Table S1 Correlation between isoaccepting tRNA gene frequencies and synonymous codon usage in the transcriptome of A. japonicus. from tRNA copy number and codon usage in the sea cucumber genome provide insights to adaptive translation for saponin biosynthesis

Genomic tRNA copy numbers determine cytoplasmic tRNA abundances, which in turn influence translation efficiency, but the underlying mechanism is not well understood. Here, using the sea cucumber <i>Apostichopus japonicus</i> as a model, we combined genomic sequence, transcriptome expression and ecological food resource data to study its codon usage adaptation. The results showed that, unlike intragenic ncRNAs, tRNAs tended to be transcribed independently. This may be attributed to their specific Pol III promoters that lack transcriptional regulation, which may underlie the correlation between genomic copy number and cytoplasmic abundance of tRNAs. Moreover, codon usage optimization was mostly restrained by a gene's amino acid sequence that might be a compromise between functionality and translation efficiency. Genes for stress responses were highly optimized for most echinoderms, while enzymes for saponin biosynthesis (LAS, CYPs and UGTs) were especially optimized in sea cucumbers, which might promote saponin synthesis as a defence strategy. The genomic tRNA content of <i>A. japonicas</i> was positively correlated to amino acid content in its natural food particles, which should promote its efficiency in protein synthesis. We propose that coevolution between genomic tRNA content and codon usage of sea cucumbers facilitate their saponin synthesis and survival on food resource with low nutrient content.