Update TRENDS in Genetics Vol.21 No.10 October 2005536

References

1 Marcuello, E. et al. (2004) Single nucleotide polymorphism in the

5 0 tandem repeat sequences of thymidylate synthase gene predicts forresponse to fluorouracil-based chemotherapy in advanced colorectalcancer patients. Int. J. Cancer 112, 733–737

2 Ueda, H. et al. (2003) Association of the T-cell regulatory gene CTLA4with susceptibility to autoimmune disease. Nature 423, 506–511

3 Lazzaro, B.P. et al. (2004) Genetic basis of natural variation inD. melanogaster antibacterial immunity. Science 303, 1873–1876

4 Tournamille, C. et al. (1995) Disruption of a GATA motif in the Duffygene promoter abolishes erythroid gene expression in Duffy-negativeindividuals. Nat. Genet. 10, 224–228

5 Davidson, E.H. (2001)Genomic Regulatory Systems: Development and

Evolution, Academic Press6 Wittkopp, P.J. et al. (2004) Evolutionary changes in cis and trans gene

regulation. Nature 430, 85–887 Knight, J.C. (2005) Regulatory polymorphisms underlying complex

disease traits. J. Mol. Med. 83, 97–109

Corresponding author: Miller, D.J. (david.miller@jcu.edu.au).Available online 11 August 2005

www.sciencedirect.com

8 Carey, M. and Smale, S.T. (2000) Transcriptional Regulation inEukaryotes: Concepts, Strategies and Techniques, Cold Spring HarborLaboratory Press

9 Lee, T.I. et al. (2002) Transcriptional regulatory networks inSaccharomyces cerevisiae. Science 298, 799–804

10 Chin, C.S. et al. (2005) Genome-wide regulatory complexity in yeastpromoters: separation of functionally conserved and neutral sequence.Genome Res. 15, 205–213

11 Keightley, P.D. et al. (2005) Evidence for widespread degradation ofgene control regions in hominid genomes. PLoS Biol. 3, e42

12 Carter, A.J. and Wagner, G.P. (2002) Evolution of functionallyconserved enhancers can be accelerated in large populations:a population-genetic model. Proc Biol Sci 269, 953–960

13 Keightley, P.D. and Johnson, T. (2004) MCALIGN: stochasticalignment of noncoding DNA sequences based on an evolutionarymodel of sequence evolution. Genome Res. 14, 442–450

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doi:10.1016/j.tig.2005.08.001

Cnidarians and ancestral genetic complexity in theanimal kingdom

David J. Miller1, Eldon E. Ball2 and Ulrich Technau3

1Comparative Genomics Centre, Molecular Sciences Building 21, James Cook University, Townsville, Queensland 4811, Australia2Centre for the Molecular Genetics of Development and Molecular Genetics and Evolution Group,

Research School of Biological Sciences, Australian National University, P.O Box 475, Canberra, ACT2601, Australia3Sars International Centre for Marine Molecular Biology, Thormøhlensgt. 55, 5008 Bergen, Norway

Eleven of the twelve recognized wingless (Wnt) sub-

families are represented in the seaanemoneNematostella

vectensis, indicating that this developmentally important

gene family was already fully diversified in the common

ancestor of ‘higher’ animals. In deuterostomes, although

duplications have occurred, no novel subfamilies of Wnts

have evolved. By contrast, the protostomes Drosophila

and Caenorhabditis have lost half of the ancestral Wnts.

This pattern – loss of genes from an ancestrally complex

state –might bemore important in animal evolution than

previously recognized.

Glossary

Cnidaria: a basal phylum, traditionally characterized as having two body layers,

radial symmetry and being at the tissue grade of morphological organisation.

The defining characteristic of the phylum is the presence of a nematocyst, or

stinging cell. There are two basic morphologies; the sessile polyp and the

swimming medusa or jellyfish. The phylum contains four classes, the basal

Anthozoa, to which the sea anemone Nematostella and the coral Acropora

belong, the Cubozoa or ‘sea wasps’, the Scyphozoa, or ‘true’ jellyfish, and the

Hydrozoa, which includes the familiar freshwater Hydra.

