Old Cell, New Trick? Cnidocytes as a Model for the Evolution of

Integrative and Comparative Biology
Integrative and Comparative Biology, volume 54, number 4, pp. 714–722
doi:10.1093/icb/icu027
Society for Integrative and Comparative Biology
SYMPOSIUM
Old Cell, New Trick? Cnidocytes as a Model for the Evolution of
Novelty
Leslie S. Babonis1 and Mark Q. Martindale
Whitney Laboratory for Marine Bioscience, University of Florida, 9505 N Oceanshore Blvd, St. Augustine, FL 32080, USA
From the symposium ‘‘The Cell’s View of Animal Body Plan Evolution’’ presented at the annual meeting of the Society
for Integrative and Comparative Biology, January 3–7, 2014 at Austin, Texas.
1
E-mail: [email protected]
Synopsis Understanding how new cell types arise is critical for understanding the evolution of organismal complexity.
Questions of this nature, however, can be difficult to answer due to the challenge associated with defining the identity of
a truly novel cell. Cnidarians (anemones, jellies, and their allies) provide a unique opportunity to investigate the molecular regulation and development of cell-novelty because they possess a cell that is unique to the cnidarian lineage and
that also has a very well-characterized phenotype: the cnidocyte (stinging cell). Because cnidocytes are thought to differentiate from the cell lineage that also gives rise to neurons, cnidocytes can be expected to express many of the same
genes expressed in their neural ‘‘sister’’ cells. Conversely, only cnidocytes posses a cnidocyst (the explosive organelle that
gives cnidocytes their sting); therefore, those genes or gene-regulatory relationships required for the development of the
cnidocyst can be expected to be expressed uniquely (or in unique combination) in cnidocytes. This system provides an
important opportunity to: (1) construct the gene-regulatory network (GRN) underlying the differentiation of cnidocytes,
(2) assess the relative contributions of both conserved and derived genes in the cnidocyte GRN, and (3) test hypotheses
about the role of novel regulatory relationships in the generation of novel cell types. In this review, we summarize
common challenges to studying the evolution of novelty, introduce the utility of cnidocyte differentiation in the model
cnidarian, Nematostella vectensis, as a means of overcoming these challenges, and describe an experimental approach that
leverages comparative tissue-specific transcriptomics to generate hypotheses about the GRNs underlying the acquisition of
the cnidocyte identity.
Why study novelty?
The development of novel traits (structures and/or
functions) is one critical way in which morphological
and functional diversity is generated across taxa;
indeed, many of the novel features of greatest interest
are complex multicellular traits responsible for major
evolutionary transitions (e.g., evolution of the tetrapod limb) (Shubin et al. 1997). Yet a complete understanding of how these complex evolutionary
novelties arise (and, ultimately, how animal diversity
arises) necessitates an understanding of how new cell
types are generated. From a developmental perspective, new cell types are generated when ‘‘error’’ is
introduced during the process of differentiation,
such that a daughter cell with a new phenotype is
produced. From an evolutionary perspective, novel
phenotypes of cells may arise either with the
advent of novel genes (e.g., by gene duplication followed by neofunctionalization, introduction of transposable elements, and/or lateral gene transfer) (for
review, see Hall and Kerney 2012) or as a consequence of novel relationships among deeply homologous genes (resulting in heterochrony, novel
regulatory networks, or novel protein–protein interactions) (Hoekstra and Coyne 2007; Wray, 2007;
Shubin et al. 2009; Wagner and Lynch 2010). A
recent study modeling diversity in types of cells as
a function of new regulatory relationships among
conserved genes suggests that this latter hypothesis
is sufficient to generate extensive novelty and diversity among cell types (Lobo and Vico 2010). Still,
many additional examples of novel traits emerging
as a consequence of novel genes exist (Khalturin
et al. 2009; Milde et al. 2009; Johnson and Tsutsui
Advanced Access publication April 25, 2014
ß The Author 2014. Published by Oxford University Press on behalf of the Society for Integrative and Comparative Biology. All rights reserved.
For permissions please email: [email protected].
Cnidocytes model novelty
715
2011), thereby supporting a diverse array of mechanisms responsible for generating diversity at the cellular and tissue level (Oakley 2007). An important
future area of study of this topic lies at the intersection of these processes. In particular, how novel
genes become incorporated into novel or existing
GRNs is a critical next step in revealing the mechanisms that result in the generation of new cell types.
Herein, we propose that cnidocytes may be uniquely
suited to model the interaction of structural and regulatory novelties and suggest a means by which to
capitalize on recent efforts in sequencing across diverse cnidarian taxa to develop hypotheses about the
evolution of this important cnidarian-specific cell
novelty.
Cnidocyte differentiation in
Nematostella vectensis: a model
for the evolution of novel cells
Using the simple terminology of Peterson and Muller
(2013), we consider cnidocytes, the stinging cells in
cnidarians, a classic example of an evolutionary
(phenotypic) novelty. Found in no other organisms,
cnidocytes have been studied for decades, in part
because of their unique function. Following stimulation of the sensory cilium at the apex of the cnidocyte (Fig. 1), the cnidocyst (the organelle from which
the cnidocyte derives its ‘‘sting’’) extrudes from the
cell with an acceleration that exceeds that of perhaps
any other biological process (Holstein and Tardent
1984). Ultimately, these explosive organelles ensnare,
envenomate, or adhere to their target, providing a
means by which to capture/subdue prey, defend
against predators, or locomote through substrate.
