Supplementary Fig. 1

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Supplementary Fig. 1
Supplementary Figure 1. Distributions of (A)
exon and (B) intron lengths in O. sativa and A.
thaliana genes. Green bars are used for O.
sativa and orange bars for A. thaliana. Our
data suggests that both exons and introns are on
average longer in rice than their counterparts in
Arabidopsis thaliana (Supplementary Table 2).
This tendency was especially prevalent among the
first and last exons (Supplementary Table 2). It
is possible that transposon insertions in their
UTRs may have led to the observed differences in
exon lengths between the two species. Another
possibility is that even though the average exon
length is the same we would observe a different
image since the A. thaliana mRNA dataset used
contained a lower proportion of FLcDNAs than that
of O. sativa, the A. thaliana mRNAs perhaps
contain a percentage of incomplete UTRs which may
have biased the average. However, the almost
identical mean numbers of exons in the two
species (Supplementary Table 2) suggested that
the A. thaliana mRNA dataset used was similar to
its rice counterpart in composition. The
distributions of the predicted exon lengths were
fairly similar between the two species
(Supplementary Fig. 1A), but the predicted
introns displayed different distributions
(Supplementary Fig. 1B), which implied that only
a limited number of exons were elongated in the
rice genome or incomplete in the A. thaliana
genome. It appears that the rice introns may
have accepted more transposon inserts than the A.
thaliana introns.
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Supplementary Fig. 1 (Cont.)
(A) Exon length
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Supplementary Fig. 1 (Cont.)
(B) Intron length
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Supplementary Fig. 2
Supplementary Figure 2. Proportion of protein
lengths in five categories. The first three
categories were combined. Short proteins (lt300
a.a.) appear to be enriched in Categories IV and
V.
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Supplementary Fig. 3
Antisense npRNA candidate
BTP/POZ domain-containing protein
NAM-like protein
Supplementary Figure 3. Antisense npRNA in the
rice genome. The Os08g0103700 (AK071064) npRNA
encoded in the forward strand on chromosome 8
overlaps two sense genes Os08g0103600 (AK067168
BTP/POZ domain-containing protein gene) and
Os08g0103900 (AK110611 NAM-like protein gene).
Other features such as A. thaliana mRNAs and
expressed sequence tags (ESTs) are also shown.
See the following URL http//rappub.lab.nig.ac.jp
/g-integra/cgi-bin/f_genemap.cgi?idAK071064
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Supplementary Fig. 4
Supplementary Figure 4. Distribution of
evolutionary distances (p distance) of orthologs
detected between O. sativa and A. thaliana.
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Supplementary Fig. 5
Supplementary Figure 5. Distributions of
evolutionary distances between paralogs in O.
sativa (black bars) and A. thaliana (white bars).
The distances were estimated by the
Poisson-gamma correction with the shape parameter
of 2.25. Even though the distributions of gene
duplicates were quite similar between O. sativa
and A. thaliana (Fig. 2), the process of genome
evolution in each species may have been quite
different. If genes are duplicated and deleted
on a purely random basis without selection
pressure, exponential decay of the duplicate
genes over time should be observed. If a
large-scale duplication event occurred, we would
see a unimodal distribution that peaks at the
point of the duplication event (Blanc, G and
Wolfe K. H. 2004. Widespread paleopolyploidy in
model plant species inferred from age
distributions of duplicate genes. The Plant Cell
16 1667-1678). We estimated the Poisson-gamma
distances (shape parameter 2.25) for duplicate
protein pairs created after the divergence event
between O. sativa and A. thaliana. Here we used
only paralog clusters for two members because the
evolutionary distances between these paralog
clusters could be calculated unambiguously. The
distribution of the O. sativa proteins appeared
to be a combination of the two aforementioned
distributions, whereas in A. thaliana there seems
to be a single large peak as noted by Blanc and
Wolfe (2004), which may be characteristic of a
large-scale duplication. Hence, the different
patterns of duplication events are likely to have
led to the similar patterns of paralog cluster
sizes observed (Fig. 2).
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Supplementary Fig. 5 (Cont.)
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Supplementary Fig. 6
Supplementary Figure 6. Numbers of
lineage-specific and other proteins in five ORF
categories.
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Supplementary Fig. 7
Supplementary Figure 7. Distribution of protein
lengths in lineage-specific and other proteins.