Wu, T.; Sima, Y.-K.; Chen, S.-Y.; Fu, Y.-P.; Ma, H.-F.; Hao, J.-B.; Zhu, Y.-F. Comparative Analysis of the Chloroplast Genomes of Eight Species of the Genus Lirianthe Spach with Its Generic Delimitation Implications. Int. J. Mol. Sci.2024, 25, 3506.
Wu, T.; Sima, Y.-K.; Chen, S.-Y.; Fu, Y.-P.; Ma, H.-F.; Hao, J.-B.; Zhu, Y.-F. Comparative Analysis of the Chloroplast Genomes of Eight Species of the Genus Lirianthe Spach with Its Generic Delimitation Implications. Int. J. Mol. Sci. 2024, 25, 3506.
Wu, T.; Sima, Y.-K.; Chen, S.-Y.; Fu, Y.-P.; Ma, H.-F.; Hao, J.-B.; Zhu, Y.-F. Comparative Analysis of the Chloroplast Genomes of Eight Species of the Genus Lirianthe Spach with Its Generic Delimitation Implications. Int. J. Mol. Sci.2024, 25, 3506.
Wu, T.; Sima, Y.-K.; Chen, S.-Y.; Fu, Y.-P.; Ma, H.-F.; Hao, J.-B.; Zhu, Y.-F. Comparative Analysis of the Chloroplast Genomes of Eight Species of the Genus Lirianthe Spach with Its Generic Delimitation Implications. Int. J. Mol. Sci. 2024, 25, 3506.
Abstract
The genus Lirianthe in the family Magnoliaceae includes approximately 25 species, each with exceptional landscaping and horticultural or medical worth. Many of these plants are considered rare and protected due to their endangered status. The limited knowledge of species within this genus and the absence of research on its chloroplast genome have greatly impeded studies on the relationship between its evolution and systematics. In this study, the chloroplast genomes of 8 species from the genus Lirianthe were sequenced and analyzed, their phylogenetic relationships with other genera of the family Magnoliaceae are also elucidated. The results showed that the chloroplast genome sizes of the 8 Lirianthe species ranged from 159,548 to 159,833 bp. The genomes consisted of a large single copy region, a small single copy region, and a pair of inverted repeat sequences. The GC content was very similar across species. Gene annotation revealed that the chloroplast genomes contained 85 protein-coding genes, 37 tRNA genes, and 8 rRNA genes, totaling 130 genes. Codon usage analysis indicated that codon usage was highly conserved among the 8 Lirianthe species. Repeat sequence analysis identified 42-49 microsatellite sequences, 16-18 tandem repeats, and 50 dispersed repeats, with microsatellite sequences being predominantly single nucleotide repeats. DNA polymorphism analysis revealed 10 highly variable regions located in the large single copy and small single copy regions, among which rpl32-trnL, petA-psbJ and trnH-psbA are recommended candidate DNA barcodes for the genus Lirianthe species. The inverted repeat boundary regions show little variation between species and are generally conserved. Phylogenetic tree analysis confirmed the monophyly of the genus Lirianthe and its closest relationship with the genera, Talauma and Dugandiodendron. Morphological studies found noticeable differences between Lirianthe species in aspects including leaf indumentum, stipule scars, floral orientation, tepal number, tepal texture, and fruit dehiscence. In summary, this study elucidated the chloroplast genome evolution within Lirianthe and laid a foundation for further systematic and taxonomic research of this genus.
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