While lingering hypotheses have suggested a close
evolutionary relationship between cnidocytes and
the elaborate extrusive cells of some protists
(Shostak 1993; Denker et al. 2008a; Ozbek et al.
2009), the absence of any molecular evidence of lateral gene transfer (Technau et al. 2005) suggests this
similarity is little more than impressive homoplasy.
The autonomous ability of cnidocytes to sense the
environment and respond (by firing) led to early
hypotheses that cnidocytes are an unusual type of
dual function (sensory/effector) neuron (Pantin
1942), albeit with a highly derived neurosecretory
vesicle (the cnidocyst). Expression of many
common regulatory genes in the precursors of both
neurons and cnidocytes lends support to this idea
(e.g., cnox-2, prdl-b, and COUP-TF) (Galliot and
Quiquand 2011); however, a recent phylogenetic
study suggests that neurons may have evolved long
before cnidocytes (Ryan et al. 2013). If cnidocytes
Fig. 1 Anatomy of a cnidocyte. (A) Unfired. Stimulation of the
cnidocil activates exocytosis of the contents of the cnidocyst. (B)
Fired. The tubule is everted from the capsule of the cnidocyst.
evolved from within the lineage that gave rise to
neurons, it may be reasonable to expect conservation
of many of the molecular elements of their differentiation pathways. Understanding the GRNs that underlie the differentiation of both neurons and
cnidocytes is a critical first step in evaluating this
hypothesis.
The concept of cell identity is inherently modular,
thus, many components of cell identity may be
nested within a single cell. For example, a single
cell may at the same time be an epithelial cell, a
sensory cell, a secretory cell, and a cnidocyte.
Because of this, it may not be surprising to find
substantial conservation of GRN modules between
cnidocytes and, for example, neurons which may
also be epithelial, sensory, and secretory cells.
Understanding the evolution of novel cell identity,
then, requires first identifying the components of a
GRN that underlie a particular module of cell identity and then assessing whether these components are
shared across cell types or are unique to the novel
cell lineage. Because of their truly unique function,
studies of cnidocysts continue to attract attention
across fields ranging from venom evolutionary studies to clinical investigations of novel drug delivery
techniques (Shaoul et al. 2012; Weston et al. 2013).
These and other detailed studies of the cnidocyte
proteome (e.g., Hwang et al. 2007) have revealed
numerous taxonomically restricted genes in this
cell type, providing many possible examples of elements comprising the ‘‘cnidocyte’’ identity module.
716
Importantly, development of the cnidocyst relies
both on cnidarian-specific structural proteins (e.g.,
minicollagens, NOWA, and spinalin) (Kurz et al.,
1991; Koch et al., 1998; Engel et al., 2002) and scaffolding by conserved glycosaminoglycans, including
chondroitin sulfate (Yamada et al. 2007; Adamczyk
et al. 2010; Ozbek 2011). Thus, components comprising the cnidocyte identity module may only
need to be regulated together, rather than be
uniquely expressed in this cell type to produce a
novel phenotype. Although binding sites for conserved transcription factors have yet to be identified
in the promoter regions of any cnidocyte-specific
genes, functional assays of several conserved transcription factors suggest that the structural elements
of the cnidocyst identity module may be regulated
(directly or indirectly) by conserved transcription
factors (e.g., mef2 and NFkB) (Genikhovich and
Technau 2011; Wolenski et al. 2013). In order to
elucidate the process by which the cnidocyte identity
module became integrated with other GRNs underlying cell-type identity, it is necessary to examine the
processes upstream of cnidocyst formation, specifically the differentiation of cnidocytes from a proliferative precursor.
Like all other somatic cells, new cnidocytes arise
through mitosis of a precursor or ‘‘stem’’ cell, a
process that has been well-studied in hydrozoan cnidarians (recently reviewed by David 2012). In hydrozoans, cnidocytes are known to arise from a special
progenitor lineage that resides in the interstitium of
the body-wall’s epidermis (so-called ‘‘i-cells’’).
Following several rounds of mitosis without full
cleavage, early-stage cnidocytes are produced in
nests and remain attached to each other via cytoplasmic bridges until maturation of the cnidocyst and,
finally, migration of the mature cnidocytes to the
tentacles, where the majority of cnidocytes are
mounted. Studies of the proliferation and differentiation of stem cells in hydrozoans have benefited from
both a long history of study (Galliot 2012) and many
recent advances in molecular techniques (including
the development of i-cell transgenics, which has facilitated the extensive molecular characterization of icells and their descendents) (Wittlieb et al. 2006;
Hemmrich et al. 2012). Considering that hydrozoans
are a highly derived lineage of cnidarians, the applicability of these studies to a broader understanding of
cell biology across cnidarian taxa has been questioned
(Extavour et al. 2005; Technau et al. 2005; Steele et al.
2011). In concert with this, i-cells appear to be a type
of progenitor cell restricted to the Hydrozoa, yet even
among hydrozoans the dynamics of i-cell biology
(e.g., their embryonic origins, their contribution to
L. S. Babonis and M. Q. Martindale
regeneration, and their spatio-temporal progression
to cnidocyte development) varies (Denker et al.
