INTEGR. COMP. BIOL., 45:639–648 (2005)
Genomics of Basal Metazoans1
ROBERT E. STEELE2
Department of Biological Chemistry and the Developmental Biology Center, University of California, Irvine, California 92697-1700
SYNOPSIS.
An in-depth understanding of the biology of animals will require the generation of genomics
resources from organisms from all phyla in the metazoan phylogenetic tree. Such resources will ideally
include complete genome sequences and comprehensive EST (expressed sequence tag) datasets for each
species of interest. Of particular interest in this regard are animals in the early diverging non-bilaterian
phyla Porifera, Placozoa, Cnidaria, and Ctenophora. Publications describing the results from the use of
genomics approaches in these phyla have only recently begun to appear (Kortschak et al., 2003; Yang et al.,
2003; Steele et al., 2004). Issues to be considered here include choosing the basal metazoan species to examine
with genomics approaches, the relative advantages and disadvantages of genome sequencing versus EST
projects, and the resources and infrastructure required to carry out such projects successfully.
WHAT CAN ONE EXPECT TO LEARN BY DOING
GENOMICS ON BASAL METAZOANS?
Before discussing the issues associated with pursuing genomic studies on basal metazoans, it is important
to consider what one can expect to learn from such
studies. If the whole genome of an organism is sequenced, one obviously expects ultimately to end up
with a catalog of all of the genes for that organism.
The value of such a catalog is substantial. It allows
one to evaluate critically a number of interesting hypotheses related to evolutionary, physiological, and
developmental processes. For example the absence of
a gene from a cnidarian genome but its presence in
bilaterian genomes could indicate that the gene
evolved after the divergence of cnidarians. Alternatively, the gene could have been secondarily lost from
cnidarians. To determine which hypothesis is correct
one would then need to have information on this gene
from other taxa, particularly ones which diverged prior
to cnidarians. If, for example, sponges were found to
have the gene, then one would conclude that secondary loss explains its absence from cnidarians.
Secondary loss is not as rare as might be expected.
Kortschak et al. (2003) have provided a preliminary
sampling of the genes in the coral Acropora millepora
using an expressed sequence tag dataset of 1,376 clusters and found that 53 of the clusters represented genes
that are present in vertebrates but absent from Drosophila and Caenorhabditis elegans. A number of additional cases have been found in which a gene is present in a cnidarian and in deuterostomes, but absent
from the protostomes Drosophila and/or C. elegans
(Chan et al., 1994; Steele et al., 1999; Fedders et al.,
2004). Thus these genes were apparently lost secondarily from these protostomes. In essence, then, evolution has carried out gene knockout experiments in
worms and flies that indicate that these genes are not
required for at least some types of metazoans to survive in their natural environments. This gets around
the problem with a number of gene knockout studies
in mice, in which absence of an observable phenotype
may be due either to compensation by paralogous
genes or the failure of the laboratory to duplicate the
animal’s natural environment.
Of particular interest would be genes that are absent
from all basal metazoans but present in bilaterians.
These would presumably represent genes that were selected for their role in a bilaterian-specific biological
process. Proof of such genes would require complete
genome sequences of representatives from each of the
basal metazoan phyla. Of equal interest to biologists
would be genes found only in one or more basal metazoan taxa. These genes would be candidates for involvement in taxon-specific biological processes. Examples of such genes would include those encoding
proteins involved in taxon-specific signaling processes
(e.g., those involved in reproduction), genes involved
in taxon-specific defense against pathogens, genes involved in production of taxon-specific structures (e.g.,
the nematocysts of cnidarians), and genes involved in
taxon-specific symbioses (e.g., coral/algal symbiosis).
Having genome sequences from sponges and cnidarians in particular will potentially have far-reaching impacts on fields as diverse as ecology and medicine. For
example, our understanding of the phenomenon of coral bleaching (Hughes et al., 2003; Pandolfi et al.,
2003) might be enhanced by knowledge of a cnidarian
gene set. Our understanding of the synthesis and biological roles of the large number of natural products,
some of biomedical relevance, identified in marine cnidarians and sponges (Fingerman and Nagabhushanam,
2001) might also be enhanced by having in hand the
sequences of all of the proteins from such organisms,
presumably including the enzymes responsible for synthesis of such products.
