Results: 4

1.
Figure 3

Figure 3. From: Salmo salar and Esox lucius full-length cDNA sequences reveal changes in evolutionary pressures on a post-tetraploidization genome.

Distributions and means of ORF, 5' and 3' UTR sizes in reference FLcDNAs for (A) S. salar (B) E. lucius. Each reference FLcDNA, determined by in-house annotation methods, was examined for an ORF, 5' UTR, and 3' UTR. Means for each region were calculated (+/- standard deviation). An ORF is characterized by a start (ATG) and an in-frame stop codon (TGA, TAG, TAA). The 5' UTR is calculated as the entire area upstream of the start codon, while the 3' UTR is considered the entire area downstream of the stop codon. Any 3' polyA tails were masked and were not included in UTR length calculations.

Jong S Leong, et al. BMC Genomics. 2010;11:279-279.
2.
Figure 2

Figure 2. From: Salmo salar and Esox lucius full-length cDNA sequences reveal changes in evolutionary pressures on a post-tetraploidization genome.

Schematic of S. salar reference FLcDNA identification through individual clone assemblies. Three full-length 5'-CAP enriched libraries were created. A 4,380 clone subset of library rgf was resequenced to completion. Libraries rgg and rgh were bi-directionally sequenced and individually assembled using PHRAP (1). A BLASTX was carried out resulting in a total of 14,384 well-annotated cDNAs (2), which were further reduced to 8,469 FL annotations by increasing the stringency of the local alignment length (3). In-frame annotation-flanking start and stop codons were found from the reduced set, resulting in a set of 7,255 reference FLcDNA candidates (4). Intra-library sequence redundancy was minimized using an all versus all pairwise BLASTN comparison (5), resulting in a total set of 3,204 non-redundant reference FLcDNAs.

Jong S Leong, et al. BMC Genomics. 2010;11:279-279.
3.
Figure 1

Figure 1. From: Salmo salar and Esox lucius full-length cDNA sequences reveal changes in evolutionary pressures on a post-tetraploidization genome.

Schematic of S. salar FLcDNA contig identification and reference FLcDNA identification. Two-stage assembly of 434,384 high-quality 5'- and 3'-end ESTs identified 81,398 contigs (1-2) for FL contig identification. A BLASTX was carried out resulting in 34,451 well-annotated contigs (3), which were further reduced to 14,021 FL annotations by increasing the stringency of the local alignment length (4). In-frame annotation-flanking start and stop codons were found from the reduced set, resulting in a set of 10,026 FL contigs (5). The FL contigs represent the complete set of FL unique putative transcripts. A set of all reads and subsequently sequenced library rgf reads was mapped to the FL contigs (6). Those clones whose 5'- and 3'-end reads map to the same contig were analyzed to determine sequence overlap (complete) or non-overlap (incomplete) (7). Only complete clones are considered, and a single representative of a clone is taken for each transcript resulting in 5,953 complete reference FLcDNAs (8).

Jong S Leong, et al. BMC Genomics. 2010;11:279-279.
4.
Figure 4

Figure 4. From: Salmo salar and Esox lucius full-length cDNA sequences reveal changes in evolutionary pressures on a post-tetraploidization genome.

Frequencies of dS and ω values for comparisons within S. salar and E. lucius gene trios. (A) Distributions of dS values from pairwise comparisons within gene trios: between S. salar paralogs (green) and between each of the two S. salar paralogs and its corresponding E. lucius ortholog (gray and black). (B) Distributions of dN/dS ratios (ω) from pairwise comparisons within gene trios: between S. salar paralogs (green) and between each of the two S. salar paralogs and its corresponding E. lucius ortholog (gray and black). (C) Distributions of dS values separated into individual tree branches based on gene trios. Values from pairwise comparisons were used to calculate silent substitution rates for periods before and after the salmonid tetraploidization event. The light blue curve represents frequencies of dS values from the duplication event to one S. salar paralog, the red curve from the duplication event to the other paralog, and the black curve prior to the genome duplication to the E. lucius ortholog. (D) Distributions of dN/dS ratios separated into branches where one S. salar paralog, that which has the lower ω value, is considered to be a slow branch (light blue curve) and the other paralog (red curve) is considered to be more quickly diverging (fast branch for the purposes of labelling). The black curve displays frequencies of ω values between the E. lucius ortholog and the genome duplication.

Jong S Leong, et al. BMC Genomics. 2010;11:279-279.

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