C. elegans ORFeome Version 3.1: Increasing the Coverage of ORFeome Resources With Improved Gene Predictions

Article (PDF Available)inGenome Research 14(10B):2064-9 · November 2004with39 Reads
DOI: 10.1101/gr.2496804 · Source: PubMed
Abstract
The first version of the Caenorhabditis elegans ORFeome cloning project, based on release WS9 of Wormbase (August 1999), provided experimental verifications for approximately 55% of predicted protein-encoding open reading frames (ORFs). The remaining 45% of predicted ORFs could not be cloned, possibly as a result of mispredicted gene boundaries. Since the release of WS9, gene predictions have improved continuously. To test the accuracy of evolving predictions, we attempted to PCR-amplify from a highly representative worm cDNA library and Gateway-clone approximately 4200 ORFs missed earlier and for which new predictions are available in WS100 (May 2003). In this set we successfully cloned 63% of ORFs with supporting experimental data ("touched" ORFs), and 42% of ORFs with no supporting experimental evidence ("untouched" ORFs). Approximately 2000 full-length ORFs were cloned in-frame, 13% of which were corrected in their exon/intron structure relative to WS100 predictions. In total, approximately 12,500 C. elegans ORFs are now available as Gateway Entry clones for various reverse proteomics (ORFeome v3.1). This work illustrates why the cloning of a complete C. elegans ORFeome, and likely the ORFeomes of other multicellular organisms, needs to be an iterative process that requires multiple rounds of experimental validation together with gradually improving gene predictions.

Figures

C. elegans ORFeome Version 3.1: Increasing
the Coverage of ORFeome Resources With
Improved Gene Predictions
Philippe Lamesch,
1,2
Stuart Milstein,
1
Tong Hao,
1
Jennifer Rosenberg,
1
Ning Li,
1
Reynaldo Sequerra,
3
Stephanie Bosak,
3
Lynn Doucette-Stamm,
3
Jean Vandenhaute,
2
David E. Hill,
1
and Marc Vidal
1,4
1
Center for Cancer Systems Biology and Department of Cancer Biology, Dana-Farber Cancer Institute, and Department of
Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA;
2
Unite´ de Recherche en Biologie Mole´culaire, Faculte´s
Universitaires Notre-Dame de la Paix, 5000 Namur, Belgium;
3
Agencourt Biosciences Corporation,
Beverly, Massachusetts 01915, USA
The first version of the Caenorhabditis elegans ORFeome cloning project, based on release WS9 of Wormbase (August
1999), provided experimental verifications for 55% of predicted protein-encoding open reading frames (ORFs). The
remaining 45% of predicted ORFs could not be cloned, possibly as a result of mispredicted gene boundaries. Since
the release of WS9, gene predictions have improved continuously. To test the accuracy of evolving predictions, we
attempted to PCR-amplify from a highly representative worm cDNA library and Gateway-clone 4200 ORFs missed
earlier and for which new predictions are available in WS100 (May 2003). In this set we successfully cloned 63% of
ORFs with supporting experimental data (“touched” ORFs), and 42% of ORFs with no supporting experimental
evidence (“untouched” ORFs). Approximately 2000 full-length ORFs were cloned in-frame, 13% of which were
corrected in their exon/intron structure relative to WS100 predictions. In total, 12,500 C. elegans ORFs are now
available as Gateway Entry clones for various reverse proteomics (ORFeome v3.1). This work illustrates why the
cloning of a complete C. elegans ORFeome, and likely the ORFeomes of other multicellular organisms, needs to be an
iterative process that requires multiple rounds of experimental validation together with gradually improving gene
predictions.
[Supplemental material is available online at www.genome.org.]
The Caenorhabditis elegans genome sequence, released in Decem-
ber 1998, was nearly complete and highly accurate, with an error
rate estimated at 1/30,000 (The C. elegans Sequencing Consor-
tium 1998). The finished sequence was eventually released in
November 2002, comprising 100,258,171 bp in six contiguous
segments corresponding to the six C. elegans chromosomes (J.
Sulston, pers com; http://elegans.swmed.edu/Announcements/
genome_complete.html).
Although the technology required for rapid and accurate
whole-genome sequencing is mature, the gene prediction tools
currently available to identify protein-encoding open reading
frames (ORFs) and to define their exon/intron structures still
need improvements. For exon prediction in mammalian ge-
nomes, these tools have an overall sensitivity and specificity of
only 60% (Burset and Guigo 1996), and 40% for the 5 and 3
gene boundaries specifically (Korf et al. 2001). Predicted genes
can be truncated, extended, split, or merged (see Reboul et al.