1 From the Symposium Model Systems for the Basal Metazoans:
Cnidarians, Ctenophores, and Placozoans presented at the Annual
Meeting of the Society for Integrative and Comparative Biology, 5–
9 January 2004, at New Orleans, Louisiana.
2 E-mail: [email protected]
GENOME SEQUENCING VERSUS ESTS
If one wants to make unequivocal statements about
the gene content of an organism, a complete, fully annotated genome sequence is the only acceptable data639
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ROBERT E. STEELE
TABLE 1.
Genome Sequencing Projects.
Advantages
Sequences of all genes are obtained if a finished sequence is produced.
Sequences of potential transcriptional regulatory regions are obtained.
Genome organization information is obtained.
Disadvantages
Expensive, particularly if done to finished quality.
Draft quality sequence will lack genes.
A large genome size can make sequencing prohibitively expensive.
Difficulty in demonstrating biomedical relevance may affect priority.
EST Projects
Advantages
Potentially less expensive than a genome sequence.
Gene identification is easier due to absence of introns.
Small-scale EST projects don’t require the involvement of a large sequencing center.
Disadvantages
Higher sequencing error rate than for genome sequencing.
Multiple cDNA libraries and/or various technical procedures (e.g., normalization) needed to ensure that one achieves good coverage of the
gene set.
Yields only partial sequences for cDNAs less than about 1,000 base pairs (assuming both ends of a cDNA clone are sequenced).
Don’t get genome organization information.
Don’t get transcriptional regulatory sequences.
Don’t get all of the genes in the organism.
set. An alternative approach to obtain information
about the gene set of an organism is to generate an
EST dataset. ESTs are produced by single pass sequencing from one or both ends of randomly selected
clones from a cDNA library (Adams et al., 1992). The
presence of a gene in an organism is confirmed if an
EST for it is identified even in the absence of a complete genome sequence. However, the absence of a
gene can be demonstrated only if the whole genome
has been sequenced. Given this requirement, a complete genome sequence from each of the basal metazoan phyla is an obvious goal. In addition, complete
genome sequences allow one to ask a variety of important questions related to evolution of genome organization and gene regulation. Some of the advantages and disadvantages of genome projects and EST projects are listed in Table 1.
Despite their incompleteness, EST datasets are powerful resources that allow one to pursue a variety of
interesting questions. In basal metazoans, with their
relatively simple cell compositions and life cycles, one
has a chance of achieving close to saturation coverage
of the gene set with an EST project of sufficiently
large size and thus a reasonable approximation of a
genome sequence with regard to gene content, a socalled ‘‘poor man’s genome’’ (Rudd, 2003). For bilaterians this would require very large EST datasets
from a variety of developmental stages and from as
many adult tissues and organs as possible. Thus EST
projects with basal metazoans can have significant advantages over those done with bilaterians. Obviously
the best situation would be to have a complete genome
sequence and a near-saturation EST dataset from a given organism since an EST dataset is an essential tool
for gene prediction and high quality annotation of a
genomic sequence (Clark et al., 2003; Poustka et al.,
2003). Automated computational methods for gene
prediction have their value (Mathe et al., 2002), but
comparison between the genome sequence and a large
EST dataset is the only sure way to confirm that one
has correctly identified protein-coding genes.
BOTH GENOME AND EST PROJECTS GENERATE
VALUABLE RESOURCES IN ADDITION TO THE
SEQUENCES THEMSELVES
While the sequences are the goal of genome and
EST projects, valuable research resources are generated as a product of such projects. These include libraries containing large pieces of genomic DNA—bacterial artificial chromosome (BAC) (Shizuya et al.,
1992) and fosmid libraries (Kim et al., 1992). Such
libraries provide material for doing transgenic experiments (promoters for driving expression of cloned
genes introduced into embryos and adult tissues).
cDNA clones identified by EST projects can provide
reagents for examining gene expression via high
throughput in situ hybridization studies (Pollet and
Niehrs, 2001), protein interactions via yeast two-hybrid assays (Li et al., 2004; Formstecher et al., 2005),
antibody generation by immunization with proteins expressed in bacteria (Baneyx, 1999), and production of
proteins for structural studies (Finley et al., 2004).
