Comparative and Phylogenetic Analysis Based on the Chloroplast Genome of Coleanthus subtilis (Tratt.) Seidel, a Protected Rare Species of Monotypic Genus

Abstract

Coleanthus subtilis (Tratt.) Seidel (Poaceae) is an ephemeral grass from the monotypic genus Coleanthus Seidl, which grows on wet muddy areas such as fishponds or reservoirs. As a rare species with strict habitat requirements, it is protected at international and national levels. In this study, we sequenced its whole chloroplast genome for the first time using the next-generation sequencing (NGS) technology on the Illumina platform, and performed a comparative and phylogenetic analysis with the related species in Poaceae. The complete chloroplast genome of C. subtilis is 135,915 bp in length, with a quadripartite structure having two 21,529 bp inverted repeat regions (IRs) dividing the entire circular genome into a large single copy region (LSC) of 80,100 bp and a small single copy region (SSC) of 12,757 bp. The overall GC content is 38.3%, while the GC contents in LSC, SSC, and IR regions are 36.3%, 32.4%, and 43.9%, respectively. A total of 129 genes were annotated in the chloroplast genome, including 83 protein-coding genes, 38 tRNA genes, and 8 rRNA genes. The accD gene and the introns of both clpP and rpoC1 genes were missing. In addition, the ycf1, ycf2, ycf15, and ycf68 were pseudogenes. Although the chloroplast genome structure of C. subtilis was found to be conserved and stable in general, 26 SSRs and 13 highly variable loci were detected, these regions have the potential to be developed as important molecular markers for the subfamily Pooideae. Phylogenetic analysis with species in Poaceae indicated that Coleanthus and Phippsia were sister groups, and provided new insights into the relationship between Coleanthus, Zingeria, and Colpodium. This study presents the initial chloroplast genome report of C. subtilis, which provides an essential data reference for further research on its origin.

Characterization and Comparative Analysis of Chloroplast Genomes in Five Uncaria Species Endemic to China

“…The GC content was identical to the other Rubiaceae family members [ 26 , 44 , 45 ]. The IR areas contained four rRNA genes with high GC content, which supported the hypothesis of previous research [ 46 , 47 , 48 , 49 ]. A previous study found that the GC content was substantially higher, most likely due to the abundance of rRNA in the IR regions [ 50 ].…”

“…During the evolution of terrestrial plants, the chloroplast genome’s IR region frequently experiences length variations, which results in the formation of a variety of boundary features [ 32 , 49 , 53 ]. Furthermore, the primary causes of the size change in cp genomes are the contraction and expansion of IR regions and the single-copy (SC) border regions, which influences the cp genome’s rate of evolution [ 54 , 55 ].…”

“…Contraction and expansion as well as variation at the SC-IR boundary were identified, suggesting that gene location information in the SC-IR region can reveal the distance between species to some extent. During the evolution of terrestrial plants, length variation in the IR region of the chloroplast genome was a frequent occurrence, which resulted in the formation of a variety of boundary features [ 32 , 49 , 53 ]. Furthermore, the contraction and expansion of IR regions and the single-copy (SC) border regions are also the main contributors to the size variation in cp genomes, which influences the evolutionary rate of the cp genome [ 54 , 55 ].…”

“…This research will not only help shed lighter on the evolutionary position of Uncaria but also offer useful chloroplast genomic data for future investigations into the genesis and diversification of Rubiaceae. Overall, our phylogenomic investigations using chloroplast genomes have made the first successful effort to clarify intrageneric connections within the Uncaria genus [ 49 ].…”

Comparative and phylogenetic analyses of the chloroplast genome reveal the taxonomy of the Morus genus

“…Twenty-two intron-containing genes out of 125 genes were detected in these CP genomes. Among them, the trnK-UUU gene embodied the matK genes and had the largest intron (over 2,500 bp), which has been reported in previous studies (Li X. et al, 2019;Souza et al, 2020;Ren et al, 2022). matK is a well-known gene that is often used for molecular identification and analysis of genetic relationships in plants (Hilu and Liang, 1997;Ramesh et al, 2022), including Morus (Venkateswarlu et al, 2012).…”