Artificial wetlands are now constructed to be used for wastewater treatment, water quality improvement of reservoirs, and landscape reintegration purposes. The removal and degradation of enriched nutrients and pollutants from them are efficiently done by the activity of wetland plants. Most studies are focused on the purification capacity; the identification and classification of these species are lacking. In the present research, chloroplast genomes (cp genome) of three wetland plants namely, Cyperus alternifolius L., Thalia dealbata Fraser, and Canna indica L. were examined. The cp genomes of these species were sampled and sequenced using Illumina HiSeq platform with a 300-bp paired-end sequencing followed by the analysis of codon usage pattern. In the experiment, 3.86 Gb clean data were obtained and 310 genes from each of C. alternifolius and T. dealbata and 62 genes in C. indica were predicted. In the optimal codons analysis, showed that three cp genome preferred A/U-ending and 3, 11, and 14 were identified in the C. alternifolius, T. dealbata, and C. indica cp genomes, respectively. Advanced analysis indicated that other factors (e.g., natural selection) play a major role in shaping codon usage pattern rather than mutation pressure. These results extend the codon usage bias study of plants and provide genetic data for further identification and phylogenetic studies.

中文翻译：

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三种湿地植物中完整的叶绿体基因组序列和密码子使用方式

现在建造了人工湿地，用于废水处理，改善水库水质和景观整合。湿地植物的活动可以有效地从中去除和降解丰富的养分和污染物。大多数研究都集中在净化能力上。缺乏对这些物种的识别和分类。在本研究中，三种湿地植物的叶绿体基因组（cp基因组）分别是莎草，塔利亚塔拉巴塔弗雷泽和印度大麻。L.被检查。使用Illumina HiSeq平台对这些物种的cp基因组进行采样和测序，并具有300 bp的配对末端测序，然后分析密码子使用方式。在实验中，获得3.86千兆干净的数据，并且从每个的310个基因C. alternifolius和T.银荆和62个基因美人蕉进行了预测。在最佳密码子分析，表明3个CP基因组优选的A / U-结束和3，图11，和14中所识别的C. alternifolius，T.银荆，和美人蕉cp基因组。先进的分析表明，其他因素（例如自然选择）在塑造密码子使用方式而不是突变压力方面起着主要作用。这些结果扩展了植物的密码子使用偏好研究，并为进一步的鉴定和系统发育研究提供了遗传数据。