Small Single-copy Region Research Articles

The complete chloroplast genome sequence of Rhamnella wilsonii Schneid (Rhamnaceae)

Rhamnella wilsonii Schneid 1914 is a member of the Rhamnaceae and endemic to China. In this study, the complete chloroplast genome of R. wilsonii was sequenced and assembled. The complete chloroplast genome was 160,049 bp in length, including a pair of inverted repeats (IRs) of 26,502 bp, one large single copy (LSC) region of 88,274 bp and one small single copy (SSC) region of 18,771 bp. The genome contained 129 genes, including 8 rRNA genes, 37 tRNA genes and 84 protein-coding genes. The overall GC content of the complete chloroplast genome was 37.15%. The phylogenetic analysis demonstrated that R. wilsonii is closely related to R. martinni. This study provides basic information for further studies on the identification and evolution of R. wilsonii and Rhamnella from genomic perspective.

Characterization of the complete chloroplast genome of Eutrema deltoideum (Brassicaceae)

Eutrema deltoideum (Hook. f. et Thoms.) has been recognized as a potentially important vegetable and medicinal resource. In this study, we present the complete chloroplast genome of E. deltoideum and conduct a phylogenetic analysis. The chloroplast genome is 154,051 bp long and consists of a large single-copy (LSC) region of 84,149 bp, two inverted repeat (IR) regions of 26,065 bp each, and a small single-copy (SSC) region of 17,772 bp. It contains 132 complete genes, including 87 protein-coding genes, 8 ribosomal RNA genes, and 37 tRNA genes. Additionally, we identified 78 simple sequence repeats (SSRs). The phylogenetic tree reveals that E. deltoideum is closely related to E. heterophyllum, and the Eutrema genus is monophyletic. This study provides valuable information about E. deltoideum and enhances our understanding of its taxonomic classification.

The complete chloroplast genome of Lagochilus ilicifolius Bunge ex Bentham, Labiat. Gen. 1834 (Lamiaceae) and its phylogenetic analysis

Lagochilus ilicifolius Bunge ex Bentham, Labiat. Gen is a perennial herb with much-branched stems native to Nei Mongol, Ningxia, Gansu, N Shaanxi. It can be used clinically as a hemostatic agent. The chloroplast genome length is 151,466 bp. It contained two inverted repeat regions of 25,660 bp each, a large single-copy region of length 82,504 bp, and a small single-copy region of length 17,642 bp. Also, the GC content is 38.6%. There were 133 genes annotated, including 88 known protein-coding genes, 37 tRNAs, and eight rRNAs. The phylogenetic tree was constructed using Bayesian method for plastome data of 29 species. The entire chloroplast genome of L. ilicifolius within the Lamiaceae is the first to reveal genetic taxonomy at the molecular level, and the new phylogenetic tree data can be used for future evolutionary studies.

Complete chloroplast genome of two Arabis L. species from Korea and assessment of their phylogenetic relationship in plastome based phylogeny

Arabis stelleri DC. and A. takesimana Nakai belong to the family Brassicaceae. Arabis stelleri is widely distributed in East Asia, and A. takesimana is a Korean endemic plant. In this study, we report the complete chloroplast genomes of both species, measuring 153,577 bp for A. stelleri and 153,557 bp for A. takesimana. The plastome of A. stelleri comprises two inverted repeats (IRs) of 26,421 bp, a large single-copy (LSC) region measuring 82,705 bp, and a small single-copy (SSC) region of 18,030 bp. Whereas A. takesimana has IR regions of 26,426 bp, an LSC of 82,694 bp, and an SSC of 18,011 bp. Both the plastomes contain 131 total genes, 86 protein-coding genes, 37 tRNA genes, 8 rRNA genes, and 36.4% GC content. The organization and gene content of both plastomes were found to be similar to previously reported Arabis plastomes. In addition, we have tested the phylogenetic position of both the Arabis species and the relationship of the genus Arabis with other Brassicaceae members in comprehensive family-level plastome-based phylogeny. Arabis stelleri and A. takesimana are phylogenetically placed within the Arabis clade and show a close relationship to A. flagellosa, A. nipponica, A. paniculata, and A. hirsuta.

Characterization of the complete chloroplast genome sequence of <i>Hypericum petiolulatum</i> (Hypericaceae)

<i>Hypericum</i> L. (Hypericaceae) is one of the best-selling herbal medicines in the world comprising ca. 500 species of herbs, shrubs, and small trees. <i>Hypericum petiolulatum</i> Hook. f. & Thomson ex Dyer is widely distributed in China, Vietnam, Myanmar, Nepal, India, Malaysia, and Bhutan and is used as a traditional herb to treat hemoptysis and inflammation. In this study, we sequenced and assembled the complete chloroplast (cp) genome of <i>H. petiolulatum</i>. The complete plastome of <i>H. petiolulatum</i> was 136,105 bp in length, with a large single copy region (LSC) of 93,709 bp, a small single copy region (SSC) of 11088 bp and two identical inverted repeats (IRs) of 15,654 bp. The overall GC content of the plastome was 37.0%, while GC contents of the LSC, SSC, and each IR were 35.5%, 31.0%, and 43.8%, respectively. In addition, 116 genes consisting of 76 protein-coding genes, six ribosomal RNA genes, and 34 transfer RNA genes were identified. A phylogenetic analysis of 14 taxa inferred based on cp genome sequences revealed a close relationship between <i>H. petiolulatum</i> and <i>H. perforatum</i>. The complete cp genome sequence of <i>H. petiolulatum</i> reported in this paper will facilitate population and phylogenomics studies of this medicinal plant group.

