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Species- and sex-specific patterns were observed in stress response and recovery, with pink salmon mounting a higher magnitude stress response for plasma variables and sockeye salmon exhibiting a higher and more variable gene expression profile.
In all strains, there were more variable gene clusters on chromosome II than chromosome I, even though chromosome II is smaller.
As all proposed mechanisms for local co-expression are likely to act in a distance-dependent way [ 1], this should enhance their signal compared to genomes with larger and more variable gene distances.
Studying the triangular relationship between methylation, gene expression, and GC3 (figs. 2 and 3), we observe that GC3-rich genes tend to have more variable gene expression and lesser gene-body methylation levels than the GC3-poor genes.
Land plant mitochondria are known to have more variable gene content compared to chloroplasts where functional gene transfer from the chloroplast genome to the nuclear genome is a rare event [ 78].
For HLA class II loci, HLA-DRB1 and -DPB1 encode relatively more variable gene products for HLA-DR and -DP molecules respectively, while both HLA-DQB1 and -DQA1 are variable in human population.
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Sequencing of other more variable genes and a more considered analysis would help to resolve this.
The more variable genes stamp and vmp1 encoding for surface proteins showed further differentiation.
In contrast, the more variable genes (s 2 >1.75) showed higher mRNA levels than average.
The results further suggest that the resolution at the isolate level may, subsequently be improved by targeting more variable genes.
In order to investigate the differences that these more variable genes may entail and find significant differentially expressed (DE) genes, we applied two algorithms: DEseq and Cuffdiff.
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