The DNA fragments transferred among cotton cytoplasmic genomes are highly differentiated. The wild D group cotton species have undergone much greater evolution compared with cultivated AD group. Cotton (Gossypium spp.) is one of the most economically important fiber crops worldwide. Gene transfer, nucleotide evolution, and the codon usage preferences in cytoplasmic genomes are important evolutionary characteristics of high plants. In this study, we analyzed the nucleotide sequence evolution, codon usage, and transfer of cytoplasmic DNA fragments in Gossypium chloroplast (cp) and mitochondrial (mt) genomes, including the A genome group, wild D group, and cultivated AD group of cotton species. Our analyses indicated that the differences in the length of transferred cytoplasmic DNA fragments were not significant in mitochondrial and chloroplast sequences. Analysis of the transfer of tRNAs found that trnQ and nine other tRNA genes were commonly transferred between two different cytoplasmic genomes. The Codon Adaptation Index values showed that Gossypium cp genomes prefer A/T-ending codons. Codon preference selection was higher in the D group than the other two groups. Nucleotide sequence evolution analysis showed that intergenic spacer sequences were more variable than coding regions and nonsynonymous mutations were clearly more common in cp genomes than mt genomes. Evolutionary analysis showed that the substitution rate was much higher in cp genomes than mt genomes. Interestingly, the D group cotton species have undergone much faster evolution compared with cultivated AD groups, possibly due to the selection and domestication of diverse cotton species. Our results demonstrate that gene transfer and differential nucleotide sequence evolution have occurred frequently in cotton cytoplasmic genomes.

中文翻译：

---

棉花细胞质基因组的基因转移和核苷酸序列进化表明了新的进化特征。

在棉花细胞质基因组之间转移的 DNA 片段是高度分化的。与栽培的AD组相比，野生D组棉花物种经历了更大的进化。棉花（Gossypium spp.）是全球经济上最重要的纤维作物之一。细胞质基因组中的基因转移、核苷酸进化和密码子使用偏好是高等植物的重要进化特征。在这项研究中，我们分析了棉花叶绿体 (cp) 和线粒体 (mt) 基因组中的核苷酸序列进化、密码子使用和细胞质 DNA 片段的转移，包括棉花物种的 A 基因组组、野生 D 组和栽培 AD 组。 . 我们的分析表明，转移的细胞质 DNA 片段长度的差异在线粒体和叶绿体序列中不显着。对 tRNA 转移的分析发现，trnQ 和其他九个 tRNA 基因通常在两个不同的细胞质基因组之间转移。密码子适应指数值显示棉 cp 基因组更喜欢 A/T 结尾的密码子。D组的密码子偏好选择高于其他两组。核苷酸序列进化分析表明，基因间间隔序列比编码区更具可变性，并且非同义突变在 cp 基因组中明显比 mt 基因组中更常见。进化分析表明，cp基因组中的替代率远高于mt基因组。有趣的是，与栽培的AD组相比，D组棉花物种经历了更快的进化，这可能是由于对不同棉花物种的选择和驯化。我们的研究结果表明，棉花细胞质基因组中经常发生基因转移和差异核苷酸序列进化。