Bilateria: a monophyletic group of metazoan animals characterized by bilateral

symmetry. This group, which could also be termed the ‘higher Metazoa’

excludes the Cnidaria, Ctenophora, Porifera (sponges) and Placozoa.

Oral–aboral axis: the single obvious body axis of the two ‘radiate’ phyla

(Cnidaria and Ctenophora), marked at one end by the mouth or oral pore.

Deuterostomes: those bilaterians in which the anus opens near the former site

of the blastopore.

Introduction

One of the most deep-rooted assumptions in animal biologyis that the evolution of vertebrate characteristics, such as asophisticatedhumoral immunesystem, theneural crest andahighly complexnervous system,wasenabledbynewsetsofgenes. This notion appears legitimate when mammals arecompared with the model ecdysozoans Drosophila andCaenorhabditis but, as we learn more about the geneticmakeup of additional organisms, the list of ‘vertebrate-specific’ genes seems to be shrinking by the day. Thebroadening of comparative genomics to include animalssuch as the sea anemone Nematostella vectensis, the coral

Acropora millepora (both members of the cnidarian ClassAnthozoa) and the ragworm Platynereis dumerilii(Annelida, Polychaeta) requires some radical rethinking oftraditional assumptions about the origins of many verte-brate genes. There have been intriguing hints that some‘vertebrate-specific’ genes might predate the origin of theBilateria (see Glossary) [1–4], and this point is elegantlymade in a recent paper on wingless (Wnt) gene diversity inNematostella [5], which broadens, and pushes back intime, the conclusions previously reached for the same genefamily by Prud’homme et al. [6].

Protostomes: those bilaterians in which the mouth opens near the former site

of the blastopore.

Update TRENDS in Genetics Vol.21 No.10 October 2005 537

Anthozoan cnidarians such as Nematostella are prov-ing to be particularly informative for inferring the genecontent of the common cnidarian–bilaterian ancestor,because this class of cnidarians is basal within the phylum[7] (reviewed in Ref. [8]). The genome of Nematostella hasbeen sequenced, and is currently being assembled.Undoubtedly, there are more surprises to come, but thelimited data currently available for Nematostella andother cnidarians provide some intriguing hints at theprobable genetic complexity of the common metazoanancestor. An article by Kusserow et al. [5], based on workfrom the Holstein and Martindale laboratories, revealsthat at least eleven of the twelve Wnt families known fromchordates are present in Nematostella (hence predatingthe Cnidaria–Bilateria split) and elegantly shows thatmost of these genes are expressed in serially overlappingexpression domains along the primary (oral–aboral) bodyaxis. Only six of the twelve Wnt families are representedin the model ecdysozoans, Drosophila and Caenorhabditis,which underscores the extent of gene loss in theseorganisms [3,9].

The results of Kusserow et al. [5] are important inseveral ways. First, the article is refreshingly comprehen-sive. Expression patterns of each of the twelve genes atfive stages ofNematostella development are presented andbecause all of the in situ analysis hybridisation experi-ments were performed using similar techniques in onlytwo laboratories, many of the uncertainties usuallyassociated with comparing expression patterns betweenlaboratories were eliminated. Second, as the authorsrecognize, the expression patterns of the genes indicatea system that might be capable of patterning the oral–aboral axis, because restricted zones of expression spanthe oral two-thirds of the axis in both ectoderm andendoderm. This contrasts with the expression of thecurrently known Nematostella Hox-like genes [10],which appear incapable of playing a role in patterningcomparable to the Hox genes of ‘higher’ animals, parti-cularly in the ectoderm, because they are expressed, witha single exception, exclusively in the endoderm. Third, inspite of the diverse roles of Wnts across the Bilateria,Kusserow et al. could recognize certain conserved expres-sion patterns. For example, the Nematostella ectodermalgenes, NvWnt1, NvWnt2, NvWnt4 and NvWnt7 corre-spond to the neuroectodermal Wnt genes in the higherBilateria. Another example cited, which is however lessclearcut owing to a diversity of expression patterns indeuterostomes, is that NvWnt5, NvWnt6 and NvWnt8 areexpressed in the endoderm, whereas the correspondinggenes in deuterostomes are all expressed in themesoderm.Another possible example of conservation that can beinvestigated, as a result of the sequencing of the Nemato-stella genome, is whether the chromosomally linked,evolutionarily conserved cluster of WNT1–WNT6–WNT10mentioned by Nusse [11] is conserved in Nematostella.