2008b; Plickert et al. 2012). These observations
make efforts to identify the proliferative cells in
other cnidarian lineages, and indeed the mechanism
of differentiation from these progenitors, increasingly
important (Gold and Jacobs 2013). Comparisons of
putative cnidocyte differentiation genes across
cnidarian taxa appear to reveal even more
substantial diversity; for example, the cnidarian
ortholog of the conserved achaete-scute (ash) gene
isolated from Hydra (Cnash) is known to regulate
the identity of all cells in the cnidocyte lineage
(Grens et al. 1995) whereas ash genes in N. vectensis
(NvashA-D) appear to be expressed only in neurons
or in the endodermal component of the mesenteries,
neither of which is consistent with a role in cnidocyte
development (despite suggestions to the contrary by
Layden et al. 2012). Additionally, a recent study using
subtractive library hybridization identified 16 cnidarian-specific genes in the cnidocyte lineage of Hydra,
two of which have reasonable homology with sequences in N. vectensis (Milde et al. 2009). One of
these (gene 012) is restricted to developing lineages of
two types of cnidocytes that are not found in
N. vectensis; understanding where this gene is
expressed in N. vectensis may provide information
about how the diverse repertoire of cnidocytes in
Hydra evolved. It is tempting to postulate that the
morphological diversity of cnidocytes is mirrored by
diversity at the regulatory (differentiation) level; but,
before hypotheses like these can be evaluated, it is
necessary to characterize the molecular regulation of
cnidocyte differentiation in cnidarians outside of the
Hydrozoan lineage.
Nematostella vectensis, the starlet sea anemone
(Fig. 2A), has become an important model for
molecular and developmental studies, especially
for studies of the molecular regulation of the
identity of cells and tissues (Darling et al. 2005;
Genikhovich and Technau 2011; Steele et al. 2011;
Layden et al. 2012; Nakanishi et al. 2012; Rottinger
et al. 2012; Fritz et al. 2013). Several aspects of the
biology of N. vectensis also make this animal an
attractive model for studies of cellular novelty. First,
cnidocytes are found in various tissues in this species
but are notably abundant in the epidermis on the tips
of tentacles (Fig. 2B) and in the mesenteries (Fig. 2E)
where they develop continuously throughout the lifetime of the animal (Fig. 2C and F; Zenkert et al.
2011). Although the identity of the progenitor
lineage has yet to be identified in N. vectensis
(indeed, in any non-hydrozoan cnidarian) (Gold
and Jacobs 2013), the presence of proliferative
Cnidocytes model novelty
717
Fig. 2 Cnidocyte development in Nematostella vectensis. (A) An adult polyp showing basic morphology. (B) DIC image of the tip of a
tentacle showing the abundance of mature cnidocytes (arrows) in the tentacle’s epidermis (e). (C) Fluorescent in situ hybridization
(following the protocol of Layden et al. 2012) for minicollagen 3 shows the distribution of developing cnidocytes (red) in the tentacle in
this optical section; nuclei are shown in blue (DAPI). (D) EdU (following the manufacturers’ protocol; Invitrogen USA) reveals the
presence of proliferative cells (green) in the tentacle’s epidermis; optical section. (E) DIC image of the ectodermal component of one
mesentery showing the abundance of mature cnidocytes (arrows). (F) Confocal projection showing the presence of developing
cnidocytes (red) and proliferative cells (green) in the mesentery pictured in E; nuclei as in C. (G) DIC image of an isolated nematosome
with abundant mature cnidocytes (arrows). (H) Mature cnidocytes are present in aggregations (arrows) along the mesentery before the
nematosomes have fully budded. (I) Fluorescent in situ hybridization for minicollagen 3 (red) overlaid on a DIC image shows developing
cnidocytes in the epidermis of the body wall (e) but not in the gastrodermis or nematosome (arrow); optical section. Panel A reprinted
with permission: ß SERTC, South Carolina Department of Natural Resources.
cells at the site of cnidocyte differentiation (e.g., in
the epidermis of the distal tentacle and ectodermal
mesenteries) (Fig. 2D and G) suggests that the replacement of cnidocytes occurs locally in this species.
This is an important departure from the hydrozoan
model as it suggests that progenitor cells comprise a
significant component of the epidermal tissue in
the adult, rather than being restricted to an atypical
lineage of cells found only in the interstitium of the
mid-body epidermis (as is the case for Hydrozoans).
Another important advantage of using N. vectensis
for studies of the differentiation of cnidocytes is
the opportunity to compare the molecular regulation
of this process both in adults undergoing cnidocyte
replacement and during de novo generation of the
cnidocytes through embryonic development. Studies
comparing eye development and regeneration in planarians suggest these processes may involve different
molecular pathways (summarized by Martin-Duran
et al. 2012); if this principle holds true in cnidarians,
studies aimed only at regenerating cnidocytes in
polyps may miss many important elements of the
developmental cnidocyte GRN. Comparisons of this
type can be made explicitly only after one of these
718
L. S. Babonis and M. Q. Martindale
GRNs has been characterized. Below, we discuss a
means by which to leverage tissue-specific
mRNAseq as a forward approach to characterizing
the first cnidocyte GRN in N. vectensis.
Tissue-specific transcriptomics: a
forward approach to identify
cnidocyte GRNs
A well-characterized cnidocyte GRN is a critical tool
for future testing of hypotheses about conservation
of regulatory relationships in different life stages
(e.g., adult versus embryos), across different cell
types (e.g., cnidocytes versus neurons), and among
taxa (e.g., Nematostella versus Hydra). Here, we describe a method that pairs minimal prior knowledge
of the molecular differentiation of cnidocytes with
mRNAseq technology in an unbiased approach to
identifying the elements of the cnidocyte GRN in
the adult anemone (outlined in Fig. 3). Because cnidocytes develop both locally and continuously in the
tentacles and mesenteries of adult N. vectensis
(Fig. 2) (Zenkert et al. 2011), sequencing mRNA
from these tissues provides a means by which to
sample cells at many stages of differentiation along
the cnidocyte pathway. Genes of particular interest
for the cnidocyte GRN (target genes) will be expressed in the union of the transcriptomic datasets
from these two tissues. However, because developing
cnidocytes are not the only cell types shared by these
two tissues, many transcripts that are not part of the
cnidocyte GRN will also be included in this union
(e.g., those expressed in any other cell type undergoing differentiation at the time of collection). Previous
studies of transcriptome-level changes in mRNA expression across developmental stages (Helm et al.
