Chloroplast Genome Research Articles

Analysis of chloroplast genome structure and phylogeny of the traditional medicinal of Ardisia crispa (Myrsinaceae)

Ardisia crispa(Myrsinaceae) is an ethnomedicine with horticultural and important medicinal values. Its morphology is complex, and its identification is difficult. We analyse the chloroplast genome characteristics and phylogenetic position of A. crispa to provide basic research data for the identification of A. crispa species and resource conservation. This study assemble and annotate the chloroplast genome of A. crispa and to compare it with the chloroplast genome within Ardisia. The A. crispa chloroplast genome is 156,785 bp in length, with a typical quadripartite structure containing 131 genes, including 86 protein-coding genes, 37 tRNA genes, and 8 rRNA genes; a total of 59 SSRs sites were identified, and the codon preference of this chloroplast genome is greater in A/U than in G/C, and leucine is the amino acid with the highest frequency of use. The chloroplast genomes of the nine Ardisia species are conserved in gene content and number, with more stable boundaries and less variation. In the phylogenetic tree, A. crispa is clustered on a branch with A. crispa var dielsii, and is closely related to A. mamillata and A. pedalis. In this study, we constructed and analyzed the chloroplast genome structure of A. crispa, and conducted phylogenetic analysis using the whole chloroplast genome sequence data of Ardisia plants, which is of great significance in understanding the genetic basis of A. crispa and adaptive evolution in Ardisia plants, and this will lay the foundation for the future research on A. crispa resource conservation and species identification.

Across a phylogeographic break in the Qinling Mountains-Huaihe River Line: Quaternary evolutionary history of a medicinal and edible homologous plant (Allium macrostemon) in China

Biogeographic barriers to gene flow are central to studies of plant phylogeography. There are many physical and geographic barriers in China, but few studies have used molecular ecological evidence to investigate the natural geographic isolation barrier of the Qinling Mountains-Huaihe River Line (QHL). Allium macrostemon is a precious Chinese perennial herb belonging to the Amaryllidaceae family. It is used as a food and medicine, with a variety of health and healing properties. Five SSR markers, three chloroplast DNA (cpDNA) markers (psbA-trnH, rps16 and trnL-F), one nuclear ribosomal DNA (nrDNA) marker (ITS), and simplified genome GBS sequencing were used to analyse the genetic diversity and structure of A. macrostemon. Combining SSR, cpDNA, nrDNA ITS data and GBS analysis results, we divided A. macrostemon populations into northern and southern groups, with the southern group further divided into southwestern and central-southeastern groups. Niche simulation results reveal that the distribution area of A. macrostemon will reach its maximum in the future. These data indicate that the regional separation of A. macrostemon has been maintained by the combined influence of a geographical barrier and Quaternary climate, and that the back-and-forth fluctuations of QHL and Quaternary climate have played an important role in this process. QHL acts as a north-south dividing line in phylogeography and population genetic structure, promoting physical geographic isolation. This study provides a theoretical basis for the conservation, development, and utilization of A. macrostemon resources. It further provides a reference for understanding the systematic geographical pattern of the large-scale spatial distribution of plants in China and enriches our understanding of Quaternary plant evolution in areas with complex terrain.

A comparative analysis of chloroplast genomes revealed the chloroplast heteroplasmy of Artemisia annua.

Artemisia annua L. is the main source of artemisinin, an antimalarial drug. High diversity of morphological characteristics and artemisinin contents of A. annua has affected the stable production of artemisinin while efficient discrimination method of A. annua strains is not available. The complete chloroplast (cp) genomes of 38 A. annua strains were assembled and analyzed in this study. Phylogenetic analysis of Artemisia species showed that distinct intraspecific divergence occurred in A. annua strains. A total of 38 A. annua strains were divided into two distinct lineages, one lineage containing widely-distributed strains and the other lineage only containing strains from northern China. The A. annua cp genomes ranged from 150, 953 to 150, 974bp and contained 131 genes, and no presence or absence variation of genes was observed. The IRs and SC junctions were located in rps19 and ycf1, respectively, without IR contraction observed. Rich sequence polymorphisms were observed among A. annua strains, and a total of 60 polymorphic sites representing 14 haplotypes were identified which unfolding the cpDNA heteroplasmy of A. annua. In conclusion, this study provided valuable resource for A. annua strains identification and provided new insights into the evolutionary characteristics of A. annua.

