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R E S E A R C H A R T I C L E Open Access
Nourishment level affects caste-related gene
expression in Polistes wasps
Ali J Berens
1,2*
, James H Hunt
3,4,5
and Amy L Toth
1,2,6
Abstract
Background: Social insects exhibit striking phenotypic plasticity in the form of distinct reproductive (queen) and
non-reproductive (worker) castes, which are typically driven by differences in the environment during early development.
Nutritional environment and nourishment during development has been shown to be broadly associated with caste
determination across social insect taxa such as bees, wasps, and termites. In primitively social insects such as Polistes paper
wasps, caste remains flexible throughout adulthood, but there is evidence that nourishment inequalities can bias caste
development with workers receiving limited nourishment compared to queens. Dominance and vibrational signaling are
behaviors that have also been linked to caste differences in paper wasps, suggesting that a combination of nourishment
and social factors may drive caste determination. To better understand the molecular basis of nutritional effects on caste
determination, we used RNA-sequencing to investigate the gene expression changes in response to proteinaceous
nourishment deprivation in Polistes metricus larvae.
Results: We identified 285 nourishment-responsive transcripts, many of which are related to lipid metabolism and
oxidation-reduction activity. Via comparisons to previously identified caste-related genes, we found that nourishment
restriction only partially biased wasp gene expression patterns toward worker caste-like traits, which supports the
notion that nourishment, in conjunction with social environment, is a determinant of developmental caste bias. In
addition, we conducted cross-species comparisons of nourishment-responsive genes, and uncovered largely
lineage-specific gene expression changes, suggesting few shared nourishment-responsive genes across taxa.
Conclusion: Overall, the results from this study highlight the complex and multifactorial nature of environmental
effects on the gene expression patterns underlying plastic phenotypes.
Keywords: Phenotypic plasticity, Nourishment, Social castes, Transcriptomics, Polistes
Background
Phenotypic plasticity provides an important adaptive
mechanism by which morphology, physiology, and/or be-
havior can be adjusted to biotic and abiotic environmental
factors including temperature, nutrition, population dens-
ity, and predator presence [1]. There are a number of
striking examples of phenotypic plasticity in insects: di-
morphic horn development in dung beetles [2], seasonal
color polyphenism in butterflies [3], and wing polyphen-
ism in aphids (reviewed in [4]). One of the best-studied
models of insect phenotypic plasticity is reproductive
castes in social insects, especially social Hymenoptera
(bees, ants, and wasps [5]). In most social insects, geno-
typic differences do not account for differences between
reproductive (queen) and non-reproductive (worker)
castes (reviewed in [6]). Instead, environmental factors in-
duce differences in hormone titers and gene expression
(reviewed in [6]), leading to the development of queens or
workers, which vary in physiology and behavior and for
advanced social species, in morphology [5].
One particular environmental factor, food availability, is
especially important for caste polyphenism in social in-
sects. Differential nourishment [7-10] and nutrition-
related genes and pathways (e.g. storage proteins such as
vitellogenin and hexamerin, insulin/insulin-like signaling
(IIS) pathways) have been linked to caste differences in
honey bees [11,12], paper wasps [13,14], and termites
[15,16]. This suggests that the influence of nutrition on
* Correspondence: berens.ali@gmail.com
1
Program in Bioinformatics and Computational Biology, Iowa State University,
Ames, IA 50011, USA
2
Department of Ecology, Evolution, and Organismal Biology, Iowa State
University, Ames, IA 50011, USA
Full list of author information is available at the end of the article
© 2015 Berens et al.; licensee BioMed Central. This is an Open Access article distributed under the terms of the Creative
Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and
reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain
Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article,
unless otherwise stated.
Berens et al. BMC Genomics (2015) 16:235
DOI 10.1186/s12864-015-1410-y
caste formation may be broadly shared across diverse taxa
[17]. There have been numerous studies investigating the
molecular mechanisms underlying queen-worker caste de-
termination in advanced eusocial species, especially honey
bees [18-25]. In honey bees, nutritional differences for lar-
vae fed either royal jelly or worker jelly precede a develop-
mental switch resulting in alternative caste phenotypes
[26]. Nutrition is also important for caste differences in
primitively eusocial species, which lack morphological
castes, but we know much less about the molecular mech-
anisms that underlie the formation of their more subtle
behavioral and physiological castes. In primitively eusocial
species such as paper wasps, differential nourishment does
not strictly determine caste but can lead to a caste bias,
whereby female larvae that are fed larger quantities of food
aremorelikelytobefuturereproductivequeens(called
“gynes”) as adults [27]. However, the ultimate caste fate of
a female is decided during adulthood. First-brood off-
spring of an established nest are capable of independent
reproduction, but instead they perform allomaternal care
(worker behavior) as a response to cues emitted by larvae
in the nest [28]. Subsequent social reinforcement of worker
behavior often occurs via dominance behaviors by the
queen or other workers [29,30].
Primitively eusocial taxa such as Polistes are an inform-
ative group for understanding the evolution of eusociality
andtheoriginsofcastes[31,32].Acrosstheannualcolony
cycle of primitively social wasps in the genus Polistes¸the
quantity of larval nourishment changes according to sea-
sonal changes in the adult-to-larva ratio [10,27]. First-brood
offspring produced early in the colony cycle have been
reared by a single nest-founding queen or few queens,
which also perform all colony tasks such as nest building,
foraging, egg laying, and brood rearing [30]. At this early
time in the colony cycle the adult-to-larva ratio is low
[30,33], which leads to low feeding rates and more limited
larval nourishment compared to offspring reared by
workers and produced later in the colony cycle (future
queens or “gynes”). Physiological evidence of nourishment-
related differences between workers and gynes collected
from naturally-founded colonies in the field include greater
fat body stores in gynes [34,35], greater quantities of the
storage protein hexamerin 1 in gynes [36,37], and greater
quantities of four additional proteins in gynes [14]. Experi-
mental studies show that nourishment inequalities that cor-
respond to early-season and late-season larval development
contexts are associated with development of offspring
having characteristics of worker and gyne phenotypes,
respectively [38,39].