2013; Tulin et al. 2013) or treatments (Barshis
et al. 2013) have narrowed their list of target genes
by examining only those transcripts whose expression changes through time or across treatments
using differential expression analysis. When target
genes are expressed in the union of two conditions
(e.g., in the set of genes shared by tentacles and mesenteries), it is necessary to employ an alternative
means to identify transcripts of greatest interest.
Nematostella vectensis again provides a unique opportunity for comparative tissue-specific transcriptome analysis in its possession of nematosomes
(Fig. 2G). Unique to anemones in the genus
Nematostella, nematosomes are small autonomous
cell masses that arise from the ectodermal component of the mesenteries (Fig. 2H; Williams 1975) and
circulate in the gastrovascular cavity of the adult
anemone with an unknown function (Williams
Fig. 3 Venn diagram indicating target genes of interest. Targets
captured in section A will include those expressed in mature
cnidocytes (found in all three tissues) as well as housekeeping
genes (found in all cells). Targets in section B will include the
genes of the cnidocyte developmental pathway as well as genes
from any other cell lineages downstream of the proliferating cells
shown in Fig. 2D and F.
1979; Hand and Uhlinger 1992). Although nematosomes are replete with mature cnidocytes (Fig. 2G
and H), there is no evidence to suggest that cnidocyte differentiation occurs in this tissue (Fig. 2I),
making nematosomes extremely valuable for distinguishing between genes involved in the development
of cnidocytes and genes responsible for the maintenance of mature cnidocyte identity. While the latter
category of genes (involved in mature cell maintenance) will be expressed in the union of all three
tissues (Group A; Fig. 3), those involved largely in
the development of cnidocytes will be excluded from
the nematosomes (Group B; Fig. 3). Thus, including
nematosomes in this analysis provides an important
opportunity to focus the suite of genes pursued in
downstream studies of cnidocyte development and
also provides a reciprocal opportunity for future
comparisons of the maintenance of identity in each
of the three types of cnidocytes found in the various
tissues in N. vectensis. Indeed, future analyses focused
on sequences in the union of all three tissues (Group
A) will be critical for establishing the molecular identity of mature cnidocytes and will benefit greatly
from comparative analyses incorporating recent
data on the cnidocyte proteome (Moran et al.
2013). Although simple in design, we suggest that
the approach outlined here may be particularly
useful for investigations of other emerging model
systems wherein some data have already been collected using a candidate-gene strategy but the full
Cnidocytes model novelty
GRN for the cell, tissue, or process of interest remains to be characterized. Because cnidocytes are
easy to identify using only light microscopy
(Ostman 2000), this approach may also be particularly useful for future studies aimed at characterizing
the tissue-specific generation of cnidocytes across
various cnidarian taxa.
The dramatic decrease in the cost of sequencing
over the past decade has resulted in a dramatic increase in the number of species, tissues, and cells for
which transcriptomic (mRNAseq) data have become
available. Among cnidarians, mRNAseq datasets are
now available for at least 12 different taxa representing both anthozoan and hydrozoan lineages:
Acropora millepora, A. palmata, A. hyacinthus,
Aiptasia pallida, Craspedacusta sowerbyi, Favia sp.,
Hydra vulgaris, Hydractinia symbiolongicarpus,
Nanomia bijuga, N. vectensis, Pocillopora damicornis,
and Porites australiensis (Polato et al. 2011; Siebert
et al. 2011; Traylor-Knowles et al. 2011; Hroudova
et al. 2012; Lehnert et al. 2012; Moya et al. 2012;
Barshis et al. 2013; Mehr et al. 2013; Tulin et al.
2013; Wenger and Galliot 2013; Shinzato et al.
2014; Zárate-Potes and Cadavid 2014). The parallel
increase in availability of user-friendly software for
de novo transcriptome assembly (Robertson et al.
2010; Grabherr et al. 2011; Schulz et al. 2012;
Brown et al. 2013) has greatly facilitated discovery
of novel genes (e.g., new taxonomically restricted
genes, short-ORF-containing transcripts, and pseudogenes) (Lehnert et al. 2012; Moya et al. 2012;
Mehr et al. 2013; Wenger and Galliot 2013) among
these non-model taxa. Together with newly developed modeling approaches aimed at inferring cis-regulatory relationships from sequencing data (Dresch
et al. 2013), the continued sampling of diverse cnidarian taxa with a particular emphasis on studies of
tissue-specific expression will enable future tests of
cnidocyte GRN conservation across lineages.