WHERE DO WE STAND CURRENTLY WITH REGARD TO
GENOMICS FOR THE VARIOUS BASAL METAZOAN TAXA?
Genomics studies of basal metazoans are underway,
but are still in the very early stages compared to such
studies in model bilaterian systems. Below I review
the current status of genomics efforts with basal metazoans.
GENOMICS
OF
Porifera
Genomic studies in sponges are of critical importance if we hope to understand the evolution of metazoans. Molecular biological studies with sponges have
been carried out by only a small number of groups,
and the number of sequences for protein-encoding
genes from sponges in the public databases is relatively small (569 at the time of writing). This compares with 2,716 such sequences for cnidarians, plus
about 150,000 more from the Hydra EST project
(www.hydrabase.org). An NSF-funded project to produce a BAC library from the sponge Callyspongia diffusa is underway (http://www.nsf.gov/bio/pubs/
awards/bachome.htm). This will be the first reported
BAC library from a sponge. Although there are no
entries for sponges in the EST database at GenBank
(dbEST), an EST project is being carried out on the
demosponge Suberites domuncula (Cetkovic et al.,
2004; Chevreux et al., 2004). At present these sequences can only be searched using a database that
requires registration (http://spongebase.genoserv.de/).
A recent exciting development in the area of sponge
genomics is the initiation of a sponge genome project
by the U.S. Department of Energy’s Joint Genome Institute (JGI) (http://www.jgi.doe.gov/sequencing/why/
CSP2005/reniera.html). The goal of this project is to
sequence the genome of the demosponge Reniera.
Reniera larvae will be used as the source of DNA for
this project (Leys et al., 2005) to avoid the presence
of DNA from contaminating organisms which have
plagued the characterization of sponge DNA (Costantini, 2004). Ultimately one sponge genome will not
suffice. The phylum Porifera is believed to be paraphyletic (Borchiellini et al., 2001). Thus a true understanding of this phylum from a genomic perspective
will require additional genome sequences.
Placozoa
The phylum Placozoa, with its single described species Trichoplax adhaerens, is of great interest to students of metazoan evolution because of its simple
composition (Miller and Ball, 2005) and its resistance
to secure placement within the metazoan tree (Wainright et al., 1993; Cavalier-Smith, 1998; Collins, 1998;
Brooke and Holland, 2003; Cavalier-Smith and Chao,
2003; Ender and Schierwater, 2003; Martinelli and
Spring, 2003). Placozoa has been placed in virtually
all possible positions among the basal metazoans. It
has been suggested to be a distinct phylum or to represent a secondarily reduced cnidarian. Attempts to resolve its relationship to other basal metazoans have so
far focused on comparisons based on rRNA and a
handful of protein coding genes (Schierwater and
Kuhn, 1998; Martinelli and Spring, 2003).
Until recently, it was assumed that Trichoplax adhaerens was the only known species in the phylum
Placozoa. A recent study of nuclear and mitochondrial
rDNA sequences from placozoans collected from diverse locations indicates that the genus Trichoplax
BASAL METAZOANS
641
contains multiple species (Voigt et al., 2004). The evolutionary history of placozoans is clearly more complicated than would have been guessed.
A proposal to sequence the Trichoplax genome was
submitted to the National Human Genome Research
Institute (NHGRI) in 2002 and received a moderate
priority ranking, but sequencing was not initiated. Subsequently a proposal was submitted through the Community Sequencing Program at JGI and was approved
(http://www.jgi.doe.gov/sequencing/why/CSP2005/
trichoplax.html). The small size of the Trichoplax genome, about 50 megabases (Grell and Ruthmann,
1991), means that a complete sequence of this genome
will be very easy to achieve. It will be very interesting
to see what the genome sequence has to tell us about
the evolution of this strange little creature.