In addition to the established role of nourishment in
caste differences in Polistes, social factors, such as domin-
ance behavior [29,31] and maternal influences [40-42] also
play a role. Jeanne and Suryanarayanan [40] propose a hy-
pothesis for caste determination in primitively social wasps
that incorporates not only nourishment variability, but also
social environmental inputs from maternal care, specific-
ally vibrational signals called antennal drumming. Antennal
drumming may be an example of a maternal manipulation
[43] that directs larvae toward a worker developmental tra-
jectory, and this effect may interact with nourishment in-
duced changes in caste phenotype. Thus, nourishment is
likely to act in concert with social environmental factors in
determining differences in gyne and worker caste develop-
ment in Polistes.
In this study, we investigated the effect of experimen-
tal proteinaceous nourishment deprivation during larval
development on caste-related gene expression in a
primitively eusocial species, the paper wasp Polistes
metricus.Wehadthreemaingoals.First,weexplored
the transcriptional responses of wasp larvae to high and
low nourishment levels during laboratory rearing using
RNA-sequencing. Second, we tested the hypothesis that
nourishment level relates to caste-related gene expres-
sion; specifically that low nourishment is associated
with more worker-like gene expression patterns, and
high nourishment is associated with more gyne-like ex-
pression patterns. To do this, we compared nourish-
ment differential expression to a set of nearly 800
previously identified genes associated with caste devel-
opment in field-reared P. metricus [13], and we did so
on multiple levels: individual transcripts, pathways and
biological functions. Third, we tested whether the mo-
lecular mechanisms underlying the response to nourish-
ment are conserved across taxa by comparing our
results to two other nourishment deprivation studies in
fruit flies [44] and dung beetles [45]. Our overall goal
was to better understand the extent and nature of the
role of nourishment and nourishment-related genes in
caste development in a primitively social wasp species.
Results
Differential expression analysis
To assess differential gene expression, we mapped reads
to a previously assembled de novo transcriptome for
P. metricus; the transcriptome was based on both the se-
quence data described here in conjunction with additional
samples described in a previous study [13]. By comparing
expression patterns from head samples from 8 individual
wasp larvae under high and low nourishment, we identi-
fied 284 P. metricus differentially expressed transcripts
(DETs) that differed between low and high nourishment
treatments, using DESeq (FDR ≤0.05, [46]), heretofore re-
ferred to as “P. metricus nourishment-responsive DETs”.
Of these DETs, 207 (72.9%) were upregulated in low com-
pared to high nourishment larvae (Figure 1 is a heat map
of the scaled DET read counts across P. metricus nourish-
ment samples. Additional file 1 includes the list of
P. metricus nourishment-responsive DETs). Thus, despite
Berens et al. BMC Genomics (2015) 16:235 Page 2 of 12
the fact that they had less food available, low nourishment
led to a majority of genes having higher gene expression,
and thus did not simply cause a general shutdown in
transcription.
One important feature of these results is the presence of
outlier individuals, i.e. one individual low nourishment
larva clustered with the high nourishment samples and a
high nourishment larva clustered with the low nourish-
ment samples (Figure 1). The variability of gene expres-
sion amongst biological samples is not completely
surprising; our previous work has found high inter-
individual variation in gene expression [13], effects of lab
rearing (JM Jandt, JL Thomson, AC Geffre, AL Toth:
Rearing environment may bias social traits: A case study
with Polistes wasps, submitted), and variable effects of
nourishment level on physiology [38].
Validation of select expression patterns via comparison to
qRT-PCR data
It is important to validate RNA-Seq data using another
method such as quantitative reverse transcription poly-
merase chain reaction (qRT-PCR). However, for this study,
we had limited samples and quantities of RNA [38], so we
could not perform qRT-PCR validation on actual samples
from this experiment. In lieu of the sample limitations, we
instead made a comparison to pre-existing data on
nourishment-responsive expression patterns from adult
brains of P. metricus under starved vs. ad lib food condi-
tions [47]. Although not ideal because of differences in tis-
sue type and life stage, this comparison still provides a
useful point of comparison to validate whether the expres-
sion patterns uncovered in this RNA-Seq study are robust.
Of 24 candidate genes, Daugherty et al. [47] identified
10 genes with differential expression in adult P. metricus
brains reared under low and high nourishment conditions
using qRT-PCR. We tested for a correlation (Spearman) in
the log
2
fold changes between the 24 candidate genes from
Daugherty et al. [47] and the orthologous transcripts in
this study, i.e. best BLAST hits between the primer se-
quences from Daugherty et al. [47] and the P. metricus
transcriptome (Additional file 2: Figure S3 is a visual
representation of the log
2
fold changes for both studies;
Additional file 3 lists the log
2
fold change for each gene/
transcript and the directionality for differentially expressed
genes). For some genes, there is more than one best
BLAST hit to the P. metricus transcriptome, so all tran-
scripts were used for the correlation analysis. The gene
PmTOR is absent from the P. metricus transcriptome, so
this gene was removed from the analysis. Although none
of the orthologous transcripts are significantly differen-
tially expressed in the RNA-seq study, we nonetheless
identified a significant positive correlation in log
2
fold
changes between these two studies (Spearman ρ:0.54,
p-value = 0.001), which provides support for our observed
RNA-Seq results.