As with any transcriptomic study, there are caveats
with this approach that must be considered. First, all
three target tissues (mesenteries, tentacles, and nematosomes) are comprised of many different cell types;
thus, using transcriptomics alone, it will not be possible to discriminate genes expressed in the developing
cnidocyte lineage from those expressed in any other
cell lineage that might be undergoing proliferation
and/or differentiation at the same time. It will still be
necessary therefore, to apply downstream processes to
determine (1) where/when the target transcripts (e.g.,
transcription factors and signaling molecules) are expressed relative to the timing of proliferation and of
cnidocyst development and (2) the effect of target gene
knockdown on the expression of markers of cnidocyst
719
development. Additionally, because cnidocytes develop continuously both in tentacles and inmesenteries
and because multiple types of cnidocytes are known to
develop in both of these tissues (Zenkert et al. 2011),
any single transcriptomic dataset will undoubtedly include expressed genes from multiple types of cnidocytes and from multiple times along the differentiation
pathway of these cnidocytes. To construct the relationships among transcripts in the network underlying
each type of cnidocyte (e.g., which transcription factors regulate which targets), it will be necessary to pair
downstream functional assays (e.g., gene knockdown)
with careful analysis of the ultrastructure of cnidocytes
(e.g., using electron microscopy). Recent advancements in the number and the nature of molecular
tools available for use in N. vectensis (including
double fluorescent in situ hybridization, knockdown/
overexpression techniques, and the recent development of transgenic lines) (Renfer et al. 2010;
Rottinger et al. 2012; Layden et al. 2013) have made
functional assays of this type possible in this system
and will facilitate the downstream studies of gene regulation necessary to fully construct the GRNs of each
type of cnidocyte. Because little is known about the
regulation of cnidocyte development outside of the
Hydrozoa, this approach will necessarily require extensive screening of transcription factors expressed in the
tissues of interest. Fortunately, the presence/absence of
cnidocytes is easy to assay (even when using only light
microscopy) thereby providing for a simple and unambiguous means for assessing initial effects of targetgene knockdown.
Although it is now technically and financially feasible to collect transcriptome data from numerous
samples across several treatments (indeed, even
from individual cells) (Hemmrich et al. 2012),
many challenges to the analysis of this type of data
still exist (for recent reviews, see McGettigan 2013;
Sims et al. 2014). Importantly, identifying a reasonable set of target genes to pursue in downstream
applications (e.g., knockdown/knockout experiments,
directed sequencing, or qPCR) can be a formidable
challenge. Many studies seek to identify suites of
target genes by identifying transcriptome-level differences in gene expression, but RNAseq datasets are
inherently noisy (Marinov et al. 2013; McDavid
et al. 2013; Wills et al. 2013) which can result in
increased detection of both false-positives and falsenegatives. Fortunately, many analytical approaches
have been developed to combat these challenges (Li
and Dewey 2011; Tarazona et al. 2011; McDavid
et al. 2013; Wagner et al. 2013), thereby facilitating
the application of large-scale sequencing data to a
720
diverse array of experimental conditions and across
diverse and divergent taxa.
Conclusions/Future directions
The mechanism underlying the evolution of novel
traits continues to garner interest across diverse
disciplines, and cnidocytes may make a particularly
useful model for studies of this type. Recent studies
revealing the diversity of minicollagen genes and
their non-overlapping involvement in cnidocyst development undoubtedly will inspire many future
studies aimed at understanding how the many
unique cnidocyst morphologies arose and we
hope these studies will inspire further investigations
into cnidocyte differentiation as well. Importantly,
the apparent diversity in the regulation of cnidocyte differentiation from a proliferative precursor
suggests that while cnidocytes themselves are
unique to, and ubiquitous within, the Cnidaria,
they may not be patterned the same way across
taxa. Considering that cnidocyte diversity in hydrozoan taxa exceeds that of anthozoans, it is tempting to hypothesize that the hydrozoan cnidocyte
program evolved from an ancestral GRN that
may still be represented in anthozoan taxa.
Indeed, the lack of apparent conservation between
the cnidocyte GRN in Hydra and the few other
cnidarians that are beginning to be examined suggests the process by which cnidocyte differentiation
occurs may be just as diverse as the cnidocysts
themselves. Evaluating the validity of this hypothesis awaits more extensive studies of cnidocyte differentiation in diverse cnidarian taxa and across
multiple life stages and we suggest that studies of
this type will be well-served to employ tissue-specific transcriptomic analyses, as discussed. Future
studies of cnidocyte development across cnidarian
taxa may indeed reveal the ancestral mechanisms
by which progenitor cells evolved and will further
shed light on the evolution of novel traits.
Acknowledgments
This manuscript was submitted as part of a symposium at the 2014 meeting of the Society for
Integrative and Comparative Biology (SICB).
Support for this symposium was provided by the
Society for Developmental Biology and SICB (to
the organizers).
Funding
Funding for this manuscript was provided by the
National Aeronautics and Space Administration
(to M.Q.M.).
L. S. Babonis and M. Q. Martindale
References
Adamczyk P, Zenkert C, Balasubramanian PG, Yamada S,
Murakoshi S, Sugahara K, Hwang JS, Gojobori T,
Holstein TW, Ozbek S. 2010. A non-sulfated chondroitin
stabilizes membrane tubulation in cnidarian organelles.
J Biol Chem 285:25613–23.
Barshis DJ, Ladner JT, Oliver TA, Seneca FO, TraylorKnowles N, Palumbi SR. 2013. Genomic basis for coral
resilience to climate change. Proc Natl Acad Sci USA
110:1387–92.
Brown CT, Scott C, Sheneman L. 2013. The Eel Pond
mRNAseq Protocol. https://khmer-protocols.readthedocs.
org/en/latest/mrnaseq/index.html.
Darling JA, Reitzel AR, Burton PM, Mazza ME, Ryan JF,
Sullivan JC, Finnerty JR. 2005. Rising starlet: the starlet
sea anemone, Nematostella vectensis. Bioessays 27:211–21.
