Complete chloroplast genome of a valuable medicinal plant, Huperzia serrata (Lycopodiaceae), and comparison with its congener

Abstract

Premise of the study:Here we report the complete chloroplast genome of the important medicinal species Huperzia serrata (Lycopodiaceae) and compare it to the chloroplast genome of the congeneric species H. lucidula.Methods and Results:The whole chloroplast genome of H. serrata was sequenced using an Illumina platform and assembled with Geneious version R9.0.5. The genome size of H. serrata was 154,176 bp, with 36.3% GC content. The complete chloroplast genome contained 120 unique genes, including 86 coding genes, four rRNA genes, and 30 tRNA genes. Comparison with the chloroplast genome of H. lucidula revealed three highly variable regions (rps16-chlB, ycf12-trnR, and ycf1) between these two species and 252 mutation events including 27 insertion/deletion polymorphisms and 225 single-nucleotide polymorphisms (SNPs). Ninety-two SNPs were identified in the gene-coding regions. In addition, 18 microsatellite sites were found, which can potentially be used in phylogeographic studies.Conclusions:The complete chloroplast genome of H. serrata is reported here, and will be a valuable genome resource for further phylogenetic, evolutionary, and medical studies of medicinal plants in the genus Huperzia.

The Unique Evolutionary Trajectory and Dynamic Conformations of DR and IR/DR- coexisting Plastomes of the Early Vascular Plant Selaginellaceae (Lycophyte)

“…Only 9-12 different tRNA genes remain in Selaginella , and GC content in Selaginella plastomes is significantly higher (54.8% for S. uncinata , 51% for S. moellendorffii , 54.1% for S. tamariscina , and 53.2% for S. vardei ) than the plastomes of other land plants (less than 43%) (Smith 2009; Tsuji et al 2007). Such extensive rearrangement events and extraordinary gene content have never been reported in other lycophytes and fern families (Guo et al 2016; Karol et al 2010; Mower and Vickrey 2018).…”

“…However, only four species of Selaginella , viz., S. uncinata (Tsuji et al 2007), S. moellendorffii (Smith 2009), S. tamariscina (Xu et al 2018), and S. vardei (Unpublished data), have been reported for their plastomes. Compared to the four species from Lycopodiaceae and Isoetaceae of lycophytes (Guo et al 2016; Karol et al 2010; Wolf et al 2005; Zhang et al 2017), plastomes of Selaginella are, indeed, far less conserved in both structures and gene contents. Both S. uncinata and S. moellendorffii belong to subg.…”

The First Chloroplast Genome Sequence of Boswellia sacra, a Resin-Producing Plant in Oman

“…A custom Python script (https://www.biostars.org/p/119214/) based on single-nucleotide polymorphism (SNP) definition (a variation in a single nucleotide that occurs at a specific position in the genome) was employed to call SNPs. In addition, the SNPs in coding regions were classified in two ways: synonymous and nonsynonymous as shown by Guo et al [47]. The number of synonymous (S) and nonsynonymous (N) substitutions for the B .…”

Lycophyte plastid genomics: extreme variation in GC, gene and intron content and multiple inversions between a direct and inverted orientation of the rRNA repeat

“…Given that lycophytes are the sister lineage to all other extant vascular plants and comprise three distinctive lineages (clubmosses, spikemosses, and quillworts) that have each existed for >300 million years (Larsén & Rydin, ; Testo et al ., ), it is perhaps unsurprising that their plastomes exhibit diverse characteristics. Plastomes from Huperzia lucidula and Huperzia serrata are nearly identical to one another (Guo Z. Y. et al ., ), and, except for a small expansion of the IR, they are collinear with nonvascular plant plastomes, implying a plesiomorphic retention of gene order from the land plant ancestor (Wolf et al ., ; Mower & Vickrey, ). By contrast, Isoetes and Selaginella harbor plastomes that are more rearranged (Tsuji et al ., ; Smith, ; Karol et al ., ; Xu et al ., ).…”