Intracellular gene transfer is widely recognized as one of the most important driving forces for species evolution. Here we investigated transferred cytoplasmic motifs in green plants including spore-bearing plants and seed-bearing plants (hereafter termed spore plants and seed plants) . Our analyses revealed that gene transfer in spore plants was characterized by shorter motifs than that of seed plants. Several spore species did not exhibit intracellular gene transfer. Meanwhile, high frequency transferred tRNA genes were identified with average values of minimum free energy at moderate level. From the chloroplast to the mitochondrial genome, trnP was found to have transferred with high frequency in green plants. In gene transfer from the mitochondrial to the chloroplast genome, trnN was found to be a highly transferred gene. We observed that several tRNA genes including trnF, trnW, and trnN were involved in bidirectional transfer, which may be related to application strategy of functional protein-coding genes in a plant’s adaptive evolution. Codon Adaptation Index (CAI) analysis showed that codon usage was unbalanced in spore and seed plants. CAI values for seed plants were higher than those for spore plants in general, which may reveal rapid divergence adaptability of codon usage in the former. These results provide novel insights into gene transfer and codon usage within cytoplasmic genomes.

中文翻译：

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绿色植物细胞内基因转移和细胞质基因组的密码子使用

细胞内基因转移被广泛认为是物种进化最重要的驱动力之一。在这里，我们研究了绿色植物中转移的细胞质基序，包括带有孢子的植物和带有种子的植物（以下称为孢子植物和种子植物）。我们的分析表明，孢子植物中的基因转移的特征是比种子植物的基序更短。一些孢子种类没有表现出细胞内基因转移。同时，高频转移的tRNA基因被鉴定为具有中等水平的最小自由能平均值。研究发现，trnP 在绿色植物中从叶绿体到线粒体基因组的转移频率很高。在从线粒体到叶绿体基因组的基因转移中，trnN被发现是一个高度转移的基因。我们观察到包括trnF、trnW和trnN在内的多个tRNA基因参与双向转移，这可能与功能蛋白编码基因在植物适应性进化中的应用策略有关。密码子适应指数（CAI）分析表明，孢子和种子植物中的密码子使用不平衡。一般来说，种子植物的 CAI 值高于孢子植物，这可能揭示了前者密码子使用的快速分化适应性。这些结果为细胞质基因组内的基因转移和密码子使用提供了新的见解。密码子适应指数（CAI）分析表明，孢子和种子植物中的密码子使用不平衡。一般来说，种子植物的 CAI 值高于孢子植物，这可能揭示了前者密码子使用的快速分化适应性。这些结果为细胞质基因组内的基因转移和密码子使用提供了新的见解。密码子适应指数（CAI）分析表明，孢子和种子植物中的密码子使用不平衡。一般来说，种子植物的 CAI 值高于孢子植物，这可能揭示了前者密码子使用的快速分化适应性。这些结果为细胞质基因组内的基因转移和密码子使用提供了新的见解。