Cnidaria
Cnidarians are unquestionably currently at the forefront with regard to genomics approaches using basal
metazoans. A large-scale Hydra EST project is underway in the United States and a smaller scale one has
recently been completed at the National Institute of
Genetics in Japan. Data from both projects have been
deposited in the public databases. As discussed above,
an analysis of a small-scale EST dataset from the coral
Acropora millepora has recently been published (Kortschak et al., 2003), and this study has received considerable attention (Dennis, 2003; Campbell, 2004;
Raible and Arendt, 2004) because of its unexpected
findings regarding gene loss in Drosophila and C. elegans. An arrayed BAC library from the starlet sea
anemone Nematostella vectensis has been completed
(http://www.nsf.gov/bio/pubs/awards/bachome.htm)
and is available to interested researchers from Children’s Hospital Oakland Research Institute (CHORI,
http://bacpac.chori.org/library.php?id5219). A largescale Nematostella EST project is in progress (U.
Technau and T. Holstein, personal communication).
Nematostella was chosen for construction of the first
cnidarian BAC library for several reasons, one of
which was concern about insert instability with the
more A1T-rich genomes of hydrozoans (e.g., 71%
A1T in Hydra). This concern arose as a result of the
severe insert instability problem encountered when attempts were made to produce BAC libraries from Dictyostelium discoideum (78% A1T) and Plasmodium
falciparum (82% A1T). Despite this concern, the
Bosch lab (University of Kiel, Germany) attempted to
construct a Hydra BAC library. They have succeeded
in producing a library with 23 coverage and an average insert size of 150 kb. A BAC library has also
been constructed from the colonial hydrozoan Hydractinia symbiolongicarpus with 133 coverage and an average insert size of 132 kb (Luis Cadavid, U. of New
Mexico, personal communication). Thus it now appears that the point at which base composition creates
a significant problem for BAC insert stability lies
somewhere in the narrow window between 71% and
78% A1T. Undoubtedly there will be segments of hy-
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ROBERT E. STEELE
drozoan genomes which will be unstable in BACs due
to high local A1T content, but the discovery that it is
possible to make BAC libraries from this class of cnidarians is an important step forward.
Without a doubt, the most exciting development in
regard to basal metazoan genomics was the decision
by JGI to sequence the Nematostella genome. At the
time of this writing, the sequencing part of the project
is nearly completed and assembly and annotation will
begin soon. Nematostella will be the first basal metazoan to have its genome sequenced. The Nematostella
genome project has been followed unexpectedly quickly by a project to sequence the genome of Hydra magnipapillata, the species being used for the Hydra EST
Project. The Hydra Genome Project is being funded
by NHGRI and is being carried out by the J. Craig
Venter Institute. This project is targeted for completion
by the end of 2005. Coverage has already reached
about 13, with a goal of 83 coverage. As they are
generated, the sequences are made available on the
Trace Archive at NCBI (http://www.ncbi.nlm.nih.gov/
Traces/trace.cgi?).
Ctenophora
The ctenophores have so far seen the least effort
with regard to genomics. Only 38 sequences from protein-encoding genes have been deposited in GenBank
(27 from Beroe, 6 from Pleurobrachia, and 5 from
Mnemiopsis). Only 75 ctenophore references are found
in PubMed, covering a period of 51 years. This lack
of attention relative to other basal metazoans is unfortunate since the relationship of ctenophores to other
phyla is still unclear (Medina et al., 2001; Martindale
et al., 2002; Rokas et al., 2003) and its resolution is
critical to understanding metazoan evolution. Genomics efforts with this phylum would undoubtedly contribute importantly to this. Concerted efforts to clone
homeobox genes of the Hox/Parahox class from ctenophores have been unsuccessful (Mark Martindale, personal communication), suggesting the intriguing possibility that ctenophores lack Hox/Parahox genes. A
ctenophore genome sequence would be the definitive
test of this hypothesis. Ongoing developmental studies
with ctenophores (Martindale, 1986; Martindale and
Henry, 1997; Martindale and Henry, 1999; Henry and
Martindale, 2000; Henry and Martindale, 2001; Yamada and Martindale, 2002) will provide an important
foundation for molecular studies arising out of genomics efforts with this phylum.