One reason we may not have observed statistically sig-
nificant differential expression of these candidate genes in
the RNA-Seq study, despite the strong correlation with
the qRT-PCR data, is because of the limited statistical
power. Differential expression calls are more stringent in
this RNA-Seq study compared to the qRT-PCR analysis
because familywise error correction is more severe due to
the larger number of genes (over 75,000 compared to 24
genes). Furthermore, the qRT-PCR study has a larger
Figure 1 Heat map of the relative expression (sample read counts scaled by library size then across each gene) for the 284
differentially expressed transcripts between nourishment manipulation levels by sample. Samples are clustered based on relative expression
across all differentially expressed transcripts (top), and transcripts are clustered based on relative expression across all samples (left). Transcripts that are
upregulated in high nourishment (H) are highlighted in yellow, and low nourishment (L) upregulated transcripts are highlighted in blue.
Berens et al. BMC Genomics (2015) 16:235 Page 3 of 12
sample size (n = 47) compared to the RNA-Seq study
(n = 8), which provides greater statistical power for detect-
ing differential expression.
Comparison to caste-related gene expression
Next, we investigated how P. metricus nourishment-
responsive DETs compared to caste-related gene expres-
sion. A previous study [13] compared gene expression in
field-collected, early season (worker-destined) larvae to late
season (gyne-destined) larvae, and identified 736 caste-
related DETs. Both low nourishment (described above) and
worker-destined larvae [13] show a pronounced bias to-
wards upregulated gene expression (72.9% upregulated
in low nourishment and 91.7% upregulated in worker-
destined larvae). This pattern generally agrees with
the prediction that worker-destined and nourishment-
deprived larvae have similar transcriptional states.
There was a statistically significant but relatively small
overlap (43 transcripts) between the nourishment-
responsive and caste-related DETs (Chi-square with Yates’
correction: p< 0.0001). Of these shared DETs, the direc-
tionality of gene expression change was unexpected: eight
(18.6%) were upregulated in low nourishment larvae com-
pared to high nourishment larvae, whereas 38 (88.4%)
were upregulated in worker-destined larvae relative to
queen-destined larvae (see Figure 2a for a Venn diagram
of the number of unique and overlapping caste and
nourishment-responsive DETs, Additional file 2: Figure S1
for a heatmap of the overlapping caste and nourishment-
responsive DETs, and Additional file 4 for the list of over-
lapping DETs). To further explore these data beyond
examining an overlap of gene lists, we performed a com-
bined statistical analysis of data from both the nourish-
ment level and caste contrasts, and the results also
indicate some overlap in gene expression patterns across
the two studies (see Methods, with complete description
of the approach and results in Additional file 2 and
Additional file 5). Taken together, these results partially
support our prediction of gene expression similarity be-
tween nourishment-responsive and caste-related gene ex-
pression but suggest some unanticipated dissimilarities
between them.
Pathway level analysis
Our previous study suggested gene expression similarity
across studies is more pronounced on the level of path-
ways and gene functional categories, rather than specific
genes or transcripts [13]. Therefore, we also examined our
data at the level of pathways using the Kyoto Encyclopedia
of Genes and Genomes (KEGG) [48,49]. Using best
BLAST hits to D. melanogaster, very few transcripts
(799 = 1.0% of the transcriptome) were annotated with en-
zyme codes for the KEGG analysis with Blast2GO [50]
(see Additional file 1 for a list of transcripts annotated
Figure 2 Number of A) differentially expressed transcripts
(DETs), B) KEGG pathways with at least one DET, and C)
enriched GO term unique to or shared between nourishment
and caste datasets. Directionality, i.e. upregulated treatment group,
is indicated for each dataset, where, for KEGG pathways and GO,
terms, directionality is defined as the treatment group with the
greater number of upregulated DETs per pathway or category,
respectively. * indicates statistically significant overlap between
nourishment and caste DETs (Chi-square test with Yates’correction,
p-value < 0.0001). ** indicates statistically significant overlap between
nourishment and caste enriched GO terms (Fisher’sexacttest,p-value=
4.4e-6). The fatty acid biosynthesis pathway had an equal number of
DETs upregulated in the high and low nourishment groups (one per
each group), so the directionality of this pathway is counted as one
half for each group (indicated by †).
Berens et al. BMC Genomics (2015) 16:235 Page 4 of 12
with enzyme codes by KEGG pathway). The presence
of many transcripts without homology is a shortcoming
of the dataset, but is expected and standard for
Illumina-based data from non-model species [51]. Only
7% (20) of the nourishment DETs were known mem-
bers of KEGG pathways, therefore we identified very
few (7 of 118) KEGG pathways with at least one DET.
We then looked to see if these seven pathways were
also related to caste differences [13]. Four of the seven
pathways also had caste-related DETs (including glycer-
olipid metabolism, nitrogen metabolism, and purine
metabolism; listed in Additional file 4), but this amount
of overlap was not statistically significant (Fisher’s exact
test, p-value = 0.12). The majority of the DETs are
upregulated in both low nourishment and worker-
destined larvae for all four of these shared KEGG
pathways (Figure 2b is a Venn diagram of the number
of KEGG pathways with nourishment and/or caste
DETs), which is in agreement with the prediction that
nourishment-responsive biochemical pathways are reg-
ulated in a similar direction to what is found between
castes in paper wasps.
