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

Characteristics of homology search of assembled unigenes against NR databases.

<p>(<b>A</b>) E-value distribution of BLAST hits for each unigene with a cutoff E-value of 1.0E-5. (<b>B</b>) Identity distribution of the top BLAST hits for each unigene. (<b>C</b>) BLASTx top-hit species distribution of gene annotations against NR databases. (<b>D</b>) Length of unigenes with hits compared with those without hits.</p

Frequency distribution of SNPs based on different types.

<p>A total of 8,510 putative single nucleotide polymorphisms (SNPs) included 2,328 transversions and 6,182 transitions.</p

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

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

Summary of cSSR searching results.

<p>Summary of cSSR searching results.</p

Summary of the miiuy croaker transcriptome.

<p>Summary of the miiuy croaker transcriptome.</p

Frequency distribution of cSSRs based on motif sequence types.

<p>The most abundant repeat motif in our cSSRs was AC/GT (41.90%), followed by AG/CT (15.91%), AGG/CCT (7.12%) and AGC/CTG (4.37%) among 284 motif sequence types.</p