Assembly and Comparative Analysis of the Complete Mitochondrial Genome of Saussurea inversa (Asteraceae).

Saussurea inversa is a perennial herb used in traditional Chinese medicine and is effective against rheumatoid arthritis. In this study, we sequenced the complete mitochondrial (mt) genome of S. inversa (GenBank accession number: ON584565.1). The circular mt genome of S. inversa was 335,372 bp in length, containing 62 genes, including 33 mRNAs, 22 tRNAs, 6 rRNAs, and 1 pseudogene, along with 1626 open reading frames. The GC content was 45.14%. Predictive analysis revealed substantial RNA editing, with ccmFn being the most abundantly edited gene, showing 36 sites. Gene migration between the mt and chloroplast (cp) genomes of S. inversa was observed through the detection of homologous gene fragments. Phylogenetic analysis revealed that S. inversa was clustered with Arctium tomentosum (Asteraceae). Our findings provide extensive information regarding the mt genome of S. inversa and help lay the foundation for future studies on its genetic variations, phylogeny, and breeding via the analysis of the mt genome.

Genetic and morphological analyses support the reinstatement of Schoenus vacillans (Cyperaceae) as distinct from S. apogon

ABSTRACT Schoenus vacillans is a sedge described from New Zealand in 1878 by Thomas Kirk. However, for over one hundred years, S. vacillans has been considered a synonym of the morphologically-variable S. apogon, which occurs in New Zealand, Australia, Taiwan, New Guinea and possibly Japan. Here we investigate the taxonomic status of S. vacillans by examining chloroplast and nuclear DNA sequences alongside morphology. Our analyses showed that S. vacillans and S. apogon are genetically distinct and are not sister taxa. Furthermore, S. vacillans is easily distinguished morphologically from S. apogon by its diffuse, many noded but few flowered inflorescences. Our results indicated that S. vacillans should be reinstated at species rank. Furthermore, it appears to be endemic to New Zealand and not conspecific with the Australian S. laxiflorus Steud., another putative segregate of S. apogon. Herbarium records indicate a distribution of S. vacillans from the central North Island northwards but there are few recent records and known populations are small. We suggest a threat ranking of Nationally Critical, with a Data Poor qualifier. Schoenus vacillans appears to prefer shady, damp sites on the sides of gullies and banks, particularly on slips.

Chloroplast genomes of Eriobotrya elliptica and an unknown wild loquat “YN-1”

The chloroplast genomes of wild loquat can help to determine their place in the history of evolution. Here, we sequenced and assembled two novel wild loquat’s chloroplast genomes, one is Eriobotrya elliptica, and the other is an unidentified wild loquat, which we named “YN-1”. Their sizes are 159,471 bp and 159,399 bp, respectively. We also assembled a cultivated loquat named ‘JFZ’, its chloroplast genome size is 159,156 bp. A comparative study was conducted with six distinct species of loquats, including five wild loquats and one cultivated loquat. The results showed that both E. elliptica and “YN-1” have 127 genes, one gene more than E. fragrans, which is psbK. Regions trnF-GAA-ndhJ, petG-trnP-UGG, and rpl32-trnL-UAG were found to exhibit high variability. It was discovered that there was a positive selection on rpl22 and rps12. RNA editing analysis found several chilling stress-specific RNA editing sites, especially in rpl2 gene. Phylogenetic analysis results showed that “YN-1” is closely related to E. elliptica, E. obovata and E. henryi.

The de novo assembly and characterization of the complete mitochondrial genome of bottle gourd (Lagenaria siceraria) reveals the presence of homologous conformations produced by repeat-mediated recombination.