2001), relative to their actual “observed” exon/intron structure.
Using GeneFinder, a gene prediction tool developed for C.
elegans (http://ftp.genome.washington.edu/cgi-bin/
genefinder_req.pl), a total of 19,477 ORFs were annotated in
Wormbase release WS9 (August 1999; http://www.Wormbase.
org; Stein et al. 2001). Approximately 50% of these ORFs were
predicted ab initio, without experimental support.
The C. elegans ORFeome project was launched to test the
accuracy of these gene predictions, while simultaneously creat-
ing a resource of cloned full-length predicted ORFs to be used in
various functional genomics and reverse proteomics studies
(Reboul et al. 2001, 2003). ORFs were PCR-amplified between
their 5- and 3-ends, and cloned using the Gateway recombina-
tional cloning system (Hartley et al. 2000; Walhout et al.
2000a,b). PCR amplification was performed on a highly repre-
sentative cDNA library using gene-specific primer pairs for each
of the 19,477 ORFs based on WS9 predictions. Gateway tails at-
tached to all primers allowed the cloning of the ORFs into the
pDONR201 vector, resulting in a total of 11,984 (61.5% of the
ORFs) Entry clones in the first version of the ORFeome (version
v1.1; Supplemental Table 1).
The C. elegans ORFeome version 1.1a (v1.1a) represents a
consolidated set of 10,623 ORFs cloned in-frame, 11.4% (1361
out of 11,984) of all cloned ORFs in version 1 were cloned out-
of-frame because of mispredicted gene boundaries (v1.1b). This
first version of the worm ORFeome contributed significantly to
the reannotation of C. elegans gene structure. The alignment of
OSTs (ORF Sequence Tags) to the corresponding predicted gene
sequences allowed the improvement of C. elegans annotations by
correcting the internal gene structure of 20% of v1.1a cloned
ORFs. In addition, OSTs provided experimental verification for
45% of the set of “untouched” ORFs, that is, not detected yet
by any mRNA or EST. For each gene, ORFeome v1.1a contains
4
Corresponding author.
E-MAIL marc_vidal@dfci.harvard.edu; FAX (617) 632-5739.
Article and publication are at http://www.genome.org/cgi/doi/10.1101/
gr.2496804.
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cloned pools that result from mixing 50 to 1000 Escherichia coli
transformants for each Entry clone. Thus, such Entry pools might
contain multiple splice variants and alleles corresponding to PCR
misincorporations. We are in the process of generating a new
resource, ORFeome v2 (Reboul et al. 2003), in which we isolate
individual wild-type clones for all detected splice variants of
ORFs cloned in v1.1a. We will shortly initiate similar attempts for
the ORFs cloned in the ORFeome version 3 described below.
The difficulties inherent in identifying ORFs within meta-
zoan genomes and predicting their correct structure are not spe-
cific to C. elegans. Genome annotation initiatives in the model
organisms Arabidopsis thaliana (Yamada et al. 2003) and Dro-
sophila melanogaster (Hild et al. 2003) have also shown limited
accuracy. The accuracy of current gene prediction algorithms is
also a major issue for the human genome. High numbers of splice
variants and lower signal-to-noise ratios caused by longer introns
and intergenic regions render human genome annotations even
more difficult than for the model systems experimentally vali-
dated so far. Hence, both in model organisms and in human,
functional genomic and reverse proteomics studies, which re-
quire the use of large sets of full-length ORFs, are hampered by
inaccuracies in gene prediction, limiting the usefulness of se-
quenced genomes.
Since the release of Wormbase WS9 in 1999, continuous
efforts to reannotate the C. elegans genome have occurred. Rean-
notations are mainly based on new experimental data, such as
mRNAs and ESTs (the EMBL nucleotide sequence database
[http://www.ebi.ac.uk/embl/] and the Y. Kohara DNA databank
[DDBJ, http://www.ddbj.nig.ac.jp/]), as well as splice-leader se-
quences (Blumenthal et al. 2002). Furthermore, more refined ab
initio approaches have allowed the reprediction of genes for
which no confirmatory experimental data are yet available. To
experimentally validate these new predictions, improve gene
annotation, and generate a more complete C. elegans ORFeome
resource, we attempted to clone the 4232 ORFs originally missed
in v1.1a and that have been either repredicted or newly pre-
dicted between the release of WS9 and that of WS100 (May
2003).
