Comparative and Phylogenetic Analysis of Complete Chloroplast Genomes in Leymus (Triticodae, Poaceae)

Abstract

Leymus is a perennial genus that belongs to the tribe Triticeae (Poaceae) which has an adaptive capacity to ecological conditions and strong resistance to cold, drought, and salinity. Most Leymus species are fine herbs that can be used for agriculture, conservation, and landscaping. Due to confusion taxonomy within genera, the complete chloroplast (cp) genome of 13 Leymus species was sequenced, assembled, and compared with those of three other previously published Leymus species (Leymus condensatus, Leymus angustus, and Leymus mollis) to clarify the issue. Overall, the whole cp genome size ranged between 135,057 (L. condensatus) and 136,906 bp (Leymus coreanus) and showed a typical quadripartite structure. All studied species had 129 genes, including 83 protein-coding genes, 38 transfer RNAs, and 8 ribosomal RNAs. In total, 800 tandem repeats and 707 SSR loci were detected, most of which were distributed in the large single-copy region, followed by the inverted repeat (IR) and small single-copy regions. The sequence identity of all sequences was highly similar, especially concerning the protein-coding and IR regions; in particular, the protein-coding regions were significantly similar to those in the IR regions, regardless of small sequence differences in the whole cp genome. Moreover, the coding regions were more conserved than the non-coding regions. Comparisons of the IR boundaries showed that IR contraction and expansion events were reflected in different locations of rpl22, rps19, ndhH, and psbA genes. The close phylogenetic relationship of Leymus and Psathyrostachys indicated that Psathyrostachys possibly is the donor of the Ns genome sequence identified in Leymus. Altogether, the complete cp genome sequence of Leymus will lay a solid foundation for future population genetics and phylogeography studies, as well as for the analysis of the evolution of economically valuable plants.

Characterization and Comparative Analysis of Complete Chloroplast Genomes of Four Bromus (Poaceae, Bromeae) Species

“…In total, 350 SSR sequences were detected in the eight Bromus cp genomes ( Figure 3 ). These sequences demonstrated the highest A/T content at 58.6% and the greatest number of repeats, aligning with findings reported in other plant studies [ 55 , 56 , 57 ]. The repeat units AAAAAT/ATTTTTT and ACATCT/AGATGT, unique to B. diandrus , and the repeat unit AAAAT/ATTTTT, unique to B. ciliatus , discovered in this study can serve as molecular markers to differentiate between the two species.…”

Phylogenomic analysis of Bupleurum in Western Sichuan, China, including an overlooked new species

“…In some cases, the highly variable regions worked well in resolving phylogeny and identifying species ( Dong et al., 2021 ; Song et al., 2022 ), but in some other cases they were not so effective ( Wu et al., 2020 ); more often, their effectiveness has not been evaluated ( Liu K et al., 2021 ; Liu X.J. et al., 2021 ; Wu et al., 2022 ). In order to assess whether the they can work in Bupleurum phylogenetic analysis and species identification, we checked the highly variable regions in cp genomes of the six Bupleurum species.…”

Comparative Analysis of Codon Usage Patterns in Nuclear and Chloroplast Genome of Dalbergia (Fabaceae)

“…The chloroplast (cp) genome is non-recombinant and maternally inherited, exhibiting features such as semi-autonomy and conservative gene content, organization, and structure relative to the mitochondrial and nuclear genomes [11,12]. It is relatively stable in structure and contains a large amount of genetic information specific to plants.…”