David CN. 2012. Interstitial stem cells in Hydra: multipotency
and decision-making. Int J Dev Biol 56:489–97.
Denker E, Bapteste E, Le Guyader H, Manuel M, Rabet N.
2008a. Horizontal gene transfer and the evolution of cnidarian stinging cells. Curr Biol 18:R858–9.
Denker E, Manuel M, Leclere L, Le Guyader H, Rabet N.
2008b. Ordered progression of nematogenesis from stem
cells through differentiation stages in the tentacle bulb of
Clytia hemisphaerica (Hydrozoa, Cnidaria). Dev Biol
315:99–113.
Dresch JM, Thompson MA, Arnosti DN, Chiu CC. 2013.
Two-layer mathematical modeling of gene expression: incorporating DNA-level information and system dynamics.
SIAM J Appl Math 73:804–26.
Engel U, Oezbek S, Engel R, Petri B, Lottspeich F,
Holstein TW. 2002. NOWA, a novel protein with minicollagen Cys-rich domains, is involved in nematocyst formation in Hydra. J Cell Sci 115:3923–34.
Extavour CG, Pang K, Matus DQ, Martindale MQ. 2005. vasa
and nanos expression patterns in a sea anemone and the
evolution of bilaterian germ cell specification mechanisms.
Evol Dev 7:201–15.
Fritz AE, Ikmi A, Seidel C, Paulson A, Gibson MC. 2013.
Mechanisms of tentacle morphogenesis in the sea anemone
Nematostella vectensis. Development 140:2212–23.
Galliot B. 2012. Hydra, a fruitful model system for 270 years.
Int J Dev Biol 56:411–23.
Galliot B, Quiquand M. 2011. A two-step process in the
emergence of neurogenesis. Eur J Neurosci 34:847–62.
Genikhovich G, Technau U. 2011. Complex functions of Mef2
splice variants in the differentiation of endoderm and of a
neuronal cell type in a sea anemone. Development
138:4911–9.
Gold DA, Jacobs DK. 2013. Stem cell dynamics in Cnidaria:
are there unifying principles? Dev Genes Evol 223:53–66.
Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA,
Amit I, Adiconis X, Fan L, Raychowdhury R, Zeng QD,
et al. 2011. Full-length transcriptome assembly from
RNA-Seq data without a reference genome. Nat
Biotechnol 29:644–52.
Grens A, Mason E, Marsh JL, Bode HR. 1995. Evolutionary
conservation of a cell fate specification gene: the Hydra
achaete-scute homolog has proneural activity in
Drosophila. Development 121:4027–35.
Cnidocytes model novelty
Hall BK, Kerney R. 2012. Levels of biological organization
and the origin of novelty. J Exp Zool Part B
318B:428–37.
Hand C, Uhlinger KR. 1992. The culture, sexual and asexual
reproduction, and growth of the sea anemone Nematostella
vectensis. Biol Bull 182:169–76.
Helm RR, Siebert S, Tulin S, Smith J, Dunn CW. 2013.
Characterization of differential transcript abundance
through time during Nematostella vectensis development.
BMC Genomics 14:266–75.
Hemmrich G, Khalturin K, Boehm AM, Puchert M, AntonErxleben F, Wittlieb J, Klostermeier UC, Rosenstiel P,
Oberg HH, Domazet-Loso T, et al. 2012. Molecular signatures of the three stem cell lineages in hydra and the emergence of stem cell function at the base of multicellularity.
Mol Biol Evol 29:3267–80.
Hoekstra HE, Coyne JA. 2007. The locus of evolution: evo
devo and the genetics of adaptation. Evolution
61:995–1016.
Holstein T, Tardent P. 1984. An ultra high speed analysis of
exocytosis—nematocyst discharge. Science 223:830–3.
Hroudova M, Vojta P, Strnad H, Krejcik Z, Ridl J, Paces J,
Vlcek C, Paces V. 2012. Diversity, phylogeny and expression patterns of pou and six homeodomain transcription
factors in hydrozoan jellyfish Craspedacusta sowerbyi. Plos
One 7:e36420.
Hwang JS, Ohyanagi H, Hayakawa S, Osato N, NishimiyaFujisawa C, Ikeo K, David CN, Fujisawa T, Gojobori T.
2007. The evolutionary emergence of cell type-specific
genes inferred from the gene expression analysis of
Hydra. Proc Natl Acad Sci USA 104:14735–40.
Johnson BR, Tsutsui ND. 2011. Taxonomically restricted
genes are associated with the evolution of sociality in
the honey bee. BMC Genomics 12:164–73.
Khalturin K, Hemmrich G, Fraune S, Augustin R,
Bosch TCG. 2009. More than just orphans: are taxonomically-restricted genes important in evolution? Trends Genet
25:404–13.
Koch AW, Holstein TW, Mala C, Kurz E, Engel J, David CN.
1998. Spinalin, a new glycine- and histidine-rich protein in
spines of Hydra nematocysts. J Cell Sci 111:1545–54.
Kurz EM, Holstein TW, Petri BM, Engel J, David CN. 1991.
Mini-collagens in Hydra nematocytes. J Cell Biol
115:1159–69.
Layden MJ, Boekhout M, Martindale MQ. 2012. Nematostella
vectensis achaete-scute homolog NvashA regulates embryonic ectodermal neurogenesis and represents an ancient
component of the metazoan neural specification pathway.
Development 139:1013–22.