RESULTS
Design of Version 3 of the C. elegans ORFeome
Wormbase, the central repository for the C. elegans genome an-
notation, is updated biweekly, reflecting the continuous effort
made both to correct the structure of previously predicted ORFs
(referred to here as repredicted ORFs) and to predict new pu-
tative ORFs. To identify ORFs that could not be cloned or were
cloned out-of-frame in ORFeome version 1, and have been repre-
dicted in improved versions of the genome annotation, we chose
to compare WS9 predictions to those of the recent Wormbase
release WS100 (see Methods). WS100 is the first Wormbase re-
lease that has been archived in the public domain (frozen;
http://ws100.Wormbase.org). For each of the 8854 ORFs that
were not in v1.1a, we searched for repredictions that at least
partially overlapped with the region between the previously pre-
dicted initiation and termination codons (starts and stops).
We focused only on structure differences at the 5- and 3-
boundaries, while ignoring internal structure differences.
We found 2708 ORFs with repredicted starts or stops (Fig.
1A). These were classified into three categories: 1052 ORFs rean-
notated at the start, 962 at the stop, and 694 at both ends. Of
these 2708 repredicted ORFs, 2213 correspond to uncloned ORFs,
and 495 to ORFs found to be out-of-frame in the first version of
the C. elegans ORFeome. The predicted structure of the remaining
6146 ORFs has not changed between WS9 and WS100. We also
detected 1524 new WS100 genes that did not overlap with any
predicted ORFs in WS9. In total, we attempted to clone and vali-
date the structure of 4232 repredicted (2708) or new (1524) ORFs.
These 4232 ORFs can be divided into two classes depending
on whether their predicted coding sequence has been verified, at
least partially, by EST and/or OST data (touched ORFs) or not
(untouched ORFs; Fig. 1B). Of the 4232 ORFs that we at-
tempted to clone, 2795 (66%) are
touched and 1437 (34%) are untouched.
According to the information available
in Wormbase, various approaches have
been used to reannotate untouched
genes. However, the criteria on which
these repredictions are based are neither
categorized into defined classes nor
searchable in Wormbase. Repredictions
or new predictions often seem based on
sequence alignments between C. elegans
predictions and coding sequences of
other organisms. Also, the 5-or3-ends
of ORFs are often truncated to avoid an
overlap with neighboring ORFs ex-
tended based on new ESTs. Other times
the repredictions are based solely on the
analysis of the genomic sequence. For
instance, some gene repredictions are
based on the presence of noncoding re-
petitive elements overlapping with the
coding sequence in earlier predictions.
Overall Assessment of WS100
As the quality of WS100 repredictions
and new predictions has not been ex-
perimentally validated yet, we first
tested their overall accuracy using a sub-
set of ORFs. We compared the ORF clon-
ing success rate using new WS100 pre-
Figure 1 The C. elegans genome annotation has evolved between WS9 and WS100. (A) For all ORFs
that are missing in v1.1a, those with repredicted starts and/or stops in WS100 were identified. Between
WS9 and WS100, 1052 ORFs have been repredicted at the start, 962 at the stop, and 694 at both ends.
A total of 6146 ORFs had the exact same start and stop in the two Wormbase releases. We also
identified 1524 newly predicted ORFs in WS100. (B) Venn diagram summarizing the classification of
the 4232 repredicted and new ORFs based on the experimental data available. The blue oval represents
all 4232 ORFs that we attempted to clone. The purple circle contains new predictions of which 713 are
touched by ESTs and 811 are untouched. The large orange oval represents all ORFs touched by ESTs.
The smaller oval in light yellow shows ORFs touched by OSTs. As no OST data are available for ORFs
that we did not clone in ORFeome Version 1 or for newly predicted ORFs, only ORFs that we cloned
out-of-frame earlier are touched by OSTs. A small portion (64) of the latter are not touched by any
ESTs. Of all 4232 predicted ORFs that we attempted to clone, 34% (626 repredicted and 811 new
ORFs) are not experimentally verified (untouched), whereas 66% are touched by ESTs, OSTs, or both.
C. elegans ORFeome Version 3.1
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dictions to that of the WS9 predictions from ORFeome version 1
on ORFs that could not be cloned previously. ORFs were PCR-
amplified from our highly representative C. elegans cDNA library
(Walhout 2000b) and cloned into the Gateway Entry vector
pDONR201. Following a second round of PCR amplification
from the Gateway Entry clone to confirm that inserts were pre-
sent and of the corrected size, ORF sequence tags (OSTs) were
generated.