An important need with regard to ctenophore genomics initiatives is an organized scientific constituency
which will lobby for them. A positive sign for such
efforts is the fact that the ctenophore Mnemiopsis leidyi
was one of the animals selected for BAC library construction by the National Science Foundation (http://
www.nsf.gov/bio/pubs/awards/bachome.htm). The
haploid genome size for Mnemiopsis leidyi has been
reported to be 3 3 108 base pairs (http://www.
genomesize.com/ctenophora.htm). This is about twice
the size of the Drosophila genome and thus well within the reasonable size range for sequencing.
Choanoflagellates–not metazoans, but close
Genomic investigations of the basal metazoan phyla
will tell us a lot about the evolution of animals. However, to complete the story it will be important to have
information on non-metazoan phyla whose divergence
immediately antedates the origin of metazoans. Studies
of the morphology of choanoflagellates in the 1800s
noted the similarity of the their cells to the choanocytes of sponges (Saville-Kent, 1880–82), particularly
with regard to the collar which surrounds the flagellum. This shared morphological trait suggested that
sponges may have derived from a choanoflagellate ancestor and that modern choanoflagellates constitute a
sister taxon to Metazoa. Molecular phylogenetic studies have provided strong support for such a relationship (reviewed in King, 2004). EST projects using two
choanoflagellates (Monosiga brevicollis and Proterospongia sp.) have led to the surprising finding that
choanoflagellates contain genes for a variety of signaling molecules that were thought to be restricted to
metazoans (King and Carroll, 2001; King et al., 2003).
These results make it clear that choanoflagellate genome sequences will be essential in understanding the
evolution of basal metazoans.
Both the JGI and the NHGRI have committed to
sequencing of choanoflagellate genomes. JGI will sequence the Monosiga brevicollis genome and NHGRI
is funding the sequencing of the Monosiga ovata genome. Comparison of these two genomes to each other
and to those of metazoans is certain to provide important insights into the origins of animals.
BASAL METAZOAN INTO THE
GENOMICS QUEUE
In choosing an organism with which to pursue genomic studies several criteria must be applied. EST
and genome projects are by definition expensive operations. For genome sequencing and generation of
BAC libraries, there are now well-defined routes to
follow. For EST projects, the path is less well-defined.
The NHGRI accepts proposals (called White Papers)
for genome sequencing of organisms for its comparative genomics program. Proposals are reviewed three
times a year. Instructions for submission can be found
at http://www.genome.gov/10002189. Previously submitted proposals which have received either a high or
moderate priority ranking can be examined at http://
www.genome.gov/10002154 and provide excellent
models for preparation of new proposals. Figure 1
shows the points to be addressed in a genome sequencing White Paper submitted to the NHGRI.
As Figure 1 shows, it is important that an organism
being proposed for sequencing satisfy a number of criteria. The size and other basic features of the genome
must be known. It is obviously much easier to make
a case for sequencing if resources such as BAC libraries and/or EST datasets are available or are in the
GETTING
A
GENOMICS
FIG. 1.
OF
BASAL METAZOANS
643
Points to be addressed in a genome sequencing proposal (White Paper) submitted to NHGRI (from http://www.genome.gov/11509736).
process of being generated. And it is critical that the
proposal demonstrate that there is a research community of sufficient size and vigor to make good use of
the genome sequence when it becomes available.
Whole-genome shotgun sequencing requires that the
individual sequence reads be assembled into contigs
and scaffolds. Assembly can be complicated by polymorphism in the DNA used for sequencing, even if
the DNA that is used comes from a single individual
(Dehal et al., 2002). Thus having an inbred line of the
target organism is an obvious plus.
The JGI has recently established a Community Sequencing Program which accepts proposals for sequencing projects from the research community. In-
formation on this program can be found at http://
www.jgi.doe.gov/CSP/index.html. As with the NHGRI
program, the JGI program has a well-defined proposal
submission and review process.