Bottle gourd is an annual herbaceous plant that not only has high nutritional value and many medicinal applications but is also used as a rootstock for the grafting of cucurbit crops such as watermelon, cucumber and melon. Organellar genomes provide valuable resources for genetic breeding. A hybrid strategy with Illumina and Oxford Nanopore Technology sequencing data was used to assemble bottle gourd mitochondrial and chloroplast genomes. The length of the bottle gourd mitochondrial genome was 357547 bp, and that of the chloroplast genome was 157121 bp. These genomes had 27 homologous fragments, accounting for 6.50% of the total length of the bottle gourd mitochondrial genome. In the mitochondrial genome, 101 simple sequence repeats (SSRs) and 10 tandem repeats were identified. Moreover, 1 pair of repeats was shown to mediate homologous recombination into 1 major conformation and 1 minor conformation. The existence of these conformations was verified via PCR amplification and Sanger sequencing. Evolutionary analysis revealed that the mitochondrial genome sequence of bottle gourd was highly conserved. Furthermore, collinearity analysis revealed many rearrangements between the homologous fragments of Cucurbita and its relatives. The Ka/Ks values for most genes were between 0.3~0.9, which means that most of the genes in the bottle gourd mitochondrial genome are under purifying selection. We also identified a total of 589 potential RNA editing sites on 38 mitochondrial protein-coding genes (PCGs) on the basis of long noncoding RNA (lncRNA)-seq data. The RNA editing sites of nad1-2, nad4L-2, atp6-718, atp9-223 and rps10-391 were successfully verified via PCR amplification and Sanger sequencing. In conclusion, we assembled and annotated bottle gourd mitochondrial and chloroplast genomes to provide a theoretical basis for similar organelle genomic studies.

The genome sequence of the Common Tamarisk-moss, Thuidium tamariscinum (Hedw.) Schimp. (Thuidiaceae)

We present a genome assembly from an individual Thuidium tamariscinum gametophyte (the Common Tamarisk-moss; Streptophyta; Bryopsida; Hypnales; Thuidiaceae). The genome sequence has a length of 363.00 megabases. Most of the assembly is scaffolded into 11 chromosomal pseudomolecules. The mitochondrial and plastid genome assemblies have lengths of 103.12 kilobases and 125.05 kilobases, respectively.

Comparative Chloroplast Genomes Analysis Provided Adaptive Evolution Insights in Medicago ruthenica.

A perennial leguminous forage, Medicago ruthenica has outstanding tolerance to abiotic stresses. The genome of Medicago ruthenica is large and has a complex genetic background, making it challenging to accurately determine genetic information. However, the chloroplast genome is widely used for researching issues related to evolution, genetic diversity, and other studies. To better understand its chloroplast characteristics and adaptive evolution, chloroplast genomes of 61 Medicago ruthenica were assembled (including 16 cultivated Medicago ruthenica germplasm and 45 wild Medicago ruthenica germplasm). These were used to construct the pan-chloroplast genome of Medicago ruthenica, and the chloroplast genomes of cultivated and wild Medicago ruthenica were compared and analyzed. Phylogenetic and haplotype analyses revealed two main clades of 61 Medicago ruthenica germplasm chloroplast genomes, distributed in eastern and western regions. Meanwhile, based on chloroplast variation information, 61 Medicago ruthenica germplasm can be divided into three genetic groups. Unlike the phylogenetic tree constructed from the chloroplast genome, a new intermediate group has been identified, mainly consisting of samples from the eastern region of Inner Mongolia, Shanxi Province, and Hebei Province. Transcriptomic analysis showed that 29 genes were upregulated and three genes were downregulated. The analysis of these genes mainly focuses on enhancing plant resilience and adapting adversity by stabilizing the photosystem structure and promoting protein synthesis. Additionally, in the analysis of adaptive evolution, the accD, clpP and ycf1 genes showed higher average Ka/Ks ratios and exhibited significant nucleotide diversity, indicating that these genes are strongly positively selected. The editing efficiency of the ycf1 and clpP genes significantly increases under abiotic stress, which may positively contribute to plant adaptation to the environment. In conclusion, the construction and comparative analysis of the complete chloroplast genomes of 61 Medicago ruthenica germplasm from different regions not only revealed new insights into the genetic variation and phylogenetic relationships of Medicago ruthenica germplasm, but also highlighted the importance of chloroplast transcriptome analysis in elucidating the model of chloroplast responses to abiotic stress. These provide valuable information for further research on the adaptive evolution of Medicago ruthenica.

