AUTHOR=He Ling , Xu Sujuan , Cheng Xinnian , Huang Hanlin , Dai Hongyu , Wang Xin , Ding Zhiyang , Xu Ming , Gu Haoran , Yan Na , Wang Chunyan 

TITLE=Chloroplast genomes in seven Lagerstroemia species provide new insights into molecular evolution of photosynthesis genes

JOURNAL=Frontiers in Genetics

VOLUME=15

YEAR=2024

URL=https://www.frontiersin.org/journals/genetics/articles/10.3389/fgene.2024.1378403

DOI=10.3389/fgene.2024.1378403

ISSN=1664-8021

ABSTRACT=<p><italic>Lagerstroemia indica</italic> is an important commercial tree known for the ornamental value. In this study, the complete chloroplast genome sequence of <italic>Lagerstroemia indica</italic> “Pink Velour” (<italic>Lagerstroemia</italic> “Pink Velour”) was 152,174 bp in length with a GC content of 39.50%. It contained 85 protein coding genes (PCGs), 37 tRNAs, and 8 rRNA genes. 207 simple sequence repeats (SSRs) and 31 codons with relative synonymous codon (RSCU)value &gt; 1 were detected. Phylogenetic analysis divided 10 <italic>Lagerstroemia</italic> species into evolutionary branches of clade A and clade B. We conducted a comparative analysis of <italic>Lagerstroemia</italic> “Pink Velours” complete chloroplast genome with the genomes of six closely related <italic>Lagerstroemia</italic> species from different origins. The structural features of all seven species were similar, except for the deletion of ycf1 nucleobases at the JSA boundary. The large single-copy (LSC) and the small single-copy (SSC) had a higher sequence divergence than the IR region, and 8 genes that were highly divergent (<italic>trnK-UUU</italic>, <italic>petN</italic>, <italic>psbF</italic>, <italic>psbJ</italic>, <italic>ndhE</italic>, <italic>ndhD</italic>, <italic>ndhI</italic>, <italic>ycf1</italic>) had been identified and could be used as molecular markers in future studies. High nucleotide diversity was present in genes belonging to the photosynthesis category. Mutation of single nucleic acid was mainly influenced by codon usage. The value percentage of nonsynonymous substitutions (Ka) and synonymous substitutions (Ks) in 6 <italic>Lagerstroemia</italic> species revealed that more photosynthesis genes have Ka or Ks only in <italic>Lagerstroemia fauriei</italic>, <italic>Lagerstroemia limii</italic>, and <italic>Lagerstroemia subcostata</italic>. These advances will facilitate the breeding of closely related <italic>Lagerstroemia</italic> species and deepen understanding on climatic adaptation of <italic>Lagerstroemia</italic> plants.</p>