The complete chloroplast genome of the medical plant Huperzia crispata from the Huperziaceae family: structure, comparative analysis, and phylogenetic relationships

Plastome comparison and phylogenomics of Chinese endemic Schnabelia (Lamiaceae): insights into plastome evolution and species divergence

BACKGROUND

Schnabelia species, herbaceous perennial plants within the Lamiaceae family, possess medicinal value and are endemic to China. While previous studies have focused on morphological classification, molecular systematics, and medicinal components, there has been limited research on phylogenomics. To reveal their plastid genome characteristics and phylogenetic relationships, we sequenced and assembled the plastomes of all five Schnabelia species (S. oligophylla, S. tetrodonta, S. nepetifolia, S. terniflora, S. aureoglandulosa), conducted comparative genomic analyses, and constructed a phylogenetic tree incorporating closely related taxa in subfamily Ajugoideae, as well as conducting divergence time estimation.

RESULTS

Plastome size of the five species ranged from 155,733 bp to 156,944 bp, encompassing 115 unique genes, with a GC content of 37.8% same for all species. Five intergenic spacer regions (trnH-GUG-psbA, trnK-UUU-matK, petB-petD, ndhD-psaC, ndhA-ndhH) were identified as divergence hotspots. Gene selection pressure analysis demonstrated that all genes were under negative selection. Phylogenetic relationship of Ajugoideae species based on plastomes confirmed the monophyly of Schnabelia. Two clades within Schnabelia were supported, one containing two original species and the other comprising three species transferred from Caryopteris. The stem age of the Schnabelia is estimated to be approximately 30.24 Ma, with the split of two Sections occurring around 12.60 Ma.

CONCLUSIONS

We revealed plastid genome evolutionary features for five species within the genus Schnabelia. The identified highly variable regions can provide a tool for future identification of these medicinal plants. The diversification of Schnabelia during middle Miocene and the Quaternary suggests that historical geological and climatic shifts facilitated species differentiation. These findings enhance our understanding of Schnabelia's evolution and support future research on chloroplast diversity, aiding conservation and sustainable use.

Chloroplast-nuclear genome interaction drives asymmetric inverted repeats in chloroplast genome of Huperzia

Huperzia plants are important natural medicine species that have attracted increased amounts of attention due to the presence of huperzine A (Hup A), which efficiently, selectively, and reversibly inhibits acetylcholinesterase activity. However, due to the complexity of the genome structure and lack of genetic information, the phylogenetic and evolutionary relationships of Huperzia species are still unclear. In this study, seven chloroplast genome structures of Huperzia were verified and comparatively analyzed, and the phylogenetic relationships between Huperzia and other related ferns were evaluated. The results showed that a 58 kb insertion in the middle of the IRb region in the seven chloroplast genomes led to large differences in sequence size, GC content and tRNA number between IRa and IRb. All seven chloroplast genomes exhibited asymmetric structural conformations in the IR regions. We used sequence alignment and screening of the organelle and nuclear genomes to identify the source of the gene. The inserted sequence had no homologous region with the mitochondrial genome, and the same sequence as another segment was found in the nuclear genome. Then, the chloroplast genomes of Huperzia were comparatively analyzed. Phylogenetic tree showed that Phlegmariurus and Huperzia were closely related and belonged to the same branch. H. javanica and Huperzia serrata are closely related. From the perspective of phylogenetic tree, their phylogenetic relationship is closely related to geographical distribution. In conclusion, this study provides insights into the interaction mechanism between chloroplast genome and nuclear genome and the phylogeny of Huperzia. In addition, by comparing the chloroplast genomes of Huperzia, we analyzed its genetic diversity and provided important molecular information for the protection of these endangered species.

Decoding the mitogenome of rosemary (Salvia rosmarinus): insights into genome evolution, structural dynamics and prospects for mitochondrial engineering

BACKGROUND

Rosemary (Salvia rosmarinus), an aromatic evergreen shrub of the Salvia (Lamiaceae), is native to the Mediterranean region, thriving in rocky or arid soils. Widely used in food, pharmaceuticals, and cosmetics, its clonal reproduction poses significant challenges for breeding and germplasm innovation. While mitogenome engineering holds promise for introducing heritable mutations, incomplete mitogenome information for rosemary has hindered such efforts. This study addresses this gap by assembling and analyzing the complete mitogenome of S. rosmarinus, focusing on its structure, repetitive sequences, RNA editing events, intracellular gene transfer (IGT), and phylogenetic relationships.