The genetic complexity of the common metazoan

ancestor

The Wnts are one of six families of signaling moleculesthat are responsible for most developmental cell–cellinteractions across the animal kingdom [12]. The

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Nematostella data indicate that full diversification of theWnt family preceded the origin of the Bilateria (Figure 1),and ongoing EST and genome projects for variouscnidarians will show whether this is also the case for theother five developmentally regulated signaling pathways[i.e. transforming growth factor b (TGFb), Ras–mitogen-activated protein kinase 1 (MAPK), nuclear receptor,notch and hedgehog]. Recent studies have identifiedcomponents of the TGFb [10,13], Ras–MAPK (reviewedin Ref. [1]) and nuclear hormone receptor families [14].Although uncertainties remain regarding notch andhedgehog, the currently available data imply that muchof the diversity of cell signaling associated with ‘higher’animals was actually achieved early in animal evolution.Moreover, at least some of the ‘vertebrate-specific’antagonists of these signaling pathways have muchearlier origins than was inferred based on their absencefrom Drosophila and Caenorhabditis [15]. Clear homologsof the vertebrate Wnt antagonist Dickkopf are rep-resented in EST collections for the jellyfish Cyanea [16]and Hydra ([4] and publicly available Hydra EST datasets; http://hydra.ics.uci.edu/jf). Similarly, probable homo-logs of the gene encoding the bone morphogenetic protein(BMP) antagonist Noggin have been identified in theplanarian Dugesia [17] and the sponge Suberites [18],indicating that it too might also have an ancient origin.The presence of potential antagonists means that onecannot predict that a Wnt signaling pathway is activebased solely on expression pattern because of the complexregulatory reactions of the Wnts [19]. It seems likely thatthere are certain time windows during development whenWnt expression is particularly important, but these willonly be revealed once the techniques to selectively knockout individual Wnt genes have been developed. However,in situ expression analyses of the candidate Wntantagonists using currently available techniques shouldreveal some aspects of how the system might be workingin Nematostella.

Do losses outweigh gains?

One important general implication of the NematostellaWnt study and several other recent articles is that theyhighlight the significance of gene loss during animalevolution.Drosophila andCaenorhabditis have lost half ofthe ancestral Wnt diversity [5], and many other genes [3]found in ‘lower’ animals, but chordates have also under-gone gene loss, as is most clearly evident in the lowerchordatesCiona andOikopleura [20]. Each newESTstudyreveals further examples of gene loss at every taxonomiclevel throughout the ‘higher’ Metazoa. For example, of5021 cDNAs from the honeybee (Apis mellifera), 23 wereuniquely shared with mammals, indicating that thesegenes were present in the common ancestor of ‘higher’animals, but have been lost from Drosophila, Anophelesand Caenorhabditis [21]. Furthermore, of the 674sequences identified as ‘chordate-specific’ on the basis ofbeing present in Ciona, Fugu and human but absent fromCaenorhabditis and Drosophila [22], almost half can nowbe identified in ecdysozoans. It is difficult to escape theconclusion that the genome of the common ancestor of‘higher’ animals was surprisingly complex in terms of

Bilateria

Bilateria

Linear mtgenomes

Circular mtgenomes

ChordataCiona, Oikopleura, Fugu

Hemichordata

Echinodermata

BrachiopodaMolluscaLottiaAnnelidaPlatynereis, Helobdella, Capitella

Nemertea

PlatyhelminthesDugesia

ArthropodaDrosophila, Anopheles, Apis

NematodaCaenorhabditis

Cnidaria

Ctenophora

PoriferaReniera, Suberites

HydrozoaHydra

Cubozoa

ScyphozoaCyanea

AnthozoaAcropora, Nematostella

TRENDS in Genetics

Protostomia

Ecdysozoa

Deuterostomia

Lophotrochozoa

Figure 1. Phylogenies of the animal kingdom (upper panel) and Cnidaria (lower panel). Animal phylogeny has been revised in recent years on the basis of molecular data; the

overall phylogeny shown has been modified from Ref. [23]. The positions of the Cnidaria and Ctenophora relative to the Bilateria are uncertain. The major phyla are listed and

the higher groupings discussed in the main text are indicated by the coloured boxes. Genera mentioned in the main text are listed under the phylum to which they belong.