The OSTs were then aligned to the genome to confirm the
identity of the clones. The cloning success rate was 59% (n = 111)
using newly designed primers. In contrast, only 2.7% of at-
tempted ORFs were successfully cloned using WS9-designed
primers, used here as a negative control. These results clearly
show that the C. elegans genome annotation has improved con-
siderably between WS9 and WS100, and that primers designed
based on these reannotations can amplify a substantial number
of ORFs not originally cloned in ORFeome version 1.
C. elegans ORFeome Version 3
In Version 3 of the C. elegans ORFeome project, PCR amplifica-
tions were performed for 4232 repredicted or new ORFs, using
ORF-specific primers (Supplemental Fig. 1). Alignment of the re-
sulting OSTs to the C. elegans genome revealed that 56% (2315
ORFs corresponding to 1378 repredicted ORFs and 937 new
ORFs) were successfully cloned. The cloning success for touched
ORFs is much higher (63%) than for untouched ORFs (42%), and
is slightly lower than the cloning success rate of touched ORFs in
ORFeome Version 1 (71%; Supplemental Fig. 2).
We amplified 64% of ORFs that were cloned out-of-frame in
ORFeome Version 1 (v1.1b). Among these, 87% are now cloned
in-frame. Hence, reannotation efforts led to successful repredic-
tions for 55.7% (64% 0.87) of such ORFs, whereas wrong
repredictions caused complete cloning failure in 36% of the
cases. For the remaining 8.3% of originally out-of-frame ORFs,
repredictions resulted again in out-of-frame PCR products.
Of the ORFs cloned in ORFeome Version 3, 57% were
shorter at one or both ends in WS100 relative to the gene anno-
tation in WS9 (Fig. 2A). This explains why WS9-designed primers
could not anneal to previously predicted ORF boundaries and did
not amplify these ORFs in ORFeome Version 1 (Fig. 2B). Interest-
ingly, a substantial number of ORFs (31%) extended at their 3-
and/or 5-ends in WS100 were also successfully cloned in ORFe-
ome Version 3, whereas the corresponding shorter ORFs, based
on the WS9, failed to clone in ORFeome Version 1 (Fig. 2C).
Given that these previously predicted ORFs are located com-
pletely within the repredicted genes, it seems surprising that pre-
viously designed primers failed to clone these truncated ORFs as
internal primers. However, reannotation of ORF boundaries fre-
quently alters the annotation of internal intron/exon structures
such that primers initially designed to anneal to regions pre-
dicted to be exons in WS9 actually correspond to introns in the
repredicted gene.
Corrections of Intron/Exon Organization
In ORFeome Version 3, we corrected internal exon/intron struc-
tures for 540 (23.3%) cloned ORFs. Compared with WS100 pre-
dictions, OSTs could be used to extend 141 exons, truncate 165
exons, add 85 unpredicted exons, and delete apparently wrongly
predicted 327 exons. In addition, 104 and 130 introns were
added or deleted, respectively (Fig. 3). These structural changes
underestimate the number of actual structure differences, as we
only analyzed OSTs from the 5- and 3-ends representing 1kb
of sequence in total. On the other hand, it is possible that WS100
predictions not observed here might correspond to genuine
splice variants underrepresented in the worm cDNA library used
here, and thus less likely to be represented in the Entry clone
pools.
In comparison to ORFeome Version 1, the proportion of
exons needing correction in ORFeome Version 3 decreased by
8%, which can be explained by a higher rate of EST coverage for
the cloned ORFs. However, these additional EST data did not
reduce the rate of ORFs cloned out-of-frame in ORFeome Version
3, because 11.7% (270) of all cloned ORFs display frame errors
caused by mispredicted 3- and 5-boundaries. We have thus
cloned 2045 (2315 270 out-of-frame) full-length ORFs in
ORFeome Version 3.
Correction of Truncated Clones
As mispredictions of the 5-or3-end of an ORF do not neces-
sarily affect its internal gene structure, primers designed on
mispredicted boundaries can give rise to truncated clones. Previ-
ously cloned ORFs that were subsequently merged, two or more
at a time, into one single longer ORF in WS100 represent one
class of such potentially truncated clones. Merges are typically
based on additional EST data spanning the intergenic region be-
tween two individually predicted, neighboring ORFs.