RESULTS

The S. rosmarinus mitogenome spans 384,113 bp with a GC content of 44.8%, containing 34 unique protein-coding genes and 114 simple sequence repeats. Comparative analysis revealed 28 homologous segments shared between the mitogenome and plastome, totaling 18,675 bp in length. Furthermore, homologous fragments between nuclear and organellar genomes were identified, including 1,069,255 bp of organelle-derived sequences in the nuclear genome, with 194,689 bp from nuclear plastid DNA transfers (NUPTs) and 15,192 bp from nuclear mitochondrial DNA transfers (NUMTs). NUPTs were more abundant and contributed more significantly to the total length. Synteny analysis of eight Lamiales species revealed extensive mitogenomic recombination and structural rearrangements. These findings highlight the dynamic nature of mitogenomes, offering insights into genome evolution and supporting future breeding programs to enhance the genetic diversity and adaptability of S. rosmarinus.

CONCLUSIONS

This study provides the first complete mitogenome of S. rosmarinus, revealing dispersed repeats, RNA editing, and horizontal gene transfer between the nuclear and organelle genomes. The mitogenome exhibits a typical circular structure with evidence of frequent recombination, providing valuable insights into Salvia mitochondrial genetics, genome evolution, and molecular biology.

The complete chloroplast genome of an Arctic lycophyte, Huperzia arctica (Tolm.) Sipliv. 1973 (Lycopodiaceae)

Huperzia arctica (Tolm.) Sipliv. 1973 is a lycophyte species belonging to the Lycopodiaceae family, which is widely distributed in the Arctic region of Svalbard, Norway. To determine its taxonomic position, we sequenced the chloroplast genome of H. arctica. The complete chloroplast genome of H. arctica is 153,956 bp in length with 122 annotated genes, including 87 protein-coding genes, 31 tRNA genes, and 4 rRNA genes. To evaluate its evolutionary position, we performed phylogenetic analysis using 36 conserved orthologous protein-coding gene sequences from the chloroplast genomes of H. arctica and publicly available data from other Lycopodiaceae. H. arctica formed a monophyletic group with four other Huperzia species: H. lucidula, H. serrata, H. crispata, and H. javanica. However, it appeared as a separate species with a highly supported bootstrap value.

Assembly and phylogenetic analysis of the mitochondrial genome of endangered medicinal plant Huperzia crispata

Huperzia crispata is a traditional Chinese herb plant and has attracted special attention in recent years for its products Hup A can serve as an acetylcholinesterase inhibitor (AChEI). Although the chloroplast (cp) genome of H. crispata has been studied, there are no reports regarding the Huperzia mitochondrial (mt) genome since the previously reported H. squarrosa has been revised as Phlegmariurus squarrosus. The mt genome of H. crispata was sequenced using a combination of long-read nanopore and Illumina sequencing platforms. The entire H. crispata mt genome was assembled in a circular with a length of 412,594 bp and a total of 91 genes, including 45 tRNAs, 6 rRNAs, 37 protein-coding genes (PCGs), and 3 pseudogenes. Notably, the rps8 gene was present in P. squarrosus and a pseudogene rps8 was presented in H. crispata, which was lacking in most of Pteridophyta and Gymnospermae. Intron-encoded maturase (mat-atp9i85 and mat-cobi787) genes were present in H. crispata and P. squarrosus, but lost in other examined lycophytes, ferns, and Gymnospermae plants. Collinearity analysis showed that the mt genome of H. crispata and P. squarrossus is highly conservative compared to other ferns. Relative synonymous codon usage (RSCU) analysis showed that the amino acids most frequently found were phenylalanine (Phe) (4.77%), isoleucine (Ile) (4.71%), lysine (Lys) (4.26%), while arginine (Arg) (0.32%), and histidine (His) (0.42%) were rarely found. Simple sequence repeats (SSR) analysis revealed that a total of 114 SSRs were identified in the mt genome of H. crispata and account for 0.35% of the whole mt genome. Monomer repeats were the majority types of SSRs and represent 91.89% of the total SSRs. In addition, a total of 1948 interspersed repeats (158 forward, 147 palindromic, and 5 reverse repeats) with a length ranging from 30 bp to 14,945 bp were identified in the H. crispata mt genome and the 30-39-bp repeats were the most abundant type. Gene transfer analysis indicated that a total of 12 homologous fragments were discovered between the cp and mt genomes of H. crispata, accounting for 0.93% and 2.48% of the total cp and mt genomes, respectively. The phylogenetic trees revealed that H. crispata was the sister of P. squarrosus. The Ka/Ks analysis results suggested that most PCGs, except atp6 gene, were subject to purification selection during evolution. Our study provides extensive information on the features of the H. crispata mt genome and will help unravel evolutionary relationships, and molecular identification within lycophytes.