Ragan, Mark

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Genomics and evolution of microbial eukaryotes

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Botanica Marina 51 (2008): 71–72  2008 by Walter de Gruyter • Berlin • New York. DOI 10.1515/BOT.2008.008
Article in press - uncorrected proof
2008/1501081
Book review
Genomics and evolution of microbial eukaryotes
Edited by Laura Katz and Debashish Bhattacharya
Oxford University Press, Oxford, 2006
Hardcover. 256 pp.
Price: £ 55.00/US$ 125.00
ISBN 9780198569749
Genome-scale data – complete genome sequences,
deep sequencing of cDNA libraries, expression-array
data and sequence tags – continue to revolutionise the
biological sciences. For increasingly many organisms of
interest, eukaryotes as well as prokaryotes, research pro-
grams are no longer designed as a stepwise dissection
of phenotype through successively more-fundamental
strata of pathways, protein sequences, messages,
genetic loci and finally genes. Extensive genomic,
expression and proteomic data are instead available
up-front, and the challenge has become to identify and
validate those molecular regulatory and interaction net-
works most immediately relevant to the question at hand:
production of a metabolite or biopolymer, invasion of a
host, or exploitation of an ecological niche.
For the evolutionary biologist, genome data are a
treasure-trove of evidence on shared ancestry, offering
the promise of phylogenies based no longer on the lim-
ited and perhaps biased sampling dictated by suitability
as targets for PCR primers, but rather on complete sets
of exons – or perhaps on comprehensive analyses of
protein folds, gene content or gene order. Indeed, com-
parative genomics promises much more, including a sys-
tem-wide understanding of the origins and principles of
genetic transmission, genome structure, novel and
partitioned enzyme function, conserved and unique
molecular-interaction networks, multicellularity, develop-
ment, selection, and population dynamics.
Genomics came somewhat late to microbial eukaryotic
biology. The delay came about in part because the DNA-
sequencing technologies first trialled on bacteria proved
to be highly scalable and so were quickly applied to
yeast, then worm and fly, then human, mouse, and the
major animals and plants of agricultural interest. But it
did not help that the morphologically simpler eukaryotes
present such a breathtaking diversity of specialised,
hence difficult, genetics and chromosomal biology. When
sequencing is relatively costly, resources naturally flow to
systems with organised research communities, reference
strains well-characterised at the chromosomal and
genomic levels, deep DNA and EST libraries, gene-
expression resources and experimentally tractable
genetics.
Even when genomics arrives, as it has now for some
microbial eukaryotes, it presents a moving target. Data
become available in stages – ESTs first, then individual
genomic reads, then contigs, scaffolds, and successive
builds of chromosome assembly. Annotation is focused
first on exon-intron structure, only later on motifs, path-
ways, co-regulation, and comparative analyses. cDNAs
may not be full-length, expression platforms present a
maze of hazards, and false-positive predictions abound.
More insidiously, sequence data from domesticated
strains and clonal populations are welcomed as repre-
senting ‘‘the’’ genome, whereas expression and proteo-
mic data intentionally (to maximise sampling of encoded
information) reflect a diverse admixture of life-cycle and
physiological states.
This book, edited by two outstanding younger
researchers who were early adopters of genome-scale
technology in application to ciliates and photosynthetic
protists respectively, takes aim at this moving target for
microbial eukaryotes circa mid-2005: the published
genome of Plasmodium falciparum, plus partial sequenc-
es of 11 other Plasmodium strains; the partially annotated
Tetrahymena thermophia genome, plus data from Para-
mecium tetraurelia and Oxytricha trifallax; published
genomes of Trypanosoma brucei, T. cruzi and Leishmania
major; the published but partially assembled genome of
Entamoeba histolytica; the compact Encephalitozoon
cuniculi genome, with an initial comparison with that of
Antonospora locustae (formerly Nosema locustae);
nucleomorphs of Bigellowiella natans and Guillardia
theta; the published Thalassiosira pseudonana genome,
and ESTs of Phaeodactylum tricornutum; and the pub-
lished genome of Dictyostelium discoideum. Authors
additionally had access to ESTs of Alexandrium tama-
rense, Karenia brevis and four other dinoflagellates, and
GSS and EST sequences from Spironucleus barkhanus.
Although released in April 2004, the Cyanidioschyzon
merolae genome is surprisingly not treated. The April
2004 genome of Cryptosporidium parvum is discussed
only briefly, while the October 2004 genome of Cr. homi-
nis is not mentioned (a third strain, Cr. muris, has since
been sequenced). Advanced draft genomes appearing in
2005–2007 but not covered in this book include Chla-
mydomonas reinhardtii, Giardia lamblia, two strains of
Ostreococcus tauri, Paramecium tetraurelia, Phaeodac-
tylum tricornutum, Tetrahymena thermophila, Theileria
annulata and Th. parva, four strains of Toxoplasma
gondii, Trichomonas vaginalis, and the nucleomorph of
Hemiselmis rufescens. As I write, sequencing and/or
annotation continues on Antonospora locustae, Aureo-
coccus anophagefferens, Ectocarpus siliculosus, Ente-
rocytozoon beineusi, Galdieria sulphuraria, Oxytricha
trifallax (now Sterkiella histriomuscorum) and Volvox car-
terae, while proposals are afoot for other large-scale pro-
jects including the genome of Chondrus crispus.