Our data set of 2708 repredicted
ORFs contains 324 ORFs that resulted
from a merge of two (251; Fig. 4A) or
three ORFs (73), where at least one ORF
of the pair or triplet was not cloned in
ORFeome Version 1. Although C. elegans
contains operons, it is unlikely that
these merged genes are an artifact of
polycistronic messages that are not
transspliced (Blumenthal et al. 2002).
Among the 147 merged ORFs that
were successfully cloned in-frame in
ORFeome Version 3, only 20 have been
identified as being part of an operon
(Fig. 4B).
Investigating the Existence of
Clones Missing in Version 3.1
We next investigated whether the 44%
of repredicted and newly predicted
WS100 ORFs that could not be cloned
here correspond to false-positive Gene-
Finder predictions, or genuine genes
Figure 2 Cloning success based on the nature of repredictions. (A) Of ORFs cloned in ORFeome
Version 3, 57% were repredicted to be shorter and 31% to be extended at one or both ends, whereas
12% of the cloned ORFs have been extended at one end and truncated at the other end. (B) Example
of an ORF that was successfully cloned in ORFeome Version 3 after having been truncated at the
3-end. The exon/intron structures in blue represent the old (K12H6.9WS9) and new (K12H6.9WS100)
predictions of K12H6.9. Using primers based on WS100 and sequencing the resulting PCR product, we
obtained a sequence trace (black arrow) that aligned to the WS100 prediction, showing a full-length
OST (pink) of the exact structure predicted. The translated protein is shown in green, demonstrating
that the cloned ORF is, indeed, in-frame. The primer designed for the 3-end of the WS9 prediction
cannot anneal to the coding sequence of the WS100 prediction explaining earlier cloning failure. (C)
Example of an ORF that was successfully cloned in ORFeome Version 3 after having been extended at
both ends. The 5-primer based on WS9 is annealing in the middle of an intron in the new predicted
gene model, explaining earlier cloning failure.
Lamesch et al.
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that need further exon/intron corrections. To obtain an estimate
of the rate of repredicted ORFs not cloned in ORFeome Version 3
because of mispredicted ORF boundaries, we designed internal
primers for a small subset of repredicted ORFs for which PCR
amplification had failed (Reboul et al. 2001). These internal
primers were designed to anneal to internally predicted exons,
spanning at least one intron, and to amplify PCR products of 300
bp when the cDNA library is used as a template. As internal exons
are easier to predict and hence more accurate than gene bound-
aries, many ORFs that are mispredicted at their 5- and 3-ends
should be amplifiable using internal primers.
We amplified internal PCR products of the correct length for
52% of ORFs missed in Version 3. The most likely explanation
why we could not clone these ORFs in ORFeome Version 3 is that
their 5-or3-ends are still mispredicted. There are two reasons
why we were unable to amplify internal PCR products for the
remaining 48% of ORFs: ORFs could be mispredicted at the level
of their internal exon/intron structure, which consequently may
render them undetectable in the cDNA library using internal
primers. In addition, predicted ORFs that were not amplified
might be absent from the cDNA library
because they were wrongly predicted
and do not actually exist.
We then investigated whether ORFs
that we could not clone in ORFeome
Version 3, were less supported by EST
and Pfam data than ORFs that we suc-
cessfully cloned. Of uncloned ORFs, 70%
are either touched by EST data (16.5%),
contain a Pfam motif (25.5%), or show
evidence of both EST and Pfam data
(28%). The number of cloned ORFs with
EST and/or Pfam data is only slightly
higher (74%). These results show that a
substantial number of uncloned ORFs
have experimental or bioinformatics evi-
dence of their existence, supporting our
conclusion that the main reason for
cloning failure of C. elegans ORFs is the
misprediction by Genefinder of their 3-
and 5-boundaries.
DISCUSSION
The examples presented in this paper il-
lustrate that the goal of cloning a com-
plete ORFeome should be organized in
gradual steps (Fig. 5). In consecutive
versions of the ORFeome, new, previ-
ously uncloned ORFs are added to the
ORFeome resource, and previously
cloned ORFs found to be a truncated ver-
sion of a repredicted ORF are also re-
placed by the correct full-length equiva-
lent. The updated version of the C. el-
egans ORFeome resource, ORFeome v3.1,
represents all cloned ORFs from ORFe-
ome Versions 1 and 3. Merged ORFs that
were successfully cloned replace earlier
truncated cloned versions if these are
not detectably part of an operon. Ver-
sion 3.1 of the C. elegans ORFeome con-
tains 12,541 full-length, protein-coding
clones (10,623 v1.1a + 2045 Version 3,
127 merged). For each predicted ORF,
information about the cloning status,
the cloned exon/intron structure, and the primers used for clon-
ing can be found in WorfDB (Vaglio et al. 2003; http://
worfdb.dfci.harvard.edu). Clones are available at MRC Geneser-
vices (http://www.hgmp.mrc.ac.uk/geneservice/) and at Open
Biosystems (http://www.openbiosystems.com/).