Contrasting demographic history and mutational load in three threatened whitebark pines (Pinus subsect. Gerardianae): implications for conservation.

Demographic history and mutational load are of paramount importance for the adaptation of the endangered species. However, the effects of population evolutionary history and genetic load on the adaptive potential in endangered conifers remain unclear. Here, using population transcriptome sequencing, whole chloroplast genomes and mitochondrial DNA markers, combined with niche analysis, we determined the demographic history and mutational load for three threatened whitebark pines having different endangered statuses, Pinus bungeana, P. gerardiana and P. squamata. Demographic inference indicated that severe bottlenecks occurred in all three pines at different times, coinciding with periods of major climate and geological changes; in contrast, while P. bungeana experienced a recent population expansion, P. gerardiana and P. squamata maintained small population sizes after bottlenecking. Abundant homozygous-derived variants accumulated in the three pines, particularly in P. squamata, while the species with most heterozygous variants was P. gerardiana. Abundant moderately and few highly deleterious variants accumulated in the pine species that have experienced the most severe demographic bottlenecks (P. gerardiana and P. squamata), most likely because of purging effects. Finally, niche modeling showed that the distribution of P. bungeana might experience a significant expansion in the future, and the species' identified genetic clusters are also supported by differences in the ecological niche. The integration of genomic, demographic and niche data has allowed us to prove that the three threatened pines have contrasting patterns of demographic history and mutational load, which may have important implications in their adaptive potential and thus are also key for informing conservation planning.

Assembly and comparative analysis of the complete mitochondrial genome of Fritillaria ussuriensis Maxim. (Liliales: Liliaceae), an endangered medicinal plant.

Fritillaria ussuriensis is an endangered medicinal plant known for its notable therapeutic properties. Unfortunately, its population has drastically declined due to the destruction of forest habitats. Thus, effectively protecting F. ussuriensis from extinction poses a significant challenge. A profound understanding of its genetic foundation is crucial. To date, research on the complete mitochondrial genome of F. ussuriensis has not yet been reported. The complete mitochondrial genome of F. ussuriensis was sequenced and assembled by integrating PacBio and Illumina sequencing technologies, revealing 13 circular chromosomes totaling 737,569 bp with an average GC content of 45.41%. A total of 55 genes were annotated in this mitogenome, including 2 rRNA genes, 12 tRNA genes, and 41 PCGs. The mitochondrial genome of F. ussuriensis contained 192 SSRs and 4,027 dispersed repeats. In the PCGs of F. ussuriensis mitogenome, 90.00% of the RSCU values exceeding 1 exhibited a preference for A-ended or U-ended codons. In addition, 505 RNA editing sites were predicted across these PCGs. Selective pressure analysis suggested negative selection on most PCGs to preserve mitochondrial functionality, as the notable exception of the gene nad3 showed positive selection. Comparison between the mitochondrial and chloroplast genomes of F. ussuriensis revealed 20 homologous fragments totaling 8,954 bp. Nucleotide diversity analysis revealed the variation among genes, and gene atp9 was the most notable. Despite the conservation of GC content, mitogenome sizes varied significantly among six closely related species, and colinear analysis confirmed the lack of conservation in their genomic structures. Phylogenetic analysis indicated a close relationship between F. ussuriensis and Lilium tsingtauense. In this study, we sequenced and annotated the mitogenome of F. ussuriensis and compared it with the mitogenomes of other closely related species. In addition to genomic features and evolutionary position, this study also provides valuable genomic resources to further understand and utilize this medicinal plant.

Complete mitochondrial genome of Hippophae tibetana: insights into adaptation to high-altitude environments.

