Structural Characterization of Trivalvaria costata Chloroplast Genome and Molecular Evolution of rps12 Gene in Magnoliids

Abstract

Chloroplasts (cp) are important organelles in plant cells that have been widely used in phylogenetic, molecular evolution, and gene expression studies due to their conserved molecular structure. In this study, we obtained the complete cp genome of Trivalvaria costata (Annonaceae) and analyzed its structural characteristics. Additionally, we analyzed the rps12 gene in the phylogenetic framework of magnoliids. The T. costata cp genome comprises 1,662,002 bp and contains 132 genes. We detected 48 simple sequence repeats (SSRs) and identified 29 high-frequency codons as well as 8 optimal codons. Our multiple analyses show that codon usage bias is mainly influenced by natural selection. For the first time, we found the rps12 gene to be entirely located in the IR region (in Annona). In groups with exon 1 located in the single-copy (SC) region and exons 2–3 located in the inverted repeat (IR) region, the transition rate and synonymous substitution rate of exon 1 were higher than those of exons 2–3. Adaptive evolution identified a positive selection site (116) located in the 310-helix region, suggesting that the rps12 gene may undergo adaptive changes during the evolutionary history of magnoliids. This study enhances our knowledge regarding genetic information on T. costata and provides support for reduced substitution rates in the IR region.

Comparative analysis of plastid genomes reveals rearrangements, repetitive sequence features, and phylogeny in the Annonaceae

“…Our results support Annonoideae and Malmeoideae as monophyletic groups and sister clades, with Cananga odorata outside of them, followed by Anaxagorea javanica. Additionally, we observed that the phylogenetic relationships within Malmeoideae species had low support in all trees except the BI tree, consistent with previous research (Ping et al, 2023). Furthermore, we found that Chieniodendron hainanense is located within Malmeoideae, which is consistent with the findings of Thomas et al (2012), who placed Chieniodendron within Meiogyne (Malmeoideae).…”

“…In Annonoideae, 10 to 32 protein-coding genes enter the IR region in Annonoideae, which directly increases the total number of genes. Notably, in Annona, 5'-rps12 is located in the IR region, which is rarely reported before (Ping et al, 2023). In ferns and gymnosperms, it has been found that 3'-rps12 enters or leaves the IR region as the IR region expands or contracts, and it has been shown that 3'-rps12 in the IR region has reduced substitution rates and a more conserved sequence signature (Ping et al, 2021b, c).…”

“…Wang et al (2021), through phylogenetic analysis of five chloroplast regions (psbA-trnH, trnL-F, matK, rbcL, and atpB-rbcL), explicitly placed Meiogyne kwangtungensis P. T. Li within the branch of Pseuduvaria. Ping et al (2023) constructed a phylogenetic tree of 65 magnoliid species using shared PCGs and found support for Annonoideae and Malmeoideae as sister groups. In our study, we investigated the phylogenetic relationships of 28 Annonaceae species based on 75 shared plastid PCGs.…”

“…Recently, Gan et al (2022) published the plastome of Miliusa glochidioides Hand.-Mazz. Ping et al (2023) published the plastome of the Trivalvaria costata (J. D. Hooker and Thomson) I. M. Turner and discovered variations in the IR region among different species of the Annonaceae.…”