Figure 1.
Summary of sequencing read length distributions from the A. palmata transcriptome pre and post assembly.
A) Unassembled raw sequencing read lengths (in basepairs, bp) prior to trimming. B) Size distribution of unassembled sequences (in bp) following quality trimming. C) Plot of the relationship between the length of assembled contigs (in bp) and the depth of coverage in terms of the number of raw ESTs they include (note log-log axes). D) Frequency histogram of contig lengths (in bp).
Table 1.
Summary of sequencing and assembly of the Acropora palmata transcriptome.
Figure 2.
Enrichment analysis highlighted well annotated pathways that are of interest in heat stressed embryos.
A) The five most highly enriched functional categories in the A. palmata dataset (the orange line represents the threshold for significance at p<0.05 with FDR adjustment for multiple testing. B) The top canonical pathways from the IPA library of pathways that were most significant to the dataset. The left Y axis shows the percentage of proteins in the pathway that were identified in the A. palmata data (grey bars, note that this is independent of expression levels). The right Y axis shows the corrected –log (p-values) for Fisher's exact test of the probability that the association between the pathway and the data is explained by chance.
Figure 3.
Homologs involved in canonical oxidative stress response pathways identified in the A. palmata transcriptome.
Filled symbols indicate proteins with homologs that were detected in the A. palmata dataset. Unfilled symbols indicate proteins that were not detected in our data, but are present in model vertebrate pathways.
Figure 4.
Genes involved in the various p53 mediated responses to DNA damage.
Specific pathway details are likely to differ somewhat in the Cnidaria, but the presence of these components in A. palmata suggested the capacity for similar responses in corals. Filled symbols indicate proteins with homologs that were detected in the A. palmata dataset. Unfilled symbols indicate proteins that were not detected in our data, but are present in model vertebrate pathways.
Figure 5.
Tests were performed to detect evidence of natural selection along the branch leading to the Cnidaria with the program PAML (highlighted in red). The sequences in the tree include a subset of those from Rutkowski (2010). The tree was generated in garli using the TIM2+G model.
Figure 6.
Distribution of paralog groups identified between A. palmata and N. vectensis by inparanoid.
Plotting on a gene by gene basis showed that genes with large numbers of paralogs (>5) differed between species. Groups with a single member from each species were most common, and Groups with >5 members each accounted for less than 0.5%. Only a single group with >9 members was found in A. palmata. Circle size is proportional to the number of groups of a given size class.
Table 2.
Paralog group size and identity for paralog groups identified in Acropora palmata as compared to the Nematostella vectensis proteome.
Figure 7.
Microsatellite repeat distributions show similar patterns in A. palmata (red) and A. millepora (blue).
A) Microsatellite frequency distributions showed an abundance of tri and hexanucleotide repeats in both species. B) Trinucleotide motifs were dominated by ATC repeats in both species, followed by varying proportions of AAN type repeats. GC rich repeats were rare, and no CCG repeats were found.
Figure 8.
Frequency of various single nucleotide polymorphism (SNP) types in A. palmata (red) and A. millepora (blue).
Frequencies are given per 1000 bp. Transitions are in red and transversions in blue. The overall frequency of SNPs in A. palmata was 1 per 272 bp.
Figure 9.
Variation in transition to transversion ratios (Ts/Tv) among contigs.
A) The histogram of Ts/Tv ratios showed a number of contigs with ratios <1. B) Plotting the number of transitions (Ts) against the number of transversions (Tv) showed genes that have appreciable numbers of both SNP types. The diagonal line represents a ratio of 1, points below the line have a ratio <1 that may indicate a history of positive selection.
Table 3.
Significantly enriched GO terms associated with transcripts showing especially low (<1) Ts/Tv ratios (Upper) and high (>5) Ts/Tv ratios (Lower).