Hippophae tibetana, belonging to the Elaeagnaceae family, is an endemic plant species of the Qinghai-Tibet Plateau, valued for its remarkable ecological restoration capabilities, as well as medicinal and edible properties. Despite being acknowledged as a useful species, its mitochondrial genome data and those of other species of the Elaeagnaceae family are lacking to date. In this study, we, for the first time, successfully assembled the mitochondrial genome of H. tibetana, which is 464,208 bp long and comprises 31 tRNA genes, 3 rRNA genes, 37 protein-coding genes, and 3 pseudogenes. Analysis of the genome revealed a high copy number of the trnM-CAT gene and a high prevalence of repetitive sequences, both of which likely contribute to genome rearrangement and adaptive evolution. Through nucleotide diversity and codon usage bias analyses, we identified specific genes that are crucial for adaptation to high-altitude conditions. Notably, genes such as atp6, ccmB, nad4L, and nad7 exhibited signs of positive selection, indicating the presence of unique adaptive traits for survival in extreme environments. Phylogenetic analysis confirmed the close relationship between the Elaeagnaceae family and other related families, whereas intergenomic sequence transfer analysis revealed a substantial presence of homologous fragments among the mitochondrial, chloroplast, and whole genomes, which may be linked to the high-altitude adaptation mechanisms of H. tibetana. The findings of this study not only enrich our knowledge of H. tibetana molecular biology but also advance our understanding of the adaptive evolution of plants on the Qinghai-Tibet Plateau. This study provides a solid scientific foundation for the molecular breeding, conservation, and utilization of H. tibetana genetic resources.

An overview of floral and vegetative evolution in the Asian clade of Bulbophyllum (Orchidaceae)

Background and aims – Bulbophyllum, the largest genus in Orchidaceae, exhibits a diverse morphology in both reproductive and vegetative characters. While trait diversity and evolution has been extensively studied in Malagasy species and within the Cirrhopetalum alliance clade, the evolution of reproductive and vegetative characters at the whole level of the Asian clade remains largely unexplored. Material and methods – We reconstructed the phylogeny of approximately 11% of all Asian Bulbophyllum species using Bayesian inference and maximum likelihood estimation based on nuclear (ITS) and chloroplast (matK, psbA-trnH) DNA sequence data. This phylogenetic framework allowed us to examine the evolution of two vegetative and four floral characters through ancestral state reconstruction. Key results and conclusion – The ancestral character states of the Asian clade of Bulbophyllum include a single leaf, distinct pseudobulbs, multiple-flowered inflorescences, and lateral and dorsal sepals similar in length. One-leaved pseudobulbs evolved into two-leaved pseudobulbs multiple times. Distinct pseudobulbs gave rise to indistinct pseudobulbs twice. Multiple-flowered inflorescences shifted to solitary flowers and 2–3-flowered inflorescences multiple times, with some instances of evolutionary reversal. Lateral sepal elongation also presents a convergent evolutionary scenario.

Genetic Diversity and Phylogenetic Relationships of Capsicum frutescens in the Asia–Pacific Region: The Pacific Dispersal Route

AbstractCapsicum peppers are among the oldest domesticated crops in the Americas. Columbus introduced them to Europe, from where they spread to the Far East via Africa, South Asia, and Southeast Asia. However, the details of how Capsicum peppers were introduced into the Asia–Pacific region and their subsequent dispersal remain unknown. Therefore, we investigated the genetic diversity and relationships of Capsicum frutescens in the Asia–Pacific region through restriction site-associated DNA sequencing (RAD-seq) and the sequencing of a variable chloroplast genome locus. The RAD-seq analysis showed that three accessions from Japan are most closely related to those from the Americas and Micronesia, and are distant from most of those from islands and continental Southeast Asia. Although C. frutescens has two chloroplast haplotypes (T and TC), only the T type was found in the Americas and Japan, whereas both types were distributed in other regions. Therefore, we postulate that some C. frutescens accessions were introduced into the Asia–Pacific region from the Americas via the Pacific dispersal route, whereas only the T type was introduced into Japan. Evidence for this Pacific dispersal route of C. frutescens could lead to a reconsideration of the dispersal routes of other crops native to the Americas.