With the release of ORFeome v3.1, we have validated the
existence of 2045 previously uncloned ORFs. Within this set, the
internal structures of 540 ORFs were corrected. For most ORFs
that were missed in ORFeome v1.1a, we relied on experimental
data to obtain an accurate reprediction. Hence, a continuous sup-
ply of new experimental data is essential to reannotate the ge-
nome, correcting the gene structure of ORFs that were out-of-
frame, mispredicted, or missed in previous versions. Sometimes,
these data also reveal ORFs cloned in-frame that represent trun-
cated versions of longer gene structures. ORFs cloned in-frame
are thus also subject to change and consequently need to be
replaced in the ORFeome resource, underlining the fluid charac-
ter of an ORFeome resource. The reannotation of the genome
and the experimental validation of these new predictions by
cloning thus go hand in hand. Iteratively repeating these two
Figure 3 Internal structure differences observed between WS100 predictions and their aligned OSTs.
The structure of 540 ORFs has been corrected, each showing one or more differences compared with
the corresponding OSTs. OSTs may have more, fewer, longer, or shorter exons than the prediction as
well as additional or missing introns.
Figure 4 Merged genes account for a substantial number of repredictions in previously cloned ORFs.
(A) Example of two ORFs that have been repredicted and merged into one longer ORF. In ORFeome
Version 1 (upper lane), two pairs of primers were generated for the two predicted ORFs. The black
arrows represent a primer pair (mv_F09E8.3) that did not amplify the previously predicted ORF
F09E8.3. The green arrows represent primers (mv_F09E8.4) that successfully amplified a truncated
version of the merged prediction. Using a new primer pair (mv100_F09E8.3), designed on the merged
prediction in WS100 (green arrows, lower lane), this longer ORF was successfully cloned in-frame. (B)
We have attempted to clone 324 merged ORFs in ORFeome Version 3 and confirmed former mispre-
dictions of 99 pairs and 28 triplets of ORFs, each merged into one longer prediction in WS100.
C. elegans ORFeome Version 3.1
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steps increasingly generates a more complete representation of
the C. elegans ORFeome.
The first two C. elegans ORFeome projects relied on different
snapshots of the genome annotation. In both, 60% of the at-
tempted ORFs were successfully cloned as Gateway Entry clones.
The rate of wrongly predicted exons in ORFeome Version 3 de-
creased by 8% compared with ORFeome Version 1, probably as a
consequence of additional EST coverage for the ORFs in WS100.
However, the rate of cloned ORFs that displayed frame errors,
indicating mispredicted ORF boundaries, remained the same
(11%). Furthermore, the comparison of internal primer experi-
ments performed in ORFeome Versions 1 and 3 showed a drop in
the success rate of PCR amplification (73% vs. 52%) for ORFs
missed in ORFeome v1.1. Although this lower success rate might
be caused by a higher rate of false negatives and less optimal
experimental conditions in ORFeome Version 3, it is more likely
that, as the set of ORFs remaining to be cloned decreases, the
proportion of ORFs that do not exist or that are difficult to pre-
dict increases. Ongoing cloning efforts based on continuously
reannotated versions of the genome would thus have an increas-
ing cost-to-benefit ratio.
The continuous efforts made to improve the C. elegans ge-
nome annotation during the last four years increased the size of
the C. elegans ORFeome resource by 20%. A third iterative clon-
ing step, based on a new snapshot of Wormbase predictions,
might only marginally improve the resource. A coming leap in
improved gene annotations will likely result from comparative
genomics, which has proven useful for genome reannotations in
yeast (Cliften et al. 2001, 2003; Kellis et al. 2003) and will soon be
applied to the worm. The comparison of the C. elegans genome to
the newly sequenced Caenorhabditis briggsae genome (Stein et al.