Gene ontology (GO) enrichment analysis
On the level of gene functional categories, fifty-two GO
terms were significantly enriched within the P. metricus
nourishment-responsive DETs compared to the remainder
of transcriptome (Figure 3; Additional file 1 includes the
list of enriched GO terms). These included functions re-
lated to lipoprotein metabolism, oxidation reduction activ-
ity, and polysaccharide metabolism. More than 30% of GO
terms (including terms related to oxidoreductase activity
and carbohydrate metabolism) were common to both
caste- and nourishment manipulation-related DETs,
representing a significant overlap (Chi-square test with
Yate s ’correction, p < 0.0001; Figure 2b; Additional file 4
lists the shared caste and nourishment enriched GO
terms). However, if we examine the direction of differen-
tial expression of DETs associated with these GO terms,
we do not consistently see the predicted pattern of the
same directional bias to both low nourishment larvae and
worker-destined larvae (Figure 2b; Additional file 4 lists
the direction).
Cross-species comparisons
Because nourishment is an important driver of phenotypic
plasticity in many species, we were interested in determin-
ing whether the molecular mechanisms underlying the re-
sponse to nourishment identified in paper wasps are
conserved in other taxa. After an extensive literature
search, we identified two studies from other insects that
also examined transcriptional responses to nutritional
stress: 1) a microarray study of tissue-specific (fat body
and muscle) gene expression derived from fruit fly larvae
[44] and 2) a microarray study of thoracic horn develop-
ment in female dung beetle pupae [45]. Although not ideal
comparisons to our paper wasp dataset because of differ-
ences in life stages and sampled tissues, these studies
still provide useful preliminary comparisons to begin
addressing whether there are any conserved of
nourishment-responsive transcripts.
When comparing P. metricus nourishment-responsive
transcripts with nourishment-responsive transcripts in
D. melanogaster fat body and muscle tissues [44], we
identified small, non-significant overlaps: only 18 and
13 common DETs, respectively (Figure 4a and c; Chi-square
tests with Yates’correction; fat body: p-value = 0.84; muscle:
p-value = 0.19). For both tissue types in fruit flies, most
transcripts are down-regulated with low nourishment
(Additional file 6 lists the common DETs and direction-
ality for each species). Of these shared DETs, the major-
ity are expressed in the same direction in both species:
56% (10 DETs for the fat body dataset; Fisher’sExact
Test, p-value = 0.676) and 54% (7 DETs for the muscle;
Fisher’s Exact Test, p-value = 0.730).
At the level of GO categories, there is a statistically sig-
nificant overlap (six GO terms including carbohydrate
metabolic processes [GO:0005975] and oxidation-reduction
process [GO:0055114]; see Additional file 6 for the
complete list of overlapping GO categories) in the GO
terms associated with nourishment-responsive transcripts
for P. metricus and D. melanogaster fat bodies (Figure 4b;
chi-squared test with Yates’correction, p-value = 9.557e-
11). The consistency in directionality between shared P.
metricus and D. melanogaster fat body GO categories (i.e.
up-regulation in low nourishment samples for all GO cat-
egories, except carbohydrate metabolism with up-
regulation in high nourishment samples) further supports
common functional changes related to nourishment ma-
nipulation in both species. However, this signal is not ob-
served in the comparison between P. metricus
nourishment-enriched GO terms and D. melanogaster
nourishment-enriched GO terms in the muscle tissue.
There is only one common nourishment-enriched GO
term (oxidation-reduction process [GO:0055114]; Chi-
square test with Yates’correction, p-value = 0.4235), which
is upregulated in the P. metricus low nourishment larvae
but upregulated in the high nourishment samples for the
D. melanogaster muscle tissue (Figure 4d).
Out of 18,061 homologous transcripts between P. metri-
cus and a dung beetle Onthophagus taurus [45], we again
identified a very small overlap (4 transcripts; not significant;
Chi-square test, p-value = 0.57) in the nourishment-
responsive transcripts for P. metricus female larvae and
nourishment-responsive transcripts in O. taurus female
pupal thoracic horns. However, this overlap between paper
wasps and dung beetles is again consistent in the direction-
ality of nourishment-responsiveness with shared DETs
Berens et al. BMC Genomics (2015) 16:235 Page 5 of 12
being upregulated in low nourishment individuals (Figure 4e;
Additional file 6). Comparing enriched GO terms bet-
ween paper wasps and dung beetles, we found only two
shared GO categories: aminoglycan metabolic process
(GO:0006022) and chitin metabolic process (GO:0006030)
(Chi-square test with Yates’correction, p-value = 0.08;
Figure 4f), which suggests few common functional changes
related to nourishment in samples from these two species.
Discussion
In this study, we provide the first genome-wide transcrip-
tional profiling of nourishment response during develop-
ment in the genus Polistes, a model for understanding the
evolution of social castes. We identified 285 nourishment
differential expression transcripts (DETs) between larvae
raised experimentally on low vs. high nourishment, many
of which are associated with lipid metabolism and
oxidation-reduction activity. Most (73%) of the Polistes
nourishment-responsive transcripts are upregulated in lar-
vae with low nourishment, whichisoppositetothepattern
observed in other insects including fruit flies [44] and dung
beetles [45]. There were few conserved nourishment-
responsive transcripts across species, and these were related
to aminoglycan metabolism, carbohydrate metabolism, and
oxidation-reduction activity. Among transcripts corre-
sponding to those functions, our data show some cross-
Figure 3 Bar chart of GO categories significantly enriched (FDR < 0.05; one-tail) between nourishment differentially expressed
transcripts (DETs) and remaining transcriptome. All significantly enriched GO categories were over represented in the nourishment-responsive
DETs compared to the rest of the transcriptome. 17 significantly enriched GO categories were shared in common for both caste and nourishment.
