trans

24 PARASITE GENOMICS
Ascaris and C. elegans is SL1-trans-spliced, and
about 60% of C. elegans genes are trans-spliced.
The cross comparison between the freeliving
C. elegans and the parasitic nematodes
can reveal genomic features associated with
parasitism. For example, C. elegans expresses a
member of the nematode polyprotein allergen
(NPA) family of genes. In Ascaris and B. malayi
the different internal repetitive blocks of the
NPA protein are very similar, while in C. elegans
each repeat unit is strikingly different.
As the NPA protein binds lipids, this may
reflect the different requirements and environments
of the nematodes: C. elegans exploiting
a varied soil bacterial flora, and the parasites
exploiting a less variable host environment.
Several genes have apparently undergone
expansion to form a gene family in one branch
of the Nematoda, while remaining unique in
others. Filarial nematodes have but one FAR
protein gene (another lipid-binding protein)
while C. elegans has seven; conversely B. malayi
has eight ALT (abundant larval protein) genes
while C. elegans has one (B. Gregory and
M. Blaxter, unpublished observations). Emerging
microarray data for C. elegans defines sets
of genes involved in various life-cycle transitions
and tissue development. These data can
be used to cross compare with parasite EST
datasets to identify conservation of involvement
of genes in basic processes such as
gonadogenesis or development of the third
stage dauer larva/infective larva. These EST
datasets also revealed one new set of problems
in dealing with these large metazoan parasites,
those deriving from uncloned starting
organisms. The populations used for the different
libraries were not all from the same
strain, and comparison of EST sequences has
identified numerous single base changes that
are likely to have arisen through allelic variation
(rather than experimental error). For parasites
where genetics is difficult or even absent,
and where the standard laboratory strains
have not been specifically selected to be
inbred, such variation within and between
strains has to be carefully considered. Similar
problems are also seen in the schistosome
genome project (see below).
To date only limited genome sequence data
are available from nematodes other then C. elegans
and the congeneric C. briggsae. Analysis
is most advanced in B. malayi. A striking feature
of C. elegans gene organization is that
approximately 20% of the genes are arranged
as operons, where two or more genes are
cotranscribed from a single promoter. The
polycistronic pre-mRNA is then resolved into
individual mature mRNAs by linked polyadenylation
of the upstream transcript and transsplicing
of a novel family of spliced leader
exons (the SL2 family) to the 5 end of the
downstream transcript. This polycistronic
organization has also been demonstrated in
other closely related free-living nematode
species, and also in strongylid, filarid and
strongyloidoid parasites (D. Guiliano and
M. Blaxter, unpublished observations). The
functional significance of polycistrons remains
unclear, but may relate to the shared use of
strong promoters. Gene density on the chromosomes
is relatively high in C. elegans, at
approximately one per 5 kb. The regions of the
B. malayi genome that have been sequenced
(about 100 kb) have a density of one gene per
6 kb (D. Guiliano and M. Blaxter, unpublished
observations). Particularly striking is the finding
that introns in B. malayi are usually much
longer than those in C. elegans.
The C. elegans genome is organized into
five autosomes and one sex chromosome:
sex determination is by an XX (female)–XO
(male) system. While B. malayi also has five
autosomes, sex determination is by an XX
(female)–XY (male) system. Sequence analysis
of the Y chromosome (which appears
MOLECULAR BIOLOGY