Layden MJ, Rottinger E, Wolenski FS, Gilmore TD,
Martindale MQ. 2013. Microinjection of mRNA or
morpholinos for reverse genetic analysis in the starlet sea anemone, Nematostella vectensis. Nat Protoc
8:924–34.
Lehnert EM, Burriesci MS, Pringle JR. 2012. Developing the
anemone Aiptasia as a tractable model for cnidariandinoflagellate symbiosis: the transcriptome of aposymbiotic
A. pallida. BMC Genomics 13:271–80.
Li B, Dewey CN. 2011. RSEM: accurate transcript quantification from RNA-Seq data with or without a reference
genome. BMC Bioinformatics 12:323–38.
721
Lobo D, Vico FJ. 2010. Evolution of form and function in a
model of differentiated multicellular organisms with gene
regulatory networks. Biosystems 102:112–23.
Marinov GK, Williams BA, McCue K, Schroth GP, Gertz J,
Myers RM, Wold BJ. 2013. From single-cell to cell-pool
transcriptomes: stochasticity in gene expression and RNA
splicing. Genome Res. 24:496–510.
Martin-Duran JM, Monjo F, Romero R. 2012. Morphological
and molecular development of the eyes during embryogenesis of the freshwater planarian Schmidtea polychroa. Dev
Genes Evol 222:45–54.
McDavid A, Finak G, Chattopadyay PK, Dominguez M,
Lamoreaux L, Ma SS, Roederer M, Gottardo R. 2013.
Data exploration, quality control and testing in single-cell
qPCR-based gene expression experiments. Bioinformatics
29:461–7.
McGettigan PA. 2013. Transcriptomics in the RNA-seq era.
Curr Opin Chem Biol 17:4–11.
Mehr SFP, DeSalle R, Kao HT, Narechania A, Han Z,
Tchernov D, Pieribone V, Gruber DF. 2013.
Transcriptome deep-sequencing and clustering of expressed
isoforms from Favia corals. BMC Genomics 14:546–58.
Milde S, Hemmrich G, Anton-Erxleben F, Khalturin K,
Wittlieb J, Bosch TCG. 2009. Characterization of taxonomically restricted genes in a phylum-restricted cell type.
Genome Biol 10:R8–R8.16.
Moran Y, Praher D, Schlesinger A, Ayalon A, Tal Y,
Technau U. 2013. Analysis of soluble protein contents
from the nematocysts of a model sea anemone sheds light
on venom evolution. Mar Biotechnol 15:329–39.
Moya A, Huisman L, Ball EE, Hayward DC, Grasso LC,
Chua CM, Woo HN, Gattuso JP, Foret S, Miller DJ.
2012. Whole transcriptome analysis of the coral Acropora
millepora reveals complex responses to CO2-driven acidification during the initiation of calcification. Mol Ecol
21:2440–54.
Nakanishi N, Renfer E, Technau U, Rentzsch F. 2012.
Nervous systems of the sea anemone Nematostella vectensis
are generated by ectoderm and endoderm and shaped by
distinct mechanisms. Development 139:347–57.
Oakley TH. 2007. Today’s multiple choice exam: (a)
gene duplication; (b) structural mutation; (c) co-option;
(d) regulatory mutation; (e) all of the above. Evol Dev
9:523–4.
Ostman C. 2000. A guideline to nematocyst nomenclature
and classification, and some notes on the systematic value
of nematocysts. Sci Mar 64:31–46.
Ozbek S. 2011. The cnidarian nematocyst: a miniature extracellular matrix within a secretory vesicle. Protoplasma
248:635–40.
Ozbek S, Balasubramanian PG, Holstein TW. 2009. Cnidocyst
structure and the biomechanics of discharge. Toxicon
54:1038–45.
Pantin CFA. 1942. Excitation of nematocysts. Nature
149:109–109.
Peterson T, Muller GB. 2013. What is evolutionary novelty?
Process versus character based definitions. J Exp Zool Part
B 320:345–50.
Plickert G, Frank U, Muller WA. 2012. Hydractinia, a pioneering model for stem cell biology and reprogramming
somatic cells to pluripotency. Int J Dev Biol 56:519–34.
722
Polato NR, Vera JC, Baums IB. 2011. Gene discovery in the
threatened elkhorn coral: 454 sequencing of the Acropora
palmata transcriptome. PLoS One 6:e28634.
Renfer E, Amon-Hassenzahl A, Steinmetz PRH, Technau U.
2010. A muscle-specific transgenic reporter line of the sea
anemone, Nematostella vectensis. Proc Natl Acad Sci USA
107:104–8.
Robertson G, Schein J, Chiu R, Corbett R, Field M,
Jackman SD, Mungall K, Lee S, Okada HM, Qian JQ,
et al. 2010. De novo assembly and analysis of RNA-seq
data. Nat Methods 7:909–12.
Rottinger E, Dahlin P, Martindale MQ. 2012. A framework
for the establishment of a cnidarian gene regulatory network for ‘‘endomesoderm’’ specification: the inputs of
beta-catenin/TCF signaling. PLoS Genet 8:e1003164.
Ryan JF, Pang K, Schnitzler CE, Nguyen AD, Moreland RT,
Simmons DK, Koch BJ, Francis WR, Havlak P, Smith SA,
et al. 2013. The genome of the ctenophore Mnemiopsis
leidyi and its implications for cell type evolution. Science
342:1336.
Schulz MH, Zerbino DR, Vingron M, Birney E. 2012. Oases:
robust de novo RNA-seq assembly across the dynamic
range of expression levels. Bioinformatics 28:1086–92.