Directionality is indicated for the enriched GO categories and defined as the treatment group with the greater number of upregulated DETs per
category.
Berens et al. BMC Genomics (2015) 16:235 Page 6 of 12
species consistency in the direction of expression in re-
sponse to nourishment deprivation. The overall picture
from our preliminary cross-species comparisons is that it is
largely different genes that show transcriptional responses
to nourishment stress across insect orders. However, it is
importanttonotethattranscriptional similarities across
these three systems may be underestimated from our ana-
lysis because of inconsistencies in the datasets such as ana-
lyzing different life stages and tissue types. Further work
with directly comparable datasets is needed in order to bet-
ter understand the extent of conservation of nourishment-
responsive gene expression across taxa.
Figure 4 Number and overlap of nourishment-responsive differentially expressed transcripts (DETs) between Polistes metricus (paper
wasp) and A) Drosophila melanogaster (fruit fly) fat body, C) fruit fly muscle, or E) Onthophagus taurus (dung beetle) female thoracic
horn. Number and overlap of of enriched GO terms between paper wasps and B) fruit fly fat body, D) fruit fly muscle, or F) dung beetle thoracic
horn. Directionality, i.e. which nourishment treatment group showed upregulation, is indicated for each dataset. There is only a statistically significant
overlap between paper wasp and fruit fly wild-type fat body enriched GO terms (indicated by *, Chi-squared test with Yates’correction, p-value =
9.557e-11). All other comparisons were not significant (Chi-squared tests with Yates’corrections, p-values > 0.05).
Berens et al. BMC Genomics (2015) 16:235 Page 7 of 12
Nourishment inequalities have long been considered
the most important environmental determinant of castes
in Polistes [8,14,27,39]. If nourishment plays a major role
in caste bias in P. metricus, we predicted that worker-
destined larvae from natural nests in the field would
have similar transcript expression patterns as experi-
mental low nourishment larvae. With respect to direc-
tionality of overall transcript expression, this was the
case —most DETs were upregulated in worker-destined
larvae (92.1%) and in low nourishment larvae (72.9%).
This work agrees with previous work in honey bees that
also showed more genes with worker-biased expression
in larvae, but more genes with queen-biased expression
later in development (pupal stage) [18,21]. We also
found a small but statistically significant overlap (43
common transcripts) between nourishment-responsive
and caste-related DETs in Polistes (Chi-square with
Yates’correction: p < 0.0001; Figure 2; Additional file 2:
Figure S1). Focusing on the 43 common DETs, however,
shows that the majority of these were upregulated in
worker-destined larvae but down-regulated in low nour-
ishment larvae, which is opposite to our prediction and
to the pattern of all DETs. This suggests that while nour-
ishment restriction in the laboratory may lead to upreg-
ulation of transcript expression in some of the same
pathways that are related to worker development, this
manipulation did not succeed in causing a full shift to
worker-like transcript expression patterns.
There was also a significant overlap in nourishment-
responsive and caste-related expression at the GO func-
tional level, with terms related to metabolism, protein
binding, and oxidation reduction activity (Figures 2 and 3;
Additional file 2: Figure S2; Additional file 4). On the level
of pathways, we identified a few shared KEGG pathways
between nourishment and caste datasets (Figure 2; Add-
itional file 4), which may be due to the low annotation rate
of nourishment-responsive DETs. Although there is lim-
ited overlap at the level of KEGG pathways, we did ob-
serve the expected pattern of directionality in gene
expression, with the majority of DETs upregulated in low
nourishment and worker-destined larvae for all pathways.
Overall, our data suggest that nourishment level caused
a partial shift in gene expression, with low nourishment
individuals being more worker-like and high nourishment
individuals being more gyne-like. However, it is pertinent
to note that the nourishment manipulation may not have
resulted in a strong nutritional stress; i.e., wasps may have
compensated for low proteinaceous food availability by
consuming more sugar. In a recent study examining adult
wasps reared from the same nests as the larvae analyzed
here, the nourishment manipulation caused only a partial
shift in caste-related physiology [38]. In that study, total
lipid and protein hemolymph levels in adults were not af-
fected by low nourishment, whereas adults that had been
reared with low nourishment showed greater ovary devel-
opment after two weeks of being fed while in isolation.
This counterintuitive observation corresponds to previous
studies showing that adult workers collected in the field
have greater ovary development than better-nourished
gynes [52] and substantial evidence that workers are in a
physiological state ready to reproduce upon emergence
[38], whereas gynes are in reproductive diapause until
after the overwintering period [10]. Taken together, the
physiological data [38] and transcriptomic data (this study)
indicate that nourishment alone did not completely shift
the developmental trajectory of larvae towards one caste
or another.