Comparative Analysis of the Chloroplast Genomes of Eight Species of the Genus Lirianthe Spach with Its Generic Delimitation Implications.

Based on Sima and Lu's system of the family Magnoliaceae, the genus Lirianthe Spach s. l. includes approximately 25 species, each with exceptional landscaping and horticultural or medical worth. Many of these plants are considered rare and are 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 eight species from the genus Lirianthe were sequenced and analyzed, and their phylogenetic relationships with other genera of the family Magnoliaceae were also elucidated. The results showed that the chloroplast genome sizes of the eight 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 eight 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 were the recommended candidate DNA barcodes for the genus Lirianthe species. The inverted repeat boundary regions show little variation between species and are generally conserved. The result of phylogenetic analysis confirmed that the genus Lirianthe s. l. is a monophyletic taxon and the most affinal to the genera, Talauma and Dugandiodendron, in Sima and Lu's system and revealed that the genus Lirianthe s. s. is paraphyletic and the genus Talauma s. l. polyphyletic in Xia's system, while Magnolia subsection Gwillimia is paraphyletic and subsection Blumiana polyphyletic in Figlar and Nooteboom's system. 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 on this genus.

The newly assembled chloroplast genome of Aeluropus littoralis: molecular feature characterization and phylogenetic analysis with related species

Aeluropus littoralis, a halophyte grass, is widely distributed from the Mediterranean to the Indian subcontinent through the Mongolian Gobi. This model halophyte has garnered increasing attention owing to its use as forage and its high tolerance to environmental stressors. The chloroplast genomes of many plants have been extensively examined for molecular, phylogenetic and transplastomic applications. However, no published research on the A. littoralis chloroplast (cp) genome was discovered. Here, the entire chloroplast genome of A. littoralis was assembled implementing accurate long-read sequences. The entire chloroplast genome, with an estimated length of 135,532 bp (GC content: 38.2%), has a quadripartite architecture and includes a pair of inverted repeat (IR) regions, IRa and IRb (21,012 bp each), separated by a large and a small single-copy regions (80,823 and 12,685 bp, respectively). The features of A. littoralis consist of 133 genes that synthesize 87 peptides, 38 transfer RNAs, and 8 ribosomal RNAs. Of these genes, 86 were unique, whereas 19 were duplicated in IR regions. Additionally, a total of forty-six simple sequence repeats, categorized into 32-mono, four-di, two-tri, and eight-tetranucleotides, were discovered. Furthermore, ten sets of repeats greater than 20 bp were located primarily in the LSC region. Evolutionary analysis based on chloroplast sequence data revealed that A. littoralis with A. lagopoides and A. sinensis belong to the Aeluropodinae subtribe, which is a sister to the Eleusininae in the tribe Cynodonteae and the subfamily Chloridoideae. This subfamily belongs to the PACMAD clade, which contains the majority of the C4 photosynthetic plants in the Poaceae. The newly constructed A. littoralis cp genome offers valuable knowledge for DNA barcoding, phylogenetic, transplastomic research, and other biological studies.

Three complete chloroplast genomes from two north American Rhus species and phylogenomics of Anacardiaceae

BackgroundThe suamc genus Rhus (sensu stricto) includes two subgenera, Lobadium (ca. 25 spp.) and Rhus (ca. 10 spp.). Their members, R. glabra and R. typhina (Rosanae: Sapindales: Anacardiaceae), are two economic important species. Chloroplast genome information is of great significance for the study of plant phylogeny and taxonomy.ResultsThe three complete chloroplast genomes from two Rhus glabra and one R. typhina accessions were obtained with a total of each about 159k bp in length including a large single-copy region (LSC, about 88k bp), a small single-copy regions (SSC, about 19k bp) and a pair of inverted repeats regions (IRa/IRb, about 26k bp), to form a canonical quadripartite structure. Each genome contained 88 protein-coding genes, 37 transfer RNA genes, eight ribosomal RNA genes and two pseudogenes. The overall GC content of the three genomes all were same (37.8%), and RSCU values showed that they all had the same codon prefers, i.e., to use codon ended with A/U (93%) except termination codon. Three variable hotspots, i.e., ycf4-cemA, ndhF-rpl32-trnL and ccsA-ndhD, and a total of 152–156 simple sequence repeats (SSR) were identified. The nonsynonymous (Ka)/synonymous (Ks) ratio was calculated, and cemA and ycf2 genes are important indicators of gene evolution. The phylogenetic analyses of the family Anacardiaceae showed that the eight genera were grouped into three clusters, and supported the monophyly of the subfamilies and all the genera. The accessions of five Rhus species formed four clusters, while, one individual of R. typhina grouped with the R. glabra accessions instead of clustering into the two other individuals of R. typhina in the subgenus Rhus, which showed a paraphyletic relationship.ConclusionsComparing the complete chloroplast genomes of the Rhus species, it was