Phylogenetic tree of the seven <i>mll</i> and <i>setd1</i> paralogues found in vertebrates.

<p>Numbers at the nodes indicate posterior probability and approximate likelihood-ratio values obtained from Bayesian (left) and maximum likelihood (right) methods, respectively. Species abbreviations are as follows: <i>Bt, Bos Taurus; Ce, Caenorhabditis elegans; Cl, Canis lupus familiaris; Dr, Danio rerio; Gg, Gallus gallus; Gm, Gadus morhua; Hs, Homo sapiens; Mm, Mus musculus; On, Oreochromis niloticus; Pt, Pan troglodytes; Rn, Rattus norvegicus; Xt, Xenopus tropicalis.</i> GenBank accession numbers for <i>mll</i> sequences are listed in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0036908#pone.0036908.s010" target="_blank">Table S1</a>.</p

Representative tissue distribution of <i>mll</i> paralogues in adult Atlantic cod.

<p>cDNAs from various tissues (brain, gill, heart, head kidney, kidney, liver, spleen, stomach, mid gut, gas bladder, testis, ovary, fast skeletal muscle, skin and blood) were used for semi-quantitative RT-PCR. <i>Actb</i> and <i>eef1a</i> were used as endogenous references. Expression patterns were determined using three biological replicates.</p

Quantification of <i>mll</i> paralogues and key myogenic genes (<i>myog</i>, <i>myf5</i> and <i>pax7</i>) in fast muscle of Atlantic cod juveniles reared under continuous light (red bars, LD 24:0) or natural photoperiod conditions (blue bars, LDN) for 6 months.

<p>In general, <i>mll</i> genes were differentially expressed between the two light groups and there was a decrease in <i>mll</i> transcript levels with continuous illumination as early as 12 hours, compared to the natural photoperiod group. Myog transcript levels were consistently higher in the constant light group compared to natural photoperiod. Asterisks * and ** indicate significant differences at p<0.05 and p<0.01, respectively (n = 6).</p

Growth history of Atlantic cod juveniles reared under continuous light (LD 24:0, red bars) or natural photoperiod conditions (LDN, blue bars) for six months.

<p>Details of the light regimes are shown by red diamonds or green triangles for LD 24:0 and LDN groups, respectively. Sea water temperature is also indicated by blue circles. Significant differences in mean weight between the two light groups at a particular time point (two-tailed t-test, n = 123) are highlighted by an asterisk.</p

Gene name, GenBank accession number, primer sequences (5′ to 3′), amplicon sizes (bp) and PCR efficiency (%) of <i>mll,</i> s<i>et1d</i> and myogenic genes cloned in Atlantic cod.

<p>Reference genes used are also indicated.</p

Partial synteny map of the genomic region surrounding <i>mll2</i>.

<p>Synteny was disrupted between teleosts and tetrapods. Orthologous genes in <i>Gadus morhua</i>, <i>Oryzias latipes</i>, <i>Gasterosteus aculeatus</i>, <i>Takifugu rubripes</i>, <i>Tetraodon nigroviridis</i> and <i>Danio rerio</i> are colour coded and represented by block arrows that show their orientation in the genome. <i>Mll2</i> paralogues are indicated by the arrow. Additional synteny results for other <i>mll</i> paralogues can be found in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0036908#pone.0036908.s001" target="_blank">Figures S1</a>–<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0036908#pone.0036908.s009" target="_blank">9</a>.</p

Heat maps from pathway enrichment analysis of differentially regulated genes during the transport process.

<p>Significantly regulated genes - at each of the time point [immediately after packing (0 h), and at 48 and 72 h during transport] compared to the values prior to transport (basal) - were subjected to pathway enrichment analysis. Pathways which showed an enrichment of P<0.05 in at least one of the time points are displayed. Columns and rows in the heat map indicate time points and pathways, respectively. Color scale represents P values of enrichment test and gray cells indicate P>0.05.</p

Heat maps from GO enrichment analysis of differentially regulated genes during the transport process.

<p>Significantly regulated genes - at each of the time point [immediately after packing (0 h), and at 48 and 72 h during transport] compared to the values prior to transport (basal) - were subjected to GO enrichment analysis. Representative biological process GO terms with P<0.05 were selected mostly from 3^rd or 4^th levels of GO trees in at least one of the time points. Columns and rows in the heat map indicate time points and GO terms, respectively. Color scale represents P values of enrichment test and gray cells indicate P>0.05.</p

Validation of microarray results by quantitative real time PCR.

<p>Correlation plots indicating the relationship between qPCR results (fold change; Y- axis)) of six selected genes and the corresponding data from microarray analysis (X- axis). Fold changes of genes immediately after packing (0 h), and at 48 and 72 h during transport compared to the values prior to transport (basal) are displayed in the figure. Note that the fold changes for <i>scd</i> are 1/10^th of the actual changes.</p

Physiological parameters measured in zebrafish at various stages during the transport process and prior to transport.

<p>Whole body cortisol (n = 15), blood glucose (n = 15), whole body ammonia (n = 7) and liver ammonia (n = 7) were analyzed prior to transport (basal), immediately after packing (0 h), and at 48 and 72 h of transport.</p><p>Different letters indicate statistically significant differences among the different time points (P<0.05).</p><p>Values are given as means ± s.e.m.</p