Pathway assignment based on KEGG.

<p>(<b>A</b>) Distribution of assembled unigenes based on 6 main categories pathways. (<b>B</b>) Classification based on Immune System classification.</p

Comparison of the number of unigene annotations obtained from the different databases.

<p>The number of unigene annotations hits from the Nt, Nr, Swiss-Prot and Gene databases (E-value ≤1E-5), respectively.</p

Evidence of positive Darwinian selection from site-specific model analyses for the HAMP gene of fish.

<p><b>Note:</b><i>P</i> number of parameters in the <i>ω</i> distribution, <i>K</i> estimated transition/transversion rate ration, <i>ω</i> selection parameter, and <i>p</i>_n proportion of sites that fall into the <i>ω_n</i> site class. <i>p</i>, <i>q</i> shape parameters of the β function (for models M7 and M8). Only positively selected sites with posterior probability >0.95 are shown.</p

Characteristics of homology search of assembled unigenes against Nr protein database.

<p>(<b>A</b>) FPKM distribution for each assembled unigene. (<b>B</b>) Score distribution of BLAST hits for each unigene with a cutoff E-value of 1E-5. (<b>C</b>) E-value distribution of BLAST hits for each unigene with a cutoff E-value of 1E-5. (<b>D</b>) Identity distribution of the top BLAST hits for each unigene. (<b>E</b>) Similarity distribution of the top BLAST hits for each unigene. (<b>F</b>) Length of unigenes with hits compared with those without hits.</p

Putative gene name, primer sequences and the expected size for RT-PCR of the twelve unigenes.

<p>Putative gene name, primer sequences and the expected size for RT-PCR of the twelve unigenes.</p

Length distribution of cSSRs based on the number of repeat units.

<p>Length distribution of cSSRs based on the number of repeat units.</p

SOXs gene phylogeny and amino acid alignment.

<p>(<b>A</b>) Bootstrap values next to the nodes represent the percentage of 1000 replicate trees supporting the corresponding clade. (<b>B</b>) The predicted SOX proteins from <i>H. chinensis</i> were aligned together with <i>Xenopus (Silurana) tropicalis</i>, <i>Xenopus laevis, Bufo marinus, Rana chensinensis</i> and <i>Andrias davidianus</i> SOX proteins using DNAman multiple alignment program.</p