Data set S3. Correlation between TAAI, stAI and gene length in different deuterostomes.; Data set S4. Protein sequences of sea cucumber-specific CYPs and UGTs and their closest homologs. 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.

基因组转运RNA（transfer RNA, tRNA）拷贝数决定胞质tRNA丰度，进而影响翻译效率，但其背后的分子机制尚未得到充分阐释。本研究以刺参（*Apostichopus japonicus*）为研究模型，整合基因组序列、转录组表达数据与生态食物资源数据，对其密码子使用适应性展开研究。研究结果显示，与基因内非编码RNA（intragenic non-coding RNA, ncRNA）不同，tRNA更倾向于独立转录。这一特征可能源于其特有的RNA聚合酶III（RNA polymerase III, Pol III）启动子缺乏转录调控，而这或许正是tRNA基因组拷贝数与胞质丰度之间存在相关性的内在机制。此外，密码子使用偏好性的优化大多受基因氨基酸序列的约束，这可能是蛋白质功能与翻译效率之间的一种权衡。对于多数棘皮动物而言，应激响应相关基因的密码子使用优化程度较高；而皂苷生物合成相关酶（LAS、CYPs与UGTs）的密码子使用在海参中尤其优化，这可能通过促进皂苷合成作为防御策略。刺参（*Apostichopus japonicus*）的基因组tRNA含量与其天然食物颗粒中的氨基酸含量呈正相关，这有助于提升其蛋白质合成效率。本研究提出，海参基因组tRNA含量与密码子使用偏好性之间的共进化，助力其皂苷合成以及在低营养食物资源环境下的生存。