Gonochoristic Bacteriophora

— Nippostrongylus brasiliensis Ostertagia ostertagi Haemonchus contortus !— Syngamus trachea . Heterorhabditis bacteriophora "■'J?

Pelliodilis typica

■ Dolichohabditis sp CEW1

Rhabditella axei Rhabditis blumi Caenorhabditis briggsae Caenorhabditis elegans Diploscapter sp Pristionchus lheritieri Pristionchus pacificus Aduncospiculum halicti

Strongylida

Rhabditida (Rhabditoidea)

Teratorhabditis palmarum

Panagrellus redivivus rQ

Panagrolaimus sp PS1159 Strongyloides stercoralis Strongyloides ratti — Steinernema carpocapsae Bursaphelenchus sp

Aphelenchus avenae -p^f: Globodera pallida Meloidogyne arenaria

Zeldia punctata Acrobeles complexus Ascaris suum Anisakis sp Toxocara canis Brugia malayi — Dirofilaria immitis Philonema sp

— Brumptaemilius justini

— Dentostomella sp Teratocephalus lirellus

Plectus aquatilis Plectus acuminatus

Diplolaimelloides meyli Bunonema sp Metachromadora sp ¿¡^

Praeacanthonchus sp

Paratrichodorus pachydermus

Paratrichodorus anemones Trichodorus primitivus Prismatolaimus intermedius if",1 Longidorus elongatus Xiphinema rivesi

Mermis nigrescens

Mylonchulus arenicolus Trichinella spiralis Trichuris muris Adoncholaimus sp

Diplogasterida

Rhabditida (Rhabditoidea)

B Rhabditida (Panagrolaimidae)

Rhabditida (Strongyloididae) Rhabditida (Steinernematidae) Aphelenchida

Tylenchida

Rhabditida (Cephalobidae) Ascaridida

Spirurida

Rhigonematida Oxyurida

Chromadorida Monhysterida

Rhabditida (Bunonematidae) Chromadorida

Triplonchida

Enoplida

Dorylaimida

Mermithida Mononchida

Trichocephalida

Enoplida

Priapulus caudatus Chordodes morgani

Figure 3.18 Phylogeny of 53 nematodes, based on sequences of the small-subunit rRNA gene. With each species an indication of the feeding habit is given (see key). The right-hand side indicates the orders of classical nematode taxonomy. After Blaxter et al. (1998), by permission of Nature Publishing Group.

in plant roots or otherwise damage below-ground plant tissues; however, none of these plant parasites is, as far as we know, on a list for a whole-genome sequencing project.

C. elegans is a 1 mm-long, transparant animal with sequential hermaphoditism and self-fertilization. Sperm cells are made first and stored in the sper-mathecae. Then the animal switches to the production of oocytes, which are fertilized by sperm from the same individual, mature partly while still in the body, and develop to the first larval stage, which emerges after the eggs have been laid. Around 10 eggs are in the body at any time, but the animal can produce more than 300 progeny during its adult lifetime, which depends on temperature (5.5 days at 15 °C, 3.5 days at 20 °C). This phenomenal reproductive capacity, within hours to days, was an important consideration when the species was chosen as a model. In addition to hermaphrodites, males sometimes occur. These males fertilize the hermaphrodites, as there are no gonochoristic females. The sex-determining system is chromosomal and the males lack one sex chromosome (hermaphrodites are XX, males are X0). The possibilities offered by this type of reproductive cycle are very convenient for genetic work, because clones can be made from hermaphroditic lines with no signs of inbreeding depression, and males can be used for cross-fertilization.

The life cycle includes four larval stages, each separated by a moult (Fig. 3.19). The development of gonads and the production of sperm are already taking place during the larval stage. In addition to the four normal larvae there is a resting stage, called the dauer larva (after the German word for endure), which is actually an arrested third larval stage, in which the animal goes into a state of torpor, and does not eat, although it can move slightly and may live for several months. The dauer larval stage is induced by adverse conditions such as crowding and food scarcety. When terminated, the dauer stage proceeds to the fourth larval stage. It is assumed that the dauer larva is the nematode's dispersal stage. Several features point towards an increased propensity to be transported, either by wind or by other animals. The dauer dries itself out, secretes an extra cucticle and develops a behaviour known as nictation (winking); it tends to crawl up objects that protrude from the surface, stands on its tail and waves its head back and forth (Riddle 1988). An important aspect of the dauer is its extreme longevity, which may reach several months, rather than the normal 20 days. The dauer stage of C. elegans is an important model for investigating the genomic basis of longevity (see Chapter 5).

A very peculiar property of C. elegans is that it has a completely determinate developmental pattern, which is fixed for all 959 cells of the body. This was the reason why the animal was initially chosen as a model for developmental studies by Sydney Brenner at the beginning of the 1960s (Brown 2004). Brenner was inspired by earlier German work on the nervous system of the intestinal parasitic nematode Ascaris suum, which had shown that the fate and location of each cell could be traced, and was the same in all individuals. The original C. elegans strain on which the research in Cambridge was started by Brenner came from the laboratory of Ellsworth Dougherty in Berkeley, who had cultured C. elegans for several years. It is assumed that the culture actually originated from mushroom compost collected near Bristol, UK (Fitch and Thomas 1997).