One important caveat of our study is that the effects of
the nourishment treatment on gene expression and physi-
ology may be influenced by laboratory rearing, which may
produce conflicting results compared to a natural field set-
ting (JM Jandt, JL Thomson, AC Geffre, AL Toth: Rearing
environment may bias social traits: A case study with
Polistes wasps, submitted). Lab-reared wasps typically have
higher lipid stores perhaps due to both overfeeding and in-
activity [47], and lab-rearing can perturb caste-related gene
expression (JM Jandt, JL Thomson, AC Geffre, AL Toth:
Rearing environment may bias social traits: A case study
with Polistes wasps, submitted). Two genes (inositol oxygen-
ase and Hsp90alpha)knowntoexhibitcaste-specificgene
expression are perturbed due to lab rearing, but neither
gene was differentially expressed in the current study. In
addition, the low and high nourishment samples in our
study were reared by single foundresses with unrestricted
access to sucrose as opposed to the two feeding levels for
caterpillars that they fed to larvae. Diets with a high carbo-
hydrate to protein ratio can cause an increase in lipid levels
intheinsectfatbody[53-55].Theeffectsoflab-rearing
could thus be a factor in some of the non-overlap we ob-
served between nourishment-responsive and caste-related
DETs in the current study. Nonetheless, our data do sug-
gest that low nourishment can trigger expression of some
of the same genes and pathways that are associated with
worker caste development in Polistes metricus.
Our results provide insight into the role of nourish-
ment in the differential gene expression patterns that
lead to different castes in Polistes. Our results also
support the notion that nourishment inequalities alone
cannot explain all caste variability in gene expression.
Instead, caste-related gene expression bias is likely to be
additionally influenced by social factors such as domin-
ance behavior [29,31], vibrational communication
[40-42], and/or epigenetically mediated environmental
influences [56]. Further work on gene expression in rela-
tion to nourishment, other influences on caste determin-
ation in Polistes, and interactions among them can
further advance our growing understanding of caste
determination in primitively social wasps.
Berens et al. BMC Genomics (2015) 16:235 Page 8 of 12
Conclusions
This study provides new data on nourishment-
responsive gene expression in the context of caste devel-
opment for Polistes metricus, a model for studying the
evolution of social insect castes. We identified suites of
nourishment-responsive transcripts in developing P.
metricus larvae. Interestingly, most transcripts were up-
regulated when larvae experienced proteinaceous nour-
ishment deprivation; thus, reduced food level did not
shut down gene expression but instead resulted in active
transcription of many genes including several involved
in lipid metabolism, carbohydrate metabolism, and
oxidation-reduction processes. By comparing to previ-
ously reported caste-related gene expression patterns
from the same species, we uncovered some similarity in
transcripts, pathways, and gene functions related to both
nourishment deprivation and worker caste-biased ex-
pression. However, many caste-associated genes were
not found to be nourishment-responsive, so there are
additional factors (likely including many social environ-
mental factors) that influence caste-related gene expres-
sion. These results support the notion that nourishment
level during development can somewhat bias develop-
ment into queen or worker caste as adults, but leave
room for other factors, and thus underscore the complex
and multifactorial nature of caste development.
Methods
Samples
We collected adult female P. metricus wasps in early
March 2009 near Raleigh, NC, as they were exiting the
attic of a house in which they had passed the winter in
behavioral quiescence and reproductive diapause. Single
wasps were placed in cages 30 cm in length, width, and
height constructed of clear plastic with plastic screen on
the top and two sides. An opening in the top was cov-
ered with a piece of hardboard 10 cm square with a nest
from a previous season attached to the underside. Nests
were trimmed to seven cells ca. 0.5 cm deep, and meco-
nia (larval feces) of the original nest occupants were re-
moved. Each seven-cell nest therefore served as a
“starter”nest on which the newly-captured wasps could
initiate construction and then expand as their own.
Construction paper was the pulp source for nest
construction.
Caged wasps were placed on wire racks in a growth
chamber 1.2 m × 2.5 m × 2.1 m in the North Carolina
State University Phytotron. The chamber contained in-
candescent lights on a 16 L/8D cycle; fluorescent lights
came on 2 h following and went off 2 h before the
incandescent lights. Light intensity was 21 micromoles/
sec/m
2
in the incandescent-only morning and evening
periods and 225 micromoles/sec/m
2
during the both-
lights midday. Chamber temperature was 20°C at night
and 30°C during full light, with a gradual ramp-up in the
morning and ramp-down in the evening. Each day, we
repositioned cages in a rotation pattern to distribute any
light or temperature variation in the chamber across all
colonies over the course of the experiment.
Each cage was provided with ad libitum sucrose (rock
candy) and a water source (15 ml tube plugged with
cotton). Both high and low nourishment groups had equal
access to sucrose, but differed in the amount of protein-
aceous food provided. Proteinaceous nourishment was
provided in the form of late 3
rd
or early 4
th
-instar
Manduca sexta larva ca. 2.0 cm in length. Low nourish-
ment foundresses received one caterpillar every fourth
day. After May 22, the feeding schedule for low nourish-
ment foundresses was accelerated to one caterpillar every
three days. In the high nourishment treatment, foun-
dresses were provided with caterpillars ad lib,adjusted
each day to one caterpillar above the number that had
been consumed since the previous day’s provisioning. For
this experiment, we collected the largest final instar larva
in each nest immediately following spinning of a cocoon
by the third larva in the nest to do so. Those three larvae
were allowed to develop into adults that then were ana-
lyzed for developmental and physiological characteristics.
These results were published separately [38]. For our
study, four larvae per treatment were flash frozen in liquid
nitrogen and stored at -80°C prior to RNA extraction.