Shaoul E, Ayalon A, Tal Y, Lotan T. 2012. Transdermal delivery of scopolamine by natural submicron injectors:
in vivo study in pig. PLoS One 7:e31922.
Shinzato C, Inoue M, Kusakabe M. 2014. A snapshot of a
coral ‘‘holobiont’’: a transcriptome assembly of the scleractinian coral, Porites, captures a wide variety of genes from
both the host and symbiotic zooxanthellae. PLoS One
9:e85182.
Shostak S. 1993. A symbiogenetic theory for the origins of
cnidocysts in cnidaria. Biosystems 29:49–58.
Shubin N, Tabin C, Carroll S. 1997. Fossils, genes and the
evolution of animal limbs. Nature 388:639–48.
Shubin N, Tabin C, Carroll S. 2009. Deep homology and the
origins of evolutionary novelty. Nature 457:818–23.
Siebert S, Robinson MD, Tintori SC, Goetz F, Helm RR,
Smith SA, Shaner N, Haddock SHD, Dunn CW. 2011.
Differential gene expression in the siphonophore Nanomia
bijuga (Cnidaria) assessed with multiple next-generation sequencing workflows. PLoS One 6:e22953.
Sims D, Sudbery I, Ilott NE, Heger A, Ponting CP. 2014.
Sequencing depth and coverage: key considerations in genomic analyses. Nat Rev Genet 15:121–32.
Steele RE, David CN, Technau U. 2011. A genomic view of
500 million years of cnidarian evolution. Trends Genet
27:7–13.
Tarazona S, Garcia-Alcalde F, Dopazo J, Ferrer A, Conesa A.
2011. Differential expression in RNA-seq: a matter of
depth. Genome Res 21:2213–23.
Technau U, Rudd S, Maxwell P, Gordon P, Saina M, Grasso L,
Hayward D, Sensen C, Saint R, Holstein T. 2005.
Maintenance of ancestral complexity and non-metazoan
genes in two basal cnidarians. Trends Genet 21:633–9.
Traylor-Knowles N, Granger BR, Lubinski TJ, Parikh JR,
Garamszegi S, Xia Y, Marto JA, Kaufman L, Finnerty JR.
L. S. Babonis and M. Q. Martindale
2011. Production of a reference transcriptome and transcriptomic database (PocilloporaBase) for the cauliflower
coral, Pocillopora damicornis. BMC Genomics 12:585–95.
Tulin S, Aguiar D, Istrail S, Smith J. 2013. A quantitative
reference transcriptome for Nematostella vectensis early embryonic development: a pipeline for de novo assembly in
emerging model systems. EvoDevo 4:16–30.
Wagner GP, Kin K, Lynch VJ. 2013. A model based criterion
for gene expression calls using RNA-seq data. Theor Biosci
132:159–64.
Wagner GP, Lynch VJ. 2010. Evolutionary novelties. Curr Biol
20:R48–52.
Wenger Y, Galliot B. 2013. RNAseq versus genome-predicted
transcriptomes: a large population of novel transcripts
identified in an Illumina-454 Hydra transcriptome. BMC
Genomics 14:204.
Weston AJ, Chung R, Dunlap WC, Morandini AC,
Marques AC, Moura-da-Silva AM, Ward M, Padilla G, da
Silva LF, Andreakis N, et al. 2013. Proteomic characterisation of toxins isolated from nematocysts of the South
Atlantic jellyfish Olindias sambaquiensis. Toxicon 71:11–7.
Williams RB. 1975. Redescription of brackish water sea anemone Nematostella vectensis Stephenson, with an appraisal of
congeneric species. J Nat Hist 9:51–64.
Williams RB. 1979. Studies on the nematosomes of
Nematostella vectensis Stephenson (Coelenterata Actiniaria).
J Nat Hist 13:69–80.
Wills QF, Livak KJ, Tipping AJ, Enver T, Goldson AJ,
Sexton DW, Holmes C. 2013. Single-cell gene expression
analysis reveals genetic associations masked in whole-tissue
experiments. Nat Biotechnol 31:748.
Wittlieb J, Khalturin K, Lohmann JU, Anton-Erxleben F,
Bosch TCG. 2006. Transgenic Hydra allow in vivo tracking
of individual stem cells during morphogenesis. Proc Natl
Acad Sci USA 103:6208–11.
Wolenski FS, Bradham CA, Finnerty JR, Gilmore TD. 2013.
NF-kappa B is required for cnidocyte development in the
sea anemone Nematostella vectensis. Dev Biol 373:205–15.
Wray GA. 2007. The evolutionary significance of cis-regulatory mutations. Nat Rev Genet 8:206–16.
Yamada S, Morirnoto H, Fujisawa T, Sugahara K. 2007.
Glycosaminoglycans in Hydra magnipapillata (Hydrozoa,
Cnidaria): demonstration of chondroitin in the developing nematocyst, the sting organelle, and structural characterization of glycosaminoglycans. Glycobiology 17:
886–94.
Zárate-Potes A, Cadavid LF. 2014. Transcriptomics of the
immune system of hydrozoan Hydractinia symbiolongicarpus using high throughput sequencing methods.
In: Castillo LF, Cristancho M, Isaza G, Pinzón A,
Rodrı́guez JMC, editors. Advances in computational biology. Switzerland: Springer International Publishing.
p. 239–45.
Zenkert C, Takahashi T, Diesner MO, Ozbek S. 2011.
Morphological and molecular analysis of the Nematostella
vectensis cnidom. PLoS One 6:e22725.