Table 1.
Summary of generated transcriptome data.
Fig 1.
High accumulation of Cd in the P. viridis byssus.
Table 2.
Summary of the RNA-seq based assembly, functional annotation and coding sequences (CDs) from the foot transcriptomes of P. viridis.
Fig 2.
Annotation of unigenes from the P. viridis foot transcriptomes.
Venn diagrams of annotated unigenes (A) and Nr species distribution of unigenes (B) are useful for assessment of the transcriptome assemblies.
Fig 3.
DEG number for Cd_50 vs Control and Cd_100 vs Control.
(A) Up-regulated gene numbers at the three time points; (B) Down-regulated gene numbers at the three time points; (C) Heatmap representation of cluster analysis for the expression patterns of over 9,000 DEGs between the control and different concentrations of Cd stimulation (48-h treatment). The RPKM change patterns of the two concentration of Cd stimulation (Cd_50 and Cd_100) were shown to be clustered together.
Fig 4.
Function classification of DEGs in the P. viridis transcriptomes (48-h treatment).
(A) KEGG metabolic pathway annotation of DEGs; (B) Histogram presentations of the COG classification.
Fig 5.
Validation of byssus protein coding genes by qRT-PCR. β-actin was used as an internal control and each value represents average of 3 separate biological replicates.
Real-time PCR validates the byssus protein coding genes (A) between the Cd_50 and Control and (B) between the Cd_100 and Control (48-h).
Fig 6.
Hierarchical cluster and structure analysis of DEGs for the byssus metal accumulation.
The cysteine (Cys, C), tyrosine (Tyr, Y) and glycine (Gly, G) are highlighted in yellow, pink and green colors respectively. (A) The color key represents RPKM normalized log2 transformed counts in control, Cd_50 and Cd_100. (B) Amino acid sequence of the P. viridis antistasin-like protein (ALP) with 8 highly conserved patterns of CPXXCXXGXXXXXXXXGCXXCXCXXCXX; (C) Comparison of P. viridis PTMP1 with its homologus sequence reported from M. galloprovincialis. The amino acids of the putative MIDAS motif are boxed; (D) Comparison of P. viridis Pvfp-2 with its homologus sequence from M. edulis. Note that the red box is a calcium binding motif. (E) Amino acid sequence of P. viridis foot proteins (Pvfp-3, 5–1, 6), which are rich of Cys and Tyr residues. The underlined regions are signal sequences.