Two high-quality Prototheca zopfii genomes provide new insights into their evolution as obligate algal heterotrophs and their pathogenicity.

The genus Prototheca, characterized by its heterotrophic nature and pathogenicity, serves as an exemplary model for investigating pathobiology. The limited understanding of the protothecosis infectious disease is attributed to the lack of genomic resources. Using HiFi long-read sequencing, both nuclear and plastid genomes were generated for two strains of P. zopfii. The findings revealed a concurrent reduction in both plastid and nuclear genome size, accompanied by the loss of genes associated with photosynthesis, carotenoid oxygenase, basic leucine-zipper (bZIP) transcription factors, and others. The analysis of horizontal gene transfer revealed the presence of 1.37% and 1.49% bacterial genes, including malate synthase and isocitrate lyase, which play crucial roles in carbon and nitrogen metabolism, as well as pathogenicity and obligate heterotrophy. The two high-quality P. zopfii genomes represent valuable resources for investigating their adaptation and evolution as obligate heterotrophs, as well as for developing future prevention and treatment strategies against protothecosis.

The complete chloroplast genome of Rhododendronambiguum and comparative genomics of related species.

Rhododendron Linnaeus, 1753, the largest genus of woody plants in the Northern Hemisphere, includes some of the most significant species in horticulture. Rhododendronambiguum Hemsl, 1911, a member of subsection Triflora Sleumer 1947, exemplifies typical alpine Rhododendron species. The analysis of the complete chloroplast genome of R.ambiguum offers new insights into the evolution of Rhododendron species and enhances the resolution of phylogenetic relationships. This genome is composed of 207,478 base pairs, including a pair of inverted repeats (IRs) of 47,249 bp each, separated by a large single-copy (LSC) region of 110,367 bp and a small single-copy (SSC) region of 2,613 bp. It contains 110 genes: 77 protein-coding genes, 29 tRNAs, four unique rRNAs (4.5S, 5S, 16S, and 23S), with 16 genes duplicated in the IRs. Comparative analyses reveal substantial diversity in the Rhododendron chloroplast genome structures, identifying a fourth variant pattern. Specifically, four highly divergent regions (trnI-rpoB, ndhE-psaC, rpl32-ndhF, rrn16S-trnI) were noted in the intergenic spacers. Additionally, 76 simple sequence repeats were identified. Positive selection signals were detected in four genes (cemA, rps4, rpl16, and rpl14), evidenced by high Ka/Ks ratios. Phylogenetic reconstruction based on two datasets (shared protein-coding genes and complete chloroplast genomes) suggests that R.ambiguum is closely related to R.concinnum Hemsley, 1889. However, the phylogenetic positions of subsection Triflora Pojarkova, 1952 species remain unresolved, indicating that the use of complete chloroplast genomes for phylogenetic research in Rhododendron requires careful consideration. Overall, our findings provide valuable genetic information that will enhance understanding of the evolution, molecular biology, and genetic improvement of Rhododendron spieces.

Accumulation of Large Lineage-Specific Repeats Coincides with Sequence Acceleration and Structural Rearrangement in Plantago Plastomes.

Repeats can mediate rearrangements and recombination in plant mitochondrial genomes and plastid genomes. While repeat accumulations are linked to heightened evolutionary rates and complex structures in specific lineages, debates persist regarding the extent of their influence on sequence and structural evolution. In this study, 75 Plantago plastomes were analyzed to investigate the relationships between repeats, nucleotide substitution rates, and structural variations. Extensive repeat accumulations were associated with significant rearrangements and inversions in the large inverted repeats (IRs), suggesting that repeats contribute to rearrangement hotspots. Repeats caused infrequent recombination that potentially led to substoichiometric shifting, supported by long-read sequencing. Repeats were implicated in elevating evolutionary rates by facilitating localized hypermutation, likely through DNA damage and repair processes. This study also observed a decrease in nucleotide substitution rates for loci translocating into IRs, supporting the role of biased gene conversion in maintaining lower substitution rates. Combined with known parallel changes in mitogenomes, it is proposed that potential dysfunction in nuclear-encoded genes associated with DNA replication, recombination, and repair may drive the evolution of Plantago organellar genomes. These findings contribute to understanding how repeats impact organellar evolution and stability, particularly in rapidly evolving plant lineages.