For genome sequencing projects, one provides high
quality DNA to the sequencing center and they construct the clones that are used for sequencing. In the
whole-genome shotgun approach (Adams et al., 2000;
Aparicio et al., 2002; Dehal et al., 2002), the DNA is
mechanically sheared and then cloned into a plasmid
vector. The recombinant plasmids are then end-sequenced. End-sequencing of BAC clones is done to
link the shotgun sequences together.
For EST projects, there is no standard process for
644
ROBERT E. STEELE
project proposals as there is for genome sequencing
projects. cDNA libraries for EST projects can be constructed either by individual investigators or RNA can
be provided to commercial entities for library construction. The bacterial colonies from the resulting library must then be picked and arrayed in microtiter
plates. The clones then have to be sequenced and the
data analyzed. Both non-profit and for-profit entities
can be engaged to do the sequencing.
CONSTRUCTION OF BAC LIBRARIES
BAC libraries are critical for genomics studies (Hoskins et al., 2000; Osoegawa et al., 2000, 2001; McPherson et al., 2001). Given the complexities of making high quality BAC libraries, most laboratories will
not want to tackle this task on their own. It is best to
have such libraries made by one of the four labs that
constitute the BAC Resource Network (http://
www.genome.gov/10001844). They have extensive
experience in making BAC libraries from a wide variety of organisms. The NHGRI has a program for
funding the production of BAC libraries. http://
www.genome.gov/10001845. The NSF recently funded the production of a number of BAC libraries including ones from three basal metazoans—the sponge
Callyspongia diffusa, the ctenophore Mnemiopsis leidyi, and the cnidarian Nematostella vectensis (http://
www.nsf.gov/bio/pubs/awards/bachome.htm). We
should soon have in hand high quality BAC libraries
from representative species of three of the four basal
metazoan phyla. These libraries will all be available to
interested researchers through the BACPAC Resources
Center at CHORI (http://bacpac.chori.org/). Specific
information on how to obtain copies of these libraries
when they are completed is available at http://bacpac.
chori.org/sharingpolicy.htm.
DATA PROCESSING
Securing the money and generating the sequences
are only part of the job associated with a genome or
EST project. Analysis of the data and presentation of
it to the community are next. The centers that carry
out animal genome projects have well-established data
processing pipelines and sequence release policies.
They thus take care of most of the decision-making in
this regard.
The data processing and sequence release aspects of
EST projects are not as standardized as for genome
projects. Much depends on where the sequencing is
done. Some sequencing centers may process the data
relatively extensively and may require that data be released immediately to the public databases (e.g., the
Genome Sequencing Center at Washington University). However, if the EST sequencing is done under a
contract with a commercial entity or at an investigator’s home institution, it will likely be up to the investigator to determine when the data will be made
publicly available. To facilitate deposition of the large
amounts of data typically associated with an EST project, GenBank has developed a streamlined batch sub-
mission process (http://www.ncbi.nlm.nih.gov/dbEST/
howptopsubmit.html) as well as a batch process for updating the records from an EST project once they have
appeared.
There is also the question of what to deposit in the
public databases. Obviously the sequences themselves
will be deposited. It is important that the investigators
do a careful job of removing vector, linker/adaptor, and
poor quality sequences from their datasets before submission. An additional helpful feature is to include the
highest scoring BLASTX hit for each sequence (Gish
and States, 1993). Additional information that is of
value includes a brief description of the methods used
to construct the library. An example of an EST entry
for Hydra magnipapillata is shown in Figure 2. If a
database is created to hold the EST data, the investigators should, as much as possible, use open source
software (http://www.gmod.org/) that has been used
successfully with other gene databases.
The data from EST and genome projects have their
maximum impact when high quality gene predictions
are done and the genes are expertly annotated. In some
ways this is the most difficult part of the project. Automated annotation can be of some help, but such annotations have a significant error rate. The gold standard is manual annotation by expert annotators. This
is obviously both expensive and slow. Alternatives include annotation jamborees and distributed, community annotation. An important aspect of annotation is
the assignment of Gene Ontology (GO) terms (Ashburner et al., 2000), which provide a powerful tool for
organizing and comparing gene data.