The symbols used are courtesy of the Integration and Application Network (ian.umces.edu/symbols), University of Maryland Center for Environmental Science. Within the

Cnidaria, based on molecular evidence, it is clear that the Class Anthozoa is basal. Abbreviation: mt, mitochondrial.

Update TRENDS in Genetics Vol.21 No.10 October 2005538

gene content, and that gene loss has been a major factor ingenome evolution since divergence from the commonancestor.

Concluding remarks

The probable availability of complete genome sequencesfor the sponge Reniera and several cnidarians (Nemato-stella, Hydra and possibly also a coral) within the nextyear or so should clarify the extent of ancestral geneticcomplexity within the animal kingdom. One key out-standing issue concerns the other major protostomelineage, the Lophotrochozoa (Figure 1): have gene lossand sequence divergence been as extensive as in theEcdysozoa, or have ancestral states been more faithfullymaintained? There are hints from studies of specific genefamilies (e.g. Ref. [6]) that losses might have been less

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extensive in some lophotrochozoans than in those ecdyso-zoans that we are familiar with. The evo-devo communityawaits, with great interest, the completion of full genomesequencing projects in progress for several lophotrochozo-ans, including the annelids Helobdella and Capitella, andthe mollusc Lottia, which are scheduled for completionduring 2005 by the DOE’s Joint Genome Institute (http://www.jgi.doe.gov/).

References

1 Steele, R.E. et al. (1999) Appearance and disappearance of Syk familyprotein-tyrosine kinase genes during metazoan evolution. Gene 239,91–97

2 Bosch, T.C.G. and Khalturin, K. (2002) Patterning and cell differen-tiation in Hydra: novel genes and the limits to conservation. Canad.J. Zool. 80, 1670–1677

Update TRENDS in Genetics Vol.21 No.10 October 2005 539

3 Kortschak, R.D. et al. (2003) EST analysis of the cnidarian Acroporamillepora reveals extensive gene loss and rapid sequence divergencein the model invertebrates. Curr. Biol. 13, 2190–2195

4 Fedders, H. et al. (2004) A Dickkopf-3-related gene is expressed indifferentiating nematocysts in the basal metazoan Hydra. Dev. GenesEvol. 214, 72–80

5 Kusserow, A. et al. (2005) Unexpected complexity of the Wnt genefamily in a sea anemone. Nature 433, 156–160

6 Prud’homme, B. et al. (2002) Phylogenetic analysis of the Wntgene family: insights from lophotrochozoan members. Curr. Biol.12, 1395–1400

7 Collins, A.G. (2002) Phylogeny of Medusozoa and the evolution ofcnidarian life cycles. J. Evol. Biol. 15, 418–432

8 Ball, E.E. et al. (2004) A simple plan - cnidarians and the origins ofdevelopmental mechanisms. Nat. Rev. Genet. 5, 567–577

9 Coghlan, A. and Wolfe, K.H. (2002) Fourfold faster rate of genomerearrangement in nematodes than in Drosophila. Genome Res. 12,857–867

10 Finnerty, J.R. et al. (2004) Origins of bilateral symmetry: Hox and dppexpression in a sea anemone. Science 304, 1335–1337

11 Nusse, R. (2001) An ancient cluster of Wnt paralogues. Trends Genet.17, 443

12 Pires-daSilva, A. and Sommer, R.J. (2003) The evolution of signallingpathways in animal development. Nat. Rev. Genet. 4, 39–49

13 Hayward, D.C. et al. (2002) Localized expression of a DPP/BMP2-4ortholog in a coral embryo. Proc. Natl. Acad. Sci. U. S. A. 99,8106–8111

14 Grasso, L.C. et al. (2001) The evolution of nuclear receptors: evidencefrom the coral Acropora. Mol. Phylogenet. Evol. 21, 93–102

Corresponding authors: Adams, K.L. (keitha@interchange.ubc.ca), Wendel, J.F.( jfw@iastate.edu).

