Complete chloroplast genome sequences and codon usage pattern among three wetland plants

Abstract

AbstractArtificial 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.