The Complete Chloroplast Genome of Endangered Species Stemona parviflora: Insight into the Phylogenetic Relationship and Conservation Implications

Abstract

Stemona parviflora is an endangered species, narrowly endemic to Hainan and Southwest Guangdong. The taxonomic classification of S. parviflora remains controversial. Moreover, studying endangered species is helpful for current management and conservation. In this study, the first complete chloroplast genome of S. parviflora was assembled and compared with other Stemona species. The chloroplast genome size of S. parviflora was 154,552 bp, consisting of 87 protein-coding genes, 38 tRNA genes, 8 rRNA genes, and one pseudogene. The ψycf1 gene was lost in the cp genome of S. sessilifolia, but it was detected in four other species of Stemona. The inverted repeats (IR) regions have a relatively lower length variation compared with the large single copy (LSC) and small single copy (SSC) regions. Long repeat sequences and simple sequence repeat (SSR) were detected, and most SSR were distributed in the LSC region. Codon usage bias analyses revealed that the RSCU value of the genus Stemona has almost no difference. As with most angiosperm chloroplast genomes, protein-coding regions were more conservative than the inter-gene spacer. Seven genes (atpI, ccsA, cemA, matK, ndhA, petA, and rpoC1) were detected under positive selection in different Stemona species, which may result from adaptive evolution to different habitats. Phylogenetic analyses show the Stemona cluster in two main groups; S. parviflora were closest to S. tuberosa. A highly suitable region of S. parviflora was simulated by Maxent in this study; it is worth noting that the whole territory of Taiwan has changed to a low fitness area and below in the 2050 s, which may not be suitable for the introduction and cultivation of S. parviflora. In addition, limited by the dispersal capacity of S. parviflora, it is necessary to carry out artificial grafts to expand the survival areas of S. parviflora. Our results provide valuable information on characteristics of the chloroplast genome, phylogenetic relationships, and potential distribution range of the endangered species S. parviflora.

The complete chloroplast genome of Pandanus amaryllifolius Roxb. ex Lindl. (Pandanaceae) and its phylogenetic relationship

“… 2022 ), Pandanus tectorius (GenBank accession number: MH748568, ON040650; Tan et al. 2019 ), Stemona parviflora (GenBank accession number: MZ151339; Wei and Li 2022 ), and Xerophyta schlechteri (GenBank accession number: MK279914; Wang and Lanfear 2019 ).…”

Mitochondrial genome complexity in Stemona sessilifolia: nanopore sequencing reveals chloroplast gene transfer and DNA rearrangements

“…Repeat sequences played a significant role in the rearrangement of the mitogenome ( Cole et al, 2018 ). Extensive gene repeat sequences have been observed in Stemonaceae species, including S. mairei ( Lu et al, 2018a ), C. japonica ( Lu et al, 2018b ), and S. parviflora ( Wei and Li, 2022 ). The repeats analysis indicated the presence of microsatellites (SSRs), tandem repeats, and dispersed repeats within the S. sessilifolia mitogenome.…”

Characterization of the Plastid Genomes of Four Caroxylon Thunb. Species from Kazakhstan

“…The rapid advancement of next-generation sequencing technology has greatly improved the efficiency and accessibility of obtaining complete plastid genome nucleotide sequences [37]. Sequencing plastid genomes in plants is crucial for advancing various fields of research, including evolutionary biology [38], taxonomy [39], biogeography [40], breeding [41], and conservation [42]. However, despite the widespread use of plastid genome data for comparative analysis, no comparative studies have been conducted on Caroxylon plastid genomes.…”