RNA-extraction and RNA-sequencing
Polistes possess behaviorally distinct, not morphologic-
ally distinct castes, thus we were especially interested in
developmental expression changes in larval brains. This
led us to choose larval heads as the target tissue for our
analysis. Whole heads were used rather than whole
brains because of concerns about larval brain dissection
quality and low RNA yields. We acknowledge that it is
likely that the nourishment manipulation caused
additional gene expression changes in other tissues we
did not sample. However, we did not use whole bodies
for two reasons: 1) our primary interest in brains and
behavioral castes, and 2) the fact that brain gene expres-
sion differences in social insects can be subtle [57],
meaning that high levels of expression from the fat body
and other tissues could have drowned out expression
patterns from the brain.
To preserve RNA during dissection, we removed the
head region (indicated by dark coloration) of each
individual larva, while kept on dry ice, using a sterilized
razor blade. From these individual larval heads, we ex-
tracted total RNA using an RNeasy Mini Kit (Quigen),
which was quality controlled using spectrophotometry
(NanoDrop 2000) and a Bioanalyzer (Agilent). The
High-Throughput Sequencing and Genotyping Unit of
the W.M. Keck Center (University of Illinois at Urbana-
Berens et al. BMC Genomics (2015) 16:235 Page 9 of 12
Champaign) prepared 16 mRNA Seq libraries (n = 4 per
group, high and low nourishment level) derived from
two experimental nourishment levels (high and low; this
study) and unmanipulated castes (queen- and worker-
destined; [13]) using the “TruSeq RNAseq Sample Prep
kit”(Illumina). These prepared libraries were sequenced
on a HiSeq 2000 (Illumina) to generate over 1 billion
100 base paired-end reads, which we assembled de novo
into a transcriptome (deposited at DDBJ/EMBL/
GenBank under the accession GBGV00000000; this
study used the first version GBGV01000000). Raw se-
quence data has been deposited to the National Center
for Biotechnology Information’s (NCBI) Short Read
Archive (BioProject ID: PRJNA242774, [accession
numbers: NCBI:SRX511425, NCBI:SRX511426, NCBI:
SRX511427, NCBI:SRX511430, NCBI:SRX511432, NCBI:
SRX511433, NCBI:SRX511434, and NCBI:SRX511435]).
For a more details about the RNA-Sequencing and the
transcriptome assembly, see [13].
Read mapping, abundance estimation, and differential
expression analysis
As described in [13], we aligned the raw paired-end
reads to the reference transcriptome (GBGV01000000)
using Bowtie 2 (Version 2.1.0) [58] with default settings.
From these alignments, we quantified transcript abun-
dances for each library using eXpress (Version 1.3.1)
[59], which have been depositied in NCBI’sGeneEx-
pression Omnibus [60] and are accessible through GEO
Series [NCBI:GSE61960] (http://www.ncbi.nlm.nih.gov/
geo/query/acc.cgi?acc=GSE61960). From these raw read
counts, we identified differentially expressed transcripts
(FDR ≤0.05, [46]) between nourishment manipulation
levels (high and low) using the R (Version 3.0.1) [61]
statistical package DESeq (Version 1.12.0) [62] down-
loaded from the Bioconductor repository [63]. Raw read
counts were normalized by the effective library size, and
dispersion factors were determined based on the per-
condition method.
Kyoto encyclopedia of genes and genomes (KEGG) and
gene ontology (GO) analyses
From functional annotations based on best BLASTx hit
(E-value ≤1e-3) to Drosophila melanogaster sequences, we
used Blast2GO (Version 2.6.5) [50] to assign enzyme
codes, metabolic (KEGG) pathways, and GO terms to
P. metricus transcriptomic sequences (see [13]). Based on
these assignments, we identified the KEGG pathways that
contain nourishment DETs and assessed enrichment of
GO terms (FDR ≤0.05; one-tailed, [46]) between the nour-
ishment DETs compared to the background –the
complete P. metricus transcriptome.
Caste and nourishment manipulation comparison
To assess the extent that differential nourishment biased
gene expression patterns toward a particular caste pheno-
type in Polistes paper wasps, we compared molecular
signatures of nourishment manipulation and caste deter-
mination [13] at three levels: transcript differential expres-
sion, KEGG pathways with DETs, and GO enrichment. At
the transcript level, we tested for significance in overlap
between nourishment and caste DETs given the number
of DETs per each dataset and the total number of P. metri-
cus transcripts by using a Chi-square test with Yates’cor-
rection. For both the nourishment and caste datasets, we
identified which KEGG pathways had at least one DET,
and we then performed a Fisher exact test to determine
whether there is a statistically significant number of shared
KEGG pathways with DETs given the number of unique
pathways with DETs per each dataset and all pathways
without DETs. Finally, we assessed significance in the
overlap between nourishment and caste GO enriched cat-
egories in relation to the total number of annotated, not
enriched, GO terms and unique nourishment/caste
enriched GO terms using a Fisher exact test.
Alternative statistical approach to address overlap across
nourishment and caste studies
We investigated an alternative approach (beyond compari-
sons of DET lists) to test for similarity in the transcript ex-
pression patterns associated with nourishment restriction
and worker-caste development. In some sense, across the
two studies we have a replicated experiment with respect to
nourishment levels, which utilizes both the lab and field set-
ting. As described in the introduction, worker-destined typic-
ally larvae receive more limited nourishment compared to
queen-destined larvae [10,27,30,33]. Therefore, we modeled
these datasets together while controlling for location (lab or
field) to identify nourishment-responsive transcripts. Overall,
our results suggest some consistency in the modeling and list
comparison approaches. For full details and results using this
approach, please see Additional file 2 for Supplemental
Methods, Results, Table, and Figures S4-S7 and Additional
file 5 for lists of nourishment-responsive transcripts.
