Biology Reference
In-Depth Information
Clearly, one of the major, interesting aspects of the genomic structure
of some ascaridoids, including
A. suum
, is chromatin diminution,
54
wherein a proportion of the genomic content is lost from somatic tissue
relative to the germ-line. The precise mechanism governing diminution
is not understood, nor has the genomic content lost during this process
been fully characterized. However, evidence suggests a significant bias
towards the loss of repetitive sequences.
54
When we explored the repeat
content of the
A. suum
genome, we found no evidence of Tas2 trans-
posons,
11
predicted to be within the content lost during chromatin
dimunition in
A. suum
,
55
which appears to support the hypothesis that
our genome assembly reflects the somatic genome of this species, thus
explaining its low repeat content. Intriguingly, the present gene set
inferred for
A. suum
includes
fert-1
and
rpS19G
,which,althoughorigi-
nally proposed to be germ-line specific (i.e. lost from the somatic
genome during diminution),
54
were found to be highly transcribed both
in muscle and reproductive tissues in adult worms sequenced during our
study.
11
It is worthy to note that previous information on diminution for
this species is based on comparisons between germ-line and intestinal
tissues. Our findings suggest that, if the low repeat content in our
assembly is the consequence of somatic chromatin diminution, the
genomic content lost during diminution might vary among individuals
and/or tissues. We emphasize, as we proposed previously,
11
that
investigations of chromatin diminution between and among individual
cells (i.e. sperm or eggs), stages and tissues of
A. suum
would be timely,
given the availability of the current assembly, and achievable, consid-
ering that high-quality genomic DNA can be generated using a WGA-
based sequencing approach.
The Gene Set
Using transcriptomic data from adult and larval stages of
Ascaris
,
de novo
predictions and homology-based searching (see “Gene prediction
and annotation,” above), we identified 18,542 genes, with a mean length
of 6.5 kb (see
Table 11.2
). In comparison with complete genome sequence
data for other nematodes, such as
B. malayi
,
25
C. elegans
,
23
Meloidogyne
hapla
56
or
Pristionchus pacificus
,
24
the
A. suum
genes have much longer
introns than predicted previously for other nematodes, which relates to
the larger genome size of this parasite. Further analyses suggested that
our integrated approach to gene prediction was indeed robust. Almost
80% of the genes predicted in the current gene set of
A. suum
are sup-
ported by transcriptomic data. In addition, 80% have a homologue in
B. malayi
(
n
¼
12,853),
C. elegans
(
n
¼
12,779),
M. hapla
(
n
¼
10,482), and/or
P. pacificus
(
n
¼
11,865), with nearly 9000 being common among all species