2003) should result in corrected annotations for many previously
predicted genes, as well as the discovery of new genes. Genome
sequencing is currently underway for three additional Caenorhab-
ditis species, Caenorhabditis remaniae, Caenorhabditis japonica, and
CB5161, and when available should enable accurate predictions
of C. elegans ORF structures, upon which
future iterations of the ORFeome project
will be based.
The complete ORFeome for C. el-
egans is thus a long-term project relying
on combined bioinformatics and experi-
mental approaches. Besides providing a
useful tool for functional genomics and
reverse proteomics in the worm, these
efforts might eventually define better
models of metazoan genes, leading to
improved gene prediction algorithms for
numerous other genomes, including the
human genome.
METHODS
Identification of Repredicted ORFs
To find ORFs that were repredicted be-
tween versions WS9 and WS100 of
Wormbase, we compared the start and
stop coordinates of each ORF to the ge-
nome sequence. The sequencing of the
C. elegans genome was completed be-
tween those two versions, and, conse-
quently, because of nucleotide addi-
tions, some of the nonrepredicted ORFs
displayed had changed coordinates in
WS100. Hence, it was necessary to up-
date the start and stop positions of WS9
predictions by aligning their corre-
sponding primers from ORFeome Version 1 to the current ge-
nome sequence. The set of ORFs that we attempted to clone
consists of ORFs in WS100 that overlap with ORFs in WS9 while
having a repredicted start, stop, or both, as well as ORFs that are
newly predicted in WS100. We used the OSP program to design
new primers (Hillier and Green 1991). For ORFs that were repre-
dicted at only one end, we designed new primers at the repre-
dicted ends and used the primers originally synthesized for
ORFeome Version 1 (v1 primers) on the unchanged ends
(mixed primer pairs). For ORFs that were repredicted at both
ends, we designed new forward and reverse primers.
The overall quality of the v1 primers (synthesized a few
years before this work) was tested by comparing PCR amplifica-
tion of pairs of v1 primers, mixed new and v1 primers, and pairs
of all new primers using worm genomic DNA as template. Given
that the PCR success rate on genomic DNA is independent of the
quality of the annotations, similar results are expected for all
primer pairs. The comparison of v1 primer pairs to mixed and
new primer pairs showed a PCR success rate of 74%, 76%, and
83%, respectively. These results indicate that only a small portion
of old primers have decreased in quality since their synthesis,
and can be used in mixed primer pairs without biasing the re-
sults.
Gateway Cloning of C. elegans ORFeome 3.1
Primer pairs were organized by the expected size of ORFs and
aliquoted in 96-well format to optimize PCR conditions for indi-
vidual plates and to facilitate size analysis of PCR products. PCR
amplification for C. elegans ORFs was performed using Platinum
Taq DNA polymerase (Invitrogen), and PCR cycling conditions
were as previously described (Reboul et al. 2003). For one entire
plate of 77 ORFs, we failed to obtain any PCR products, leaving
4155 PCR products to be further processed.
Entry clones were produced using the pDONR201 vector
according to standard Gateway recombinant cloning technology
protocols except that BP cloning reactions were done at one-
fourth of the recommended volume (Invitrogen). Entry clones
were subsequently transformed into DH5 cells rendered chemi-
cally competent with DMSO and cultured overnight in LB liquid
Figure 5 The C. elegans ORFeome is an evolving resource. The cloning of a (nearly) complete
ORFeome will be an iterative process. At each step, predicted ORFs that are successfully cloned in-
frame (+) are added to the ORFeome resource. New attempts to clone ORFs that we cloned out-of-
frame (o.o.f.) or that we did not clone () in earlier cloning steps are based on new or updated
predictions (red box). The first two rounds of cloning, ORFeome Version 1 and Version 3, were based
on two “snapshots” of the C. elegans genome annotation, WS9 and WS100, respectively. Further
cloning steps will be based on different approaches to repredict ORFs, such as comparative genomics.
Our current ORFeome resource, v3.1, contains 12,500 cloned ORFs. At this stage, our ORFeome
resource contains pools of clones for each predicted gene. We are in the process of generating a new
resource, ORFeome v2 (Reboul et al. 2003), in which we isolate individual wild-type clones for all
detected splice variants of ORFs cloned in v1.1a.
Lamesch et al.
2068 Genome Research
www.genome.org
media containing kanamycin (50 µg/mL). Cultures were then
used to inoculate a second 1.0-mL liquid culture containing LB
and kanamycin, which was grown overnight at 37°C. Recombi-
nant products were archived for long-term storage as both bac-
terial glycerol stocks (15% glycerol in LB) and as plasmid DNA
minipreps. A Qiagen 9600 robot was used to purify plasmid DNA.
