xlsxTable S4 (Excel): Annotations of mapped
reads.ZosmaID: gene ID based on the Zostera marina genome annotation v2.1
from the ORCAE database, GenBank Accession: LFYR00000000); mRNAID: the
mapped sequence ID; name: the gene description; annotation.source: the
source of annotation (inference from homology or top BLAST hit); and
GO.terms: the associated Gene Ontology terms.TabS4.xlsxTable S5 (Excel):
Targeted GO-terms.GO-terms covered by the umbrella terms
'Heatstress' (Tab. S5a), 'Metabolism' (Tab. S5b),
'Oxidative-reductive' (Tab. S5c), 'Ribosomal' (Tab.
S5d), 'Cellwall' (Tab. S5e), and 'Photosynthesis'
(Tab. S5f) with ontologies (C: Cellular Process, F: Molecular Function, P:
Biological Process) and descriptions.TabS5.xlsxTable S6 (Excel):
Differential expression.Genes differentially expressed between Atlantic
and Mediterranean samples under control (Tab. S6a) , stress (Tab. S6b),
and recovery conditions (Tab. S6c); and genes differentially exprelssed
between Northern and Southern samples under control (Tab. S6d), stress
(Tab. S6e) and recovery conditions (Tab. S6f). Each row represents one
gene with: ZosmaID (gene ID based on the Zostera marina genome annotation
v2.1, GenBank Accession: LFYR00000000); mRNAID, the mapped sequence ID;
Source, the source of annotation (inference from homology or top BLAST
hit); Description, the gene description; baseMean, the mean of normalized
counts for all samples; log2FoldChange, the log2 fold difference in
normalized expression between Atlantic and Mediterranean (Tab. S6a-c) or
between Northern and Southern samples (Tab. S6d-f, values > 1
indicate higher expression in Mediterranean/Southern samples); lfcSE, the
standard error of the log2 fold difference; stat, the Wald test statistic
for differential expression; pvalue, the p-value; padj, the p-value
adjusted by the Benjamini-Hochberg method to control for false discovery
rate; sdcol, the standard deviation of expression counts that were
normalized by size factors for all samples; followed the regularized
log-transformed expression values of all samples that were included in the
test.TabS6.xlsxTable S7 (Excel): Genes responding to heat stress.Genes
that responded to acute heat stress (time points 2 and 3) are represented
for samples from all four populations in Tab. S7a, for Doverodde samples
Tab. S7c, for Gabicce Mare samples in Tab. S7d, and for Waquoit samples in
Tab. S7e. Genes that responded to heat in the recovery phase (time points
5, 7, and 9) are represented for all samples in Tab. S7b, for Doverodde
samples Tab. S7f, for Gabicce Mare samples in Tab. S7g, for Great Bay
samples in Tab. S7h, and for Waquoit samples in Tab. S7i. ZosmaID (column
A): the gene ID based on the Zostera marina genome annotation v2.1
(GenBank Accession: LFYR00000000); mRNAID (column B): the mapped sequence
ID; Source (column C): the source of annotation (inference from homology
or top BLAST hit); Description (column D): the gene description; baseMean
(column E): the mean of normalized counts for all samples; log2FoldChange
(column F): the log2 fold change in normalized expression between all
control samples and all stressed samples; lfcSE (column G): the standard
error of the log2 fold change; stat (column H): the Wald test statistic
for differential expression; pvalue (column I): the p-value; padj (column
J): the p-value adjusted by the Benjamini-Hochberg method to control for
false discovery rate; sdcol(column K), the standard deviation of
expression counts that were normalized by size factors for all samples.
The following columns represent regularized log-transformed expression
values of all libraries that were included in the test.TabS7.xlsxTable S8
(Excel): Enriched functions and processes under acute heat-stress and in
the recovery.GO-terms that were significantly enriched in genes that were
upregulated under acute heat stress (Tab. S8a for molecular functions MF,
Tab. S8e for biological processes BP) or downregulated under acute heat
stress (Tab. S8b for MF, Tab. S8f for BP) and in genes that were
upregulated under recovery (Tab. S8c for MF, Tab. S8g for BP) or
downregulated under recovery from heat stress (Tab. S8d for MF, Tab. S8h
for BP). Each row represents one function with: the GO-term ID; the
GO-term description, the number of annotated genes within this GO-term;
the number of significantly upregulated genes within this GO-term; the
expected number of upregulated genes; the p-value based on Fisher's
exact test for enrichment.TabS8.xlsxTable S9 (Excel): Heat-responsive
genes respresenting enriched functions and processes.Genes that were
significantly upregulated under acute heat stress and included in enriched
molecular functions (Tab. S9a) or biological processes (Tab. S9e). Genes
that were significantly downregulated under acute heat stress and included
in enriched molecular functions (Tab. S9b) or biological processes (Tab.
S9f). Genes that were significantly upregulated under recovery from heat
stress and included in enriched molecular functions (Tab. S9c) or
biological processes (Tab. S9g). Genes that were significantly
downregulated under recovery from heat stress and included in enriched
molecular functions (Tab. S9d) or biological processes (Tab. S9h). Each
row shows: the GO-term ID; the GO-term description; the gene ID (based on
the Zostera marina genome annotation v2.1, GenBank Accession:
LFYR00000000); the mapped sequence ID (mRNAID); the name of the gene; and
the source of annotation (inference from homology or top BLAST
hit).TabS9.xlsxTable S10 (Excel): Adaptively differentiated genes between
Atlantic and Mediterranean samples.Genes that were adaptively
differentiated between Atlantic and Mediterranean samples, and enriched in
biological processes (Tab. S10a) or molecular functions (Tab. S10b). Tab.
S10c represents those genes that were not represented in enriched
GO-terms. Each row represents one gene with its mapped sequence ID
(mRNAID, column A), gene ID (ZosmaID, column B, based on the Zostera
marina genome annotation v2.1, GenBank Accession: LFYR00000000), the
source (column C) of annotation (inference from homology or top BLAST
hit), and the name of the gene (column D). For Tab. S10a and Tab. S10b,
the GO-term that each gene represents is represented in column E, and the
description for this GO-term in column F.TabS10.xlsxTable S11 (Excel):
Adaptively differentiated genes between Northern and Southern
samples.Genes that were adaptively differentiated between Northern and
Southern samples, and enriched in biological processes (Tab. S11a) or
molecular functions (Tab. S11b). Tab. S11c represents those genes that
were not represented in enriched GO-terms. Each row represents one gene
with its mapped sequence ID (mRNAID, column A), gene ID (ZosmaID, column
B, based on the Zostera marina genome annotation v2.1, GenBank Accession:
LFYR00000000), the source (column C) of annotation (inference from
homology or top BLAST hit), and the name of the gene (column D). For Tab.
S11a and Tab. S11b, the GO-term that each gene represents is represented
in column E, and the description for this GO-term in column
F.TabS11.xlsxDataset S1 (vcf file): Biallelic neutral SNPsSet of 139,321
biallelic neutral SNPs with genotypes (GT), allelic depths (AD), read
depth (DP), genotype quality (GQ), and Phred-scaled likelihood for
genotypes (PL) listed for each sample.DatasetS1.vcf
North Atlantic