REAGENT DISTRIBUTION
As mentioned above, EST and genome projects create valuable reagents which the research community
will undoubtedly want access to. In the case of EST
projects, these would be arrayed cDNA clones. In the
case of genome sequencing projects, they would be
arrayed clones from BAC and fosmid libraries. Thus
an important consideration for such projects is how the
DNA clones will be archived and distributed. Archiving and distribution are expensive (freezers) and laborintensive (someone has to maintain the freezers, do the
record-keeping, and ship the clones). Thus most labs
would not want to do this themselves. Fortunately
there are centers that will archive and distribute arrayed cDNA libraries (e.g., The I.M.A.G.E. Consortium at Lawrence Livermore National Laboratory;
http://image.llnl.gov/). BAC and fosmid libraries may
be archived and distributed by the centers where they
were constructed (e.g., the BACPAC Resources Center
at CHORI). The investigator must anticipate up-front
costs of deposition of clones at a distribution center.
THE NEXT STEP—COMPARATIVE GENOMICS WITHIN
BASAL METAZOAN PHYLA
Based on efforts underway and planned, it seems all
but certain that genome sequences will eventually be
obtained for representative species from each of the
GENOMICS
FIG. 2.
OF
BASAL METAZOANS
An example of a GenBank entry for a sequence from the Hydra EST Project.
645
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ROBERT E. STEELE
FIG. 2.
basal metazoan phyla. Recently, it has become clear
that having genome sequences from several organisms
within a single taxonomic group provides a very powerful means for addressing questions of evolution
(Kellis et al., 2003; Stein et al., 2003). While we are
currently at the stage where getting a single genome
and/or large scale EST project done for each basal
metazoan phylum is the goal, the basal metazoan research community should be thinking ahead and anticipating its needs and interests with regard to genomics initiatives and resources. We should begin lining
up the next wave of organisms, paying particular attention to those which will be of the greatest immediate value for comparative studies. For example one
might want to try to get a representative done from
each of the four (and now possibly five) classes of
cnidarians (Marques and Collins, 2004) before trying
to do more members of a single cnidarian class. Alternatively one might want to concentrate on a single
class so that one can do comparisons between taxa that
are closely related but differ in life cycles. Such a comparison could be done between Hydra, which the lacks
medusa stage of most hydrozoans, and Podocoryne,
which has both medusa and polyp stages (Galliot and
Schmid, 2002).
The time is also ripe for investigators to do genome
size surveys on additional basal metazoan species and
to make attempts to bring new basal metazoan species
into laboratory culture. Such material will provide the
foundation for future genomic studies with basal metazoans.
CONCLUSION
In a period of only 15 years we have gone from the
first publications describing the cloning of protein-encoding genes from basal metazoans (Bosch et al.,
1989; Fisher and Bode, 1989) to having draft sequences of several basal metazoan genomes within reach.
The impact of genomics efforts on our understanding
Continued.
of basal metazoan biology will undoubtedly be great.
It will be particularly important for genomics researchers and organismal biologists to interact frequently and
extensively so that the wealth of information waiting
in the sequences is used as thoroughly and creatively
as possible. Functional tests are beginning to be used
successfully with genes from cnidarians (Lohmann et
al., 1999; Lohmann and Bosch, 2000; Smith et al.,
2000; Böttger et al., 2002; Miljkovic et al., 2002; Cardenas and Salgado, 2003; Jakob et al., 2004) and the
first paper describing a functional test of a gene in
Trichoplax has recently appeared (Wikramanayake et
al., 2003). The maximum benefit will come as functional tests are applied to the many interesting basal
metazoan genes that will become accessible to experimental manipulation from current and future genomics projects.
ACKNOWLEDGMENTS
This paper is dedicated to all the biologists who
have kept the faith and worked so hard to bring basal
metazoans into the genomics era, and to the genomics
researchers who have welcomed us so enthusiastically
into their community. I am grateful for the thoughtful
comments on the manuscript from the associate editor
and the two anonymous reviewers. Work in the author’s lab has been generously supported by the National Science Foundation.
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