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Fig. 4 | BMC Biology

Fig. 4

From: Speciation and adaptive evolution reshape antioxidant enzymatic system diversity across the phylum Nematoda

Fig. 4

Evolution of SOD3 and SOD3-like genes in nematodes, human, and mouse. a Phylogeny of SOD3 and SOD3-like genes and gene expression of SOD3 across developmental stages in three nematodes with available RNA-seq data. Lineage-specific expansion in the genus Angiostrongylus, T. canis, and S. papillosus was highlighted. The gene structures of SOD3-like in Clade IVa and Clade IVb, and SOD3 in Clade IVb are shown. Shapes and colors indicate different clades and subclades, as depicted in Fig. 2. Bootstrap values are shown in the node. Scale bar represents the number of amino acid substitutions per site. b, c Syntenic blocks in chromosomes or scaffolds or contigs containing SOD3 or SOD3-like in species from Clade IVa and Clade IVb. Numbers in the parentheses are gene number in blocks. d Fragments of multiple sequence alignments of EC-SOD and SOD3-like. Metal-binding sites are shown in the red box. Red triangles show disulfide bonds. Dots are used to separate blocks. Full alignment is shown in Additional file 1: Fig. S11. e Gene expression patterns of SOD3 or SOD3-like genes in Strongyloides ratti (Sra), S. stercoralis (Sst), and S. papillosus (Spa). Genes with row maximum expression (FPKM) less than 10 were not shown. Detailed expression values were shown in Additional file 6: Table S6. FPKM less than 1 was set 1 to calculate fold change. GFOLD value was calculated between free-living adult female (F_AF) and parasitic adult female (P_AF)

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