In a brief but synthetic introduction, the editors state
their intention to ‘‘convey a basic understanding of geno-
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mics and evolution in microbial eukaryotes to a wide
scientific audience’’. They envision genomics as revolu-
tionising our understanding of not only the physiology,
but also the systematics and ecology, of eukaryotes, and
see its application to the morphologically simpler repre-
sentatives as potentially challenging the principles of
genome evolution that until now have been based on a
few plant and animal lineages. Fifteen chapters are
arranged in three sections: an overview of current per-
spectives on high-level groupings of protists (one chap-
ter); evolutionary genomics of selected taxa or groupings
(seven chapters); and analyses of complete genomes
(seven chapters, one of which reviews genomic strate-
gies and technologies).
The overview chapter collects many of the better-
known eukaryotic lineages into six high-level groupings
for which some consensus exists on the basis of inferred
molecular-phylogenetic trees, shared morphological
(often ultrastructural) features, and/or discrete molecular
characters. These groupings are intentionally informal,
and the authors are careful to recognise both the provi-
sional state of some of the underlying interpretation, and
the great diversity of forms that as yet do not fit into this
framework. Judging from the coverage of this book,
microbial eukaryotes largely excludes two of these six
groupings: plantae/archaeplastida (Chlamydomonas and
Cyanidioschyzon are unmentioned) and most opistho-
konts (fungal genomes are excluded although, anoma-
lously, microsporidia are accorded a chapter).
The remaining four high-level groupings, ramicristates/
amoebozoa, stramenopiles and alveolates, rhizaria, and
excavates, do not map neatly onto the subsequent four-
teen chapters, some of which cut across groups and/or
address evolutionary themes including photosynthetic
organelles, anaerobes, gene transfer, and remnant nucle-
ar genomes. Among these four groupings rhizaria is the
least-characterised genomically, and is represented here
only by a fascinating if largely pre-genomic chapter on
diversity among foraminifera, and by the Bigelowiella
nucleomorph.
Part II treats evolutionary genomics. As presented by
these seven chapters, evolutionary genomics encom-
passes features of genome architecture, chromosome
structure, gene content variation, gene family duplication
and specialisation, serial endosymbiosis, and gene trans-
fer both between lineages and within the eukaryotic cell.
Larger themes include metabolic adaptation, establish-
ment and maintenance of host-parasite systems,
genome fusion as an evolutionary mechanism, and the
mechanics of genome duality in ciliates. This well-
considered selection would have been further enriched
by greater emphasis on within-species diversity, e.g., the
spectacular chromosomal diversity in Giardia, or
SNP and haplotype maps of Plasmodium or trypano-
somes.
The seven chapters in Part III present analyses of com-
plete genomes: trypanosomes, Entamoeba, microspori-
dia, nucleomorphs, diatoms and Dictyostelium (the
Plasmodium genomes appear in Part II). In mid-2005 the
three trypanosome genomes were the best-assembled
and annotated, and the corresponding chapter is packed
with information on genome structure, polycistronic gene
clusters, telomeres, retro-elements, haplotype informa-
tion, metabolism, cell-cycle signalling molecules and
cross-species comparisons. Gene inventories of Enta-
moeba reveal its metabolic, transport and environmental
sensing capacity, repetitive elements, laterally transferred
genes and mitosome-targeted gene products. The Tha-
lassiosira genome shows two haplotypes, a moderately
high level of sequence polymorphism, and relatively few
repetitive elements; gene inventories related to silica,
nitrogen and carbon metabolism are discussed, while
comparison with the Phaeodactylum EST library allows
preliminary comments on gene diversity between the two
diatoms. Among gene inventories for the Dictyostelium
genome we discover a wealth of G-protein-coupled
receptors, orphan receptors, receptor and other kinases,
transcriptional activators (although a low frequency of
transcription factors), transmembrane-domain proteins,
and diverse adhesion-related proteins – many of the
parts needed for multicellularity. Much more of course
remains to be discovered, not least about the structure
and regulation of transcriptional clusters and develop-
mental switches.
The genomic target continues to move. More and more
individual genomes and transcript libraries are being
sequenced, although increasingly with next-generation
technologies not anticipated by this book. Community
sequencing (metagenomics) has so far focused on pro-
karyotes and viruses, but will sooner rather than later be
applied to populations of phytoplankton or heterotrophic
flagellates. Genomic diversity within populations or
species, and genome-wide analyses of transcriptional
potential (epigenomics), feature prominently in policy
roadmaps of major funding agencies and will soon
impact on microbial genomics either directly, or via
broad-scale screens for determinants of host resistance
to pathogens. In the computational realm, it is increas-
ingly possible to infer novel metabolic pathways and
regulatory networks from a combination of sequence and
expression data. Too few of these chapters hint at the
exciting science and applications that genome-scale
technologies have in store for us in the very near future.
This highly readable book is accessible to the molec-
ularly conversant biologist, and represents a very useful
first step toward an integrated dynamics genomics of
microbial eukaryotes. Many more steps lie ahead.
Mark Ragan
Genomics and Computational Biology, Institute for
Molecular Bioscience, The University of Queensland,
Brisbane, St Lucia QLD 4072, Australia,
e-mail: m.ragan@imb.uq.edu.au
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