The Complete Chloroplast Genomic Characteristics and Phylogenetic Analysis of Abutilon theophrasti Medicus

To clarify the phylogenetic relationship between <i>Abutilon theophrasti</i> M. and other <i>Malvaceae</i> plants, the chloroplast genome of <i>A. theophrasti</i> was assembled, annotated, and analyzed. The complete chloroplast genome was sequenced using the Illumina NovaSeq 6000 platform. Bioinformatics methods were employed to systematically analyze its genomic structure, repetitive sequences, nucleic acid diversity, and codon preference. Additionally, a phylogenetic tree was constructed by integrating chloroplast genomic sequences from other <i>Malvaceae</i> species. The results showed that the chloroplast genome of <i>A. theophrasti</i> was 160,440 bp in length with a GC content of 36.89%, exhibiting a typical tetrad structure. A total of 130 coding genes were annotated, including 85 mRNA genes, 37 tRNA genes, and 8 rRNA genes, with no pseudogenes detected. Codon preference analysis indicates that leucine (Leu) is the most frequently used amino acid. There are 31 codons with a relative synonymous codon usage (RSCU) value greater than 1, most of which end with A or U. The genome contains 61 scattered repeat sequences and 288 simple repeat sequences (SSR). Ka/Ks analysis revealed that the overall chloroplast genes of <i>A. theophrasti</i> undergo purifying selection, while genes such as <i>psbK</i> and <i>rps12</i> are subjected to positive selection, which may be associated with adaptive evolution. Phylogenetically, <i>A. theophrasti</i> is most closely related to its congener <i>A. indicum</i>, followed by a clade comprising <i>M. cathayensis</i> and <i>Malva crispa</i> of the genus <i>Malva</i>. This study enhances the understanding of the phylogenetic relationship of <i>A. theophrasti</i> and provides a theoretical basis for the genetic improvement and breeding strategies of <i>A. theophrasti</i> and other <i>Malvaceae</i> plants.