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

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

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

Gene ontology (GO) analysis of Atlantic cod fast skeletal muscle transcriptome annotated to UniGene cDNA reference data.

<p>Analysis was performed with Blast2GO-PRO. a) Distribution of transcripts with major category of molecular functions at level 2. b) Distribution of transcripts with major category of cellular component. c) Distribution of transcripts with major category of biological process. The larger pie charts display the combined transcript data from six libraries, whereas smaller pie charts indicate individual data for each library.</p

Top 50 highly expressed transcripts according to combined RPKM values from all libraries.

<p>Top 50 highly expressed transcripts according to combined RPKM values from all libraries.</p

Substantial Downregulation of Myogenic Transcripts in Skeletal Muscle of Atlantic Cod during the Spawning Period - Fig 2

<p>(a) Sampling positon of fast skeletal muscle and (b) schematic representation of the data processing pipeline for annotation, gene ontology, heat map, and differential expression analyses of Atlantic cod fast skeletal muscle transcriptomes for both sexes throughout the year.</p

Overview of functional annotation results of Atlantic cod fast skeletal muscle transcriptome.

<p>Analysis was performed by Blast2GO-PRO software. a) Distribution of annotated sequence reads to UniGene cDNA reference data. b) Functional annotation results of Atlantic cod fast skeletal muscle transcriptome annotated to UniGene cDNA reference data.</p