C. elegans is a cosmopolitan species. More than 20 different strains have been isolated from soils of North America, Europe, and Australia (Fitch and Thomas 1997). Despite this broad distribution, the species is not a popular object of study among field ecologists, because it is very difficult to distinguish from other species in the same group and its distribution seems to be restricted to synanthropic habitats such as compost heaps and manure. For example, despite the fact that a good identification key of more than 600 species is available for the nematodes of the Netherlands, issued from an active university department specializing in nematology over many years (Bongers 1988), wild C. elegans have never been found in the Netherlands.

The complete genome sequence of C. elegans was the first to be published for a multicellular organism (the C. elegans Sequencing Consortium 1998). The WormBase consortium has continued to edit the sequence, brought the estimated error rate

Fertilization

Elegans Life Cycle

Figure 3.19 Life cycle (from egg to adult) of C. elegans, when cultured in the laboratory with abundant food (E. coli) at 25°C. The outer scale is marked in hours since fertilization, the inner scale in hours since hatching. L1, L2, L3, and L4 are the first to fourth larval stages. The adult can live for several days more. After Wood et al. (1980), with permission from Elsevier.

Figure 3.19 Life cycle (from egg to adult) of C. elegans, when cultured in the laboratory with abundant food (E. coli) at 25°C. The outer scale is marked in hours since fertilization, the inner scale in hours since hatching. L1, L2, L3, and L4 are the first to fourth larval stages. The adult can live for several days more. After Wood et al. (1980), with permission from Elsevier.

down to 1 in 100000, and closed the last gap in November 2002. This makes the C. elegans sequence the first and so far only metazoan genome database that has reached sequencing closure for all of the chromosomes. The interface on the World Wide Web (www.wormbase.org), described by Harris et al. (2004), offers a rich source of information, not only on the complete genome sequence but also on mutant phenotypes, genetic markers, developmental lineages of the worm, and bibliographic resources, including paper abstracts and author contact information. The genome sequence of the related species, C. briggsae, is now completely integrated into WormBase, which allows comparative analysis of orthologues and synteny. WormBase also contains extensive information from large-scale genome analyses, microarray expression studies, and the assignment of gene ontology terms to gene products. New data releases are published regularly and from time to time a 'freeze' of the software and the database is deposited, which can be downloaded. For transcription profiling, commercial microarrays are available, such as the C. elegans whole-genome GeneChip® array (Affymetrix), which targets 22500 transcripts.

The C. elegans sequence was announced in 1998 as a 'platform for investigating biology'. The consortium realized that the importance of the genome sequence of C. elegans extended beyond

Table 3.5 General features of the genome of C. elegans (C. elegans Sequencing Consortium 1998) Category Features

Protein-encoding genes Many genes (25%) organized in cistronic units (Section 3.2); three times more genes than in yeast

(see Table 3.1); more genes than was estimated from genetic studies RNA genes Many tRNAs on the X chromosome; several RNA genes in introns of protein-encoding genes;

rRNA genes in long tandem arrays Gene density Uniform GC content (see Fig. 3.7); fairly constant gene density across chromosomes

Repetitive DNA Tandem repeats account for 2.7% of the genome; inverted repeats account for 3.6% of the genome;

repeat sequences overrepresented in introns; 38 different families of dispersed repetitive sequences associated with transposition; dispersed repetitive sequences abundant on the arms of the chromosomes nematodes proper, and in fact could be considered the basic formula for constructing a multicellular animal, in the same way that the sequence of the S. cerevisiae genome contains all the information for making and maintaining a unicellular eukaryote. In addition, because nematodes branched off early in the evolutionary tree of life, the C. elegans sequence provides an outgroup for almost all other bilaterian animals (from Annelida to Chordata). For example, if a gene is identified in both C. elegans and a mollusc, it must also have been present in the ancestor of the Bilateria (Hodgkin et al. 1995). An overview of the specific features of the C. elegans genome is given in Table 3.5.

At the time of publication of the C. elegans genome sequence, information was available on only a few other eukaryote genomes. C. elegans could be compared with yeast and bacteria such as E. coli, as well as to the then-available gene content of the human genome. It turned out that 36% of the predicted C. elegans genes had a human homologue and that no less than 74% of the human genes had a homologue in C. elegans (Fig. 3.20). The similarity of C. elegans to Homo sapiens was greater than that to yeast or bacteria. This comparison demonstrated for the first time the striking unity that underlies the genomes of organisms as different as nematode and human. This tendency was reconfirmed many times when more eukar-yotic genome sequences became available.

3.3.3 Drosophila and other arthropods

In terms of numbers of species, the arthropods as a group surpass any other phylum in the animal

H. sapiens 4979

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