Complete chloroplast genomes and comparative analysis of Ligustrum species

Abstract

In this study, we assembled and annotated the chloroplast (cp) genomes of four Ligustrum species, L. sinense, L. obtusifolium, L. vicaryi, and L. ovalifolium ‘Aureum’. Including six other published Ligustrum species, we compared various characteristics such as gene structure, sequence alignment, codon preference, and nucleic acid diversity, and performed positive-selection genes screening and phylogenetic analysis. The results showed that the cp genome of Ligustrum was 162,185–166,800 bp in length, with a circular tetrad structure, including a large single-copy region (86,885–90,106 bp), a small single-copy region (11,446–11,499 bp), and a pair of IRa and IRb sequences with the same coding but in opposite directions (31,608–32,624 bp). This structure is similar to the cp genomes of most angiosperms. We found 132–137 genes in the cp genome of Ligustrum, including 89–90 protein-coding genes, 35–39 tRNAs, and 8 rRNAs. The GC content was 37.93–38.06% and varied among regions, with the IR region having the highest content. The single-nucleotide (A/T)n was dominant in simple-sequence repeats of the Ligustrum cp genome, with an obvious A/T preference. Six hotspot regions were identified from multiple sequence alignment of Ligustrum; the ycf1 gene region and the clpP1 exon region can be used as potential DNA barcodes for the identification and phylogeny of the genus Ligustrum. Branch-site model and Bayes empirical Bayes (BEB) analysis showed that four protein-coding genes (accD, clpP, ycf1, and ycf2) were positively selected, and BEB analysis showed that accD and rpl20 had positively selected sites. A phylogenetic tree of Oleaceae species was constructed based on the whole cp genomes, and the results were consistent with the traditional taxonomic results. The phylogenetic results showed that genus Ligustrum is most closely related to genus Syringa. Our study provides important genetic information to support further investigations of the phylogenetic development and adaptive evolution of Ligustrum species.

Chloroplast genome sequence of triploid Toxicodendron vernicifluum and comparative analyses with other lacquer chloroplast genomes

“…The cp genomes ranged from 158,221 bp (triploid T. vernicifluum ) to 159,710 bp [ T. vernicifluum and T. succedaneum (Ts)], with a difference in size of 1489 bp. Large variation in LSC length (742 bp) accounted for most of this genome-wide variation, which indicated that variation in genome length appears to be mainly caused by variation in LSC length [ 39 ]. The GC content of the ten Toxicodendron accessions ranged from 37.9-38.0%, which is closely related to species affinity [ 40 ].…”

Comparative analyses of Linderniaceae plastomes, with implications for its phylogeny and evolution

“…Previous studies have revealed that the expansion and contraction of the IR, LSC, and SSC regions are common during evolution and are the main reason for variations in plastome size ( Ravi et al., 2007 ; Downie and Jansen, 2015 ; Daniell et al., 2016 ). Significant contraction of IR region was observed among Linderniaceae species ( Supplementary Figure 2 ), which was also common in Lamiales, such as Gesneriaceae ( Gu et al., 2020 ), Lamiaceae ( Su et al., 2022 ), Oleaceae ( Long et al., 2023 ), Plantaginaceae ( Xie et al., 2023 ), and Scrophulariaceae ( Wang et al., 2022 ). Notably, the IR boundaries did not coincide exactly in the three populations of L. polygonoides , but they had the same plastome size.…”

Comparative analyses of complete plastid genomes from seven representative species of Convallarioideae (Asparagaceae)

“…Comparative analyses make it easy to identify mutational hotspots in plant due to their highly conservative structure. The presence of mutational hotspots surrounded by conserved sequences serves as the foundation for DNA barcodes commonly utilized in population genetic or phylogenetic research [42].…”