Available online 10 August 2005

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15 De Robertis, E.M. and Bouwmeester, T. (2001) New twists onembryonic patterning. EMBO workshop: embryonic organizer signal-ing: the next frontiers. EMBO Rep. 2, 661–665

16 Yang, Y. et al. (2003) ESTanalysis of gene expression in the tentacle ofCyanea capillata. FEBS Lett. 538, 183–191

17 Mineta, K. et al. (2003) Origin and evolutionary process of the CNSelucidated by comparative genomics analysis. Proc. Natl. Acad. Sci.

U. S. A. 100, 7666–767118 Muller, W.E.G. et al. (2003) Origin of metazoan stem cell system in

sponges: first approach to establish the model (Suberites domuncula).Biomol. Eng. 20, 369–379

19 Moon, R.T. et al. (1997) Structurally related receptors and antagonistscompete for secreted Wnt ligands. Cell 88, 725–728

20 Edvardsen, R.B. et al. (2005) Remodelling of the homeobox genecomplement in the tunicate Oikopleura dioica. Curr. Biol. 15,R12–R13

21 Nunes, F.M.F. et al. (2004) The use of open reading frames ESTs(ORESTES) for analysis of the honey bee transcriptome. BMC

Genomics 5, 8422 Dehal, P. et al. (2002) The draft genome of Ciona intestinalis: insights

into chordate and vertebrate origins. Science 298, 2157–216723 Adoutte, A. et al. (1999) Animal evolution. The end of the intermediate

taxa? Trends Genet. 15, 104–108

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doi:10.1016/j.tig.2005.08.002

Novel patterns of gene expression in polyploid plants

Keith L. Adams1 and Jonathan F. Wendel2

1UBC Botanical Garden and Centre for Plant Research, 2357 Main Mall, MacMillan Building, University of British Columbia,

Vancouver, British Colombia, Canada, V6T 1Z42Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, IA 50011, USA

Genome doubling, or polyploidy, is a major factor

accounting for duplicate genes found in most eukaryotic

genomes. Polyploidy has considerable effects on dupli-

cate gene expression, including silencing and up- or

downregulation of one of the duplicated genes. These

changes can arise with the onset of polyploidization or

within several generations after polyploid formation

and they can have epigenetic causal factors. Many

expression alterations are organ-specific. Specific

genes can be independently and repeatedly silenced

during polyploidization, whereas patterns for other

genes appear to be more stochastic. Three recent

reports have provided intriguing new insights into the

patterns, timing and mechanisms of gene expression

changes that accompany polyploidy in plants.

Introduction

Most eukaryotic genomes have numerous duplicatedgenes, many of which appear to have arisen from one or

more cycles of polyploidy (genome doubling), either byallopolyploidy or autopolyploidy (see Glossary). Well-documented examples of polyploidy exist in variousgroups of vertebrates, insects, yeasts and plants [1,2].Ancient polyploidy events (paleopolyploidy) have beeninferred to have occurred during the evolutionary historyof vertebrates, yeast and flowering plants [3]. Followingpaleopolyploidy there has been extensive loss of dupli-cated genes. Polyploidy has been especially common inflowering plants, where most species are inferred to haveexperienced at least one polyploidy event in theirevolutionary history [4]. For example, at least two andprobably three paleopolyploidy events are thought tohave occurred during the evolutionary history of Arabi-dopsis thaliana [5]. Approximately 27% of the gene pairsthat were formed by polyploidy have been retained inA. thaliana [6] and more than half of these gene pairsshow evidence of functional divergence [7].

The merging and doubling of two genomes sets inmotion extensive modifications of the genome and/or tran-scriptome, creating cascades of novel expression patterns,regulatory interactions and new phenotypic variation forevaluation by natural selection [5,8,9]. Recent studies