Complete chloroplast genome of Asarum chungbuensis (C.S. Yook & J.G. Kim) B.U. Oh 2005 (Aristolochiaceae), a Korean endemic species

Asarum chungbuensis, a species endemic to Korea, has a limited distribution across the Korean Peninsula and is used in traditional medicine. Despite its importance, the genome structure, genetic composition, and phylogenetic relationships based on its chloroplast genome have not been documented. In this study, the complete chloroplast genome of A. chungbuensis was newly assembled. The chloroplast genome is 190,179 base pairs (bp) long, and the overall GC content (%) of the plastid was 36.8%. The chloroplast genome size of A. chungbuensis is longer than that of the normal chloroplast genome (160 kb) because of an inverted small single-copy (SSC) duplication that incorporates the SSC into an inverted repeat (IR) region. By extension, this duplication event causes this chloroplast genome to lack an SSC, unlike other formal structures. The chloroplast genome, with a tripartite structure, consisted of a single-copy region of 93,351 bp with a 34.6% GC content and two IR regions, each with a length of 48,414 bp and a 38.8% GC content. Additionally, it was found to have 113 genes, including 79 PCG genes, 30 tRNA genes, and four rRNA genes. Phylogenetic analysis revealed that A. chungbuensis was grouped with A. heterotropoides var. seoulense, which diverged from the clade comprising A. koreanum and A. patens. The newly sequenced A. chungbuensis chloroplast genome could provide valuable genomic information for determining unique genome structures, especially for the assessment of genetic diversity, phylogenetic relationships, species conservation, and biogeographic studies of the genus Asarum.

The complete chloroplast genome of Semiaquilegia danxiashanensis (Ranunculaceae), a rare species endemic to Danxia landform in Guangdong, China

Semiaquilegia danxiashanensis is currently known only from the type locality, Danxia Mountain, characterized by its spectacular red sandstone cliffscape. In this study, we assembled the complete chloroplast genome sequence of S. danxiashanensis and inferred its phylogenetic relationships. Total length of the chloroplast genome was 160,548 bp, with an overall GC content of 39%. The chloroplast genome had typical quadripartite structure and contained one LSC region (89,882 bp) and one SSC region (17,386 bp), which were separated by two IRs regions (26,640 bp, respectively). It comprised 133 genes, including 84 protein coding genes, 41 tRNA genes and eight rRNA genes. The maximum likelihood phylogenetic analysis indicated that S. danxiashanensis was sister to S. adoxoides; meanwhile, Semiaquilegia was closely related to both Urophysa and Aquilegia in Ranunculaceae. This study sheds light on the evolutionary history of Semiaquilegia and provides preliminary data for future comparative analysis of chloroplast genomes.

The complete chloroplast genome of Camellia flava (Pitard) Sealy, a golden camellia of Vietnam

Camellia flava (Pit.) Sealy 1949 is a rare and precious species with golden flowers, which hold important ornamental and breeding values. In this study, the complete chloroplast genome of C. flava is reported for the first time. The chloroplast genome exhibits a typical quadripartite structure with a total length of 156,670 bp and a GC content of 37.32%, including a large single-copy region (86,250 bp), a small single-copy region (18,292 bp), and a pair of inverted repeat regions (26,064 bp). A total of 133 genes, including 88 protein-coding genes, 37 tRNA genes, and 8 rRNA genes were annotated. The phylogenetic analysis revealed a close relationship between C. flava and C. tamdaoensis. The chloroplast genome sequence of C. flava serves as a valuable resource for further breeding research and genetic phylogenetic studies.