Characteristics of <i>Thalictrum cirrhosum</i> Chloroplast Genome and Its Analysis on Codon Usage Bias

Hou Zhe; Lou Xiaoming; Li Ang; Huang Changbing

doi:10.11929/j.swfu.202205026

Journal of Southwest Forestry University > 2023 > 43(5): 47-56. > DOI: 10.11929/j.swfu.202205026

Hou Zhe, Lou Xiaoming, Li Ang, Huang Changbing. Characteristics of Thalictrum cirrhosum Chloroplast Genome and Its Analysis on Codon Usage Bias[J]. Journal of Southwest Forestry University, 2023, 43(5): 47-56. DOI: 10.11929/j.swfu.202205026

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Characteristics of Thalictrum cirrhosum Chloroplast Genome and Its Analysis on Codon Usage Bias

Suzhou Polytechnic Institute of Agriculture, Suzhou Jiangsu 215008, China

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Received Date: May 07, 2022
Revised Date: July 03, 2022
Accepted Date: September 02, 2022
Available Online: September 07, 2022
Published Date: September 19, 2023

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Abstract

This study used whole-genome resequencing data to assemble the chloroplast genome(chloroplast, cp) of T. cirrhosum and to analyse its phylogenetic relationships within the genus Thalictrum. The results showed that the chloroplast genome of T. cirrhosum is 155 969 bp in length, with a very typical quadripartite structure; the codon preference analysis showed that the average contents of GC₁, GC₂ and GC₃ were 47.97, 39.99 and 30.07, respectively, among the 48 gene sequences screened; the correlation of ENC values with GC₁ and GC₂ was not significant, while the correlation coefficient with GC₃ was significantly correlated; the neutral mapping analysis shows significant correlation between GC₃ and GC₁₂ and that codon preference is influenced by natural selection; the ENC−plot and ENC ratio frequency distribution results show that most genes have ENC values lower than expected, with only 10 genes are affected by mutations, while the remaining genes are mainly affected by natural selection; the RSCU analysis showed that 18 optimal codons have A and U endings. This study lays the foundation for the genetic engineering of the chloroplasts ofT. cirrhosum and provides reference information for the study of its genetic diversity, genetic structure and population genetics.
- Thalictrum cirrhosum,
- chloroplast genome,
- codon bias,
- optimal codon

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