Evolution of the genomes of two nematodes in the ... - Ken Wolfe

3.4 FUTURE WORK
We found ∼1650 orphans in the two worms. Some of these orphans may be novel genes that have arisen
in one of the two genomes since the species diverged (Long, 2001). However, others of the candidate
orphans may not be real orphans at all, but are either pseudogenes that have not yet been deleted, or
are very rapidly evolving genes that have diverged so rapidly that the the BLAST and Smith-Waterman
algorithms (used in the Gene Families section of Stein et al., 2003) cannot recognise their cross-species
matches. In C. elegans, orphans are clustered on the arms of chromosomes: regions with unusually high
rates of chromosomal rearrangement, amino acid substitution, and transposable element insertion (Stein
et al., 2003). I am interested in investigating whether the novel worm genes arose as by-products of
chromosomal rearrangements, since rearrangements have been implicated in the birth of some novel
genes (Long, 2001).
3.5 METHODS
3.5.1 Protein coding Gene Prediction
We predicted protein coding genes in the C. briggsae genome using Genefinder (version 980506; Phil
Green, unpublished software), Fgenesh (Salamov and Solovyev, 2000), Twinscan (Korf et al., 2001),
and the Ensembl annotation system (Clamp et al., 2003). We also ran Genefinder and Fgenesh on the
C. elegans genome.
The four gene prediction programs yielded a combined total of 430,575 exon predictions and 73,997
gene predictions in the C. briggsae assembly. Many of the predictions from different programs overlapped,
so the actual number of exons and genes is far less. The C. elegans data consisting of WS77 gene models
and Fgenesh and Genefinder predictions totalled 393,529 exon predictions and 61,525 gene predictions.
To select among overlapping predictions produced by different programs, we developed a selection
procedure that worked as follows:
1. Many of the exons predicted by different programs overlapped. We took only the longer of any two
exons that overlapped by ≥75% of their lengths and were in the same reading frame.
2. We clustered the exons within each species. Two exons were put in the same “exon cluster” if ≥1
gene prediction program placed them together in a gene prediction. Each exon-cluster consisted of
≥1 overlapping gene predictions.
3. For each exon-cluster X, we found the most homologous exon-cluster Y in the other species. Cluster
Y was the exon-cluster with the top BLASTP (Altschul et al., 1997) hit from any of the exons
in X. For example, for the C. elegans exon-cluster containing the ce-acy-4 gene, its top homologue
was the C. briggsae exon-cluster containing the cb-acy-4 gene (Figure 3.1).
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