Cross-species comparison
Based on our interest in whether nourishment differences
induce similar molecular responses in transcript expression
and biological processes, we reviewed the literature and
searched data repositories (NCBI Gene Expression
Omnibus and EMBL ArrayExpress) to identify the most
directly comparable studies to the P. metricus nourishment
manipulation dataset based on the following criteria: 1) the
datasets compared late-stage subadult insects reared on
two nourishment levels and 2) the studies used a
transcriptome-wide approach, i.e. microarray or RNA-seq.
We identified two studies that meet both of these criteria:
Berens et al. BMC Genomics (2015) 16:235 Page 10 of 12
one in fruit flies (D. melanogaster, [44]) and the other in
dung beetles (Onthophagus Taurus, [45]). For this analysis,
we compared lists of putative orthologous nourishment-
biased DETs and nourishment enriched GO terms between
paper wasps and fruit flies or dung beetles using
Chi-square tests with Yates’correction. We defined
putative orthologous sequences between P. metricus and
either D. melanogaster or O. taurus as the best BLAST hit
(E-value ≤1e-3) between pairs of species. For the fruit fly
comparison, we only used the wild-type fruit fly data, and
we compared the paper wasp dataset to both tissue types
in fruit flies (adipose and muscle). The GO terms listed in
the publication of Teleman et al. [44] were not consistent
with the current Gene Ontology database, so we identified
fruit fly nourishment enriched using Blast2Go (FDR ≤0.05;
one-tailed, [46]). For the dung beetle comparison, we fo-
cused our study on a comparison with female thoracic
horn dataset, which we felt was the most akin to the paper
wasp dataset because samples were derived from tissues in
female insects during the pupal stage of development.
Availability of supporting data
Raw sequence data has been deposited to the National
Center for Biotechnology Information’s (NCBI) Short Read
Archive (BioProject: PRJNA242774, http://www.ncbi.nlm.
nih.gov/bioproject/?term=PRJNA242774). The transcript
abundance data is available in the NCBI’sGeneExpression
Omnibus repository (Accession number: GSE61960, http://
www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE61960).
All other data sets supporting the results of this article are
included within the article and its additional files.
Additional files
Additional file 1: Polistes metricus differentially expressed
transcripts, KEGG pathways, and GO categories. Contains the results
of the differential expression analysis on the nourishment data, the list of
KEGG pathways with more than one differentially expressed transcript,
and the list of nourishment enriched GO categories.
Additional file 2: Supplemental methods, results, tables, and
figures. Includes supplemental figures for the overlap analysis of
nourishment and caste and the results of the validation by comparison
to qRT-PCR data. This file also contains the supplemental methods,
results, tables, and figures of the additional statistical approach for
determining overlap between the nourishment and caste data sets.
Additional file 3: Validation by comparison to qRT-PCR data.
Contains the log
2
fold changes for the homologous sequences between
the RNA-seq and qRT-PCR datasets. Sequences that are not differentially
expressed are listed as NDE; whereas, the directionality is listed for the
differentially expressed transcripts.
Additional file 4: Results of nourishment and caste comparison at
levels of transcripts, pathways, and biological functions. Lists the
common differentially expressed transcripts, KEGG pathways, and GO
categories between the nourishment and caste data sets.
Additional file 5: Results of additional statistical approach for
determining overlap between nourishment and caste data sets.
Includes the estimates of nourishment main effects and nourishment
by location interaction effects for the transcripts with significant effects.
Additional file 6: Nourishment comparison across species. Lists the
overlapping nourishment differentially expressed transcripts and GO
categories for the comparisons between paper wasps and fruit flies
(fat body and muscle tissue) or dung beetles.
Abbreviations
DETs: Differentially expressed transcripts; FDR: False discovery rate; GO: Gene
ontology; KEGG: Kyoto encyclopedia of genes and genomes; NCBI: National
Center for Biotechnology Information; qRT-PCR: Quantitative reverse
transcription polymerase chain reaction.
Competing interests
The authors declare that they have no competing interests.
Authors’contributions
JHH and ALT conceived the study and performed the experimental work. AJB
performed the gene expression analyses, comparative studies, and generated
the figures. AJB, JHH, and ALT wrote the manuscript. All authors have read and
approved the final manuscript.
Acknowledgements
Talbia Choudhury assisted with the wasp rearing at North Carolina State
University. Carole Saravitz and Janet Shurtleff accommodated our work at the
North Carolina State University Phytotron, including complimentary use of the
growth chamber. Manduca sexta caterpillars were provided by the North
Carolina State University Insectary, Beverley Pagura Director. Amy Geffre and
Cecile Mercado extracted RNA for sequencing. Members of the Toth laboratory
provided insightful comments during the preparation of the manuscript. This
work was supported by the National Science Foundation IOS 1146410.
Author details
1
Program in Bioinformatics and Computational Biology, Iowa State University,
Ames, IA 50011, USA.
2
Department of Ecology, Evolution, and Organismal
Biology, Iowa State University, Ames, IA 50011, USA.
3
Department of
Biological Sciences, North Carolina State University, Raleigh, NC 27695, USA.
4
Department of Entomology, North Carolina State University, Raleigh, NC
27695, USA.
5
W. M. Keck Center for Behavioral Biology, North Carolina State
University, Raleigh, NC 27695, USA.
6
Department of Entomology, Iowa State
University, Ames, IA 50011, USA.
Received: 17 December 2014 Accepted: 27 February 2015
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