PCR was performed using recovered plasmid DNA and
pDONR201 sequencing primers (Invitrogen), and the resulting
PCR products were used as template for sequencing as described
(Reboul et al. 2003).
C. elegans cDNA Library
The library used here as PCR template was described earlier (Wal-
hout 2000b).
Sequencing and Bioinformatics Analysis
All cloned ORFs were sequenced at the 5- and 3-ends resulting
in two OSTs (ORF Sequence Tags) for each ORF. ORFs that were
not successfully cloned or sequenced (phred score below 20 over
200 bases) were not included in the analysis. All OSTs were
aligned to the C. elegans genome stored in the ACeDB, using the
acembly alignment software. The comparison between OSTs and
corresponding predicted ORFs was done in two phases. First, all
alignments were analyzed using a previously described protocol
(Reboul et al. 2001), to detect OSTs that displayed a different
internal exon/intron structure than their corresponding ORFs. In
a second phase, these ORFs were analyzed manually to identify
the type of structure difference and to detect frame problems in
the OST. The information resulting from this analysis has been
stored in a MySQL database.
We found 230 ORFs in which no splicing events could be
identified. These ORFs could be categorized as having OSTs that
arose from extremely short sequencing reads that did not span
predicted introns, those that gave rise to average-length OSTs but
for which splicing had not been predicted in that region and
OSTs that were predicted to span an intron but for which no
splicing event was identified. Of the latter category, only 62 ORFs
could be interpreted in our analysis, as we require sequencing
through a splice junction. Of these ORFs, 81% were found to be
out-of-frame, suggesting that they were either mispredicted or
represent pseudogenes.
ACKNOWLEDGMENTS
We thank the C. elegans Sequencing Consortium for a complete
and highly accurate genome sequence; L. Stein, D. Lawson, R.
Durbin, K. Bradnam, N. Chen, and others from Wormbase for
continuously improving genome annotations; the participants
of the annual ORFeome meeting for their input and numerous
suggestions; M. Cusick for critical reading of the manuscript; J.-F.
Rual, N. Bertin, and T. Kishikawa for their input and help; T.
Clingingsmith and C. McCowan for superb administrative assis-
tance; the staff at Illumina and Agencourt for technical assis-
tance; and C. Fraughton for laboratory support. This work was
supported by grants 7 R33 CA81658-02 from the National Cancer
Institute and 5R01HG01715-02 from the National Human Ge-
nome Research Institute and the National Institute of General
Medical Sciences awarded to M.V.
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Received February 23, 2004; accepted in revised form June 15, 2004.
C. elegans ORFeome Version 3.1
Genome Research 2069
www.genome.org
    • "Further, molecular " toolkits " have been created for the Gateway system that provide modular DNA elements for specific applications, such as fluorophores for imaging and methods for genetic manipulation [4][5][6][7][8][9][10][11][12][13][14][15][16][17][18]. Additionally, genome-wide open reading frame libraries (ORFeomes) containing protein coding sequences from human [19][20][21][22], worm [23, 24], frog [25] and multiple bacteria [26][27][28][29] have been cloned into Gateway-compatible vectors , representing valuable resources for the characterization of individual genes. Here, we present a novel set of three-fragment MultiSite Gateway vectors which provide an expanded array of molecular tools. "
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    Full-text · Article · Aug 2016
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    Full-text · Article · Mar 2016
    • "A proteome-scale localization map was generated in budding yeast through the systematic cloning of ORFs into plasmid vectors for inducible overexpression of V5 tagged proteins, followed by immunostaining with an anti-V5 antibody [19] and similar approaches have been used in other systems202122. Due to its simplicity this approach remains very popular and large scale ORF resources are now available for many commonly used model systems, typically in vector formats that allow the easy shuffling to expression vectors containing fluorescent or epitope tags [20,23242526. However, the heterologous promoters and 3 0 regulatory elements often used with these type of vectors do not reflect the endogenous expression levels of most proteins and can disturb cellular functions. "
    [Show abstract] [Hide abstract] ABSTRACT: The localization of a protein is intrinsically linked to its role in the structural and functional organization of the cell. Advances in transgenic technology have streamlined the use of protein localization as a function discovery tool. Here we review the use of large genomic DNA constructs such as Bacterial Artificial Chromosomes as a transgenic platform for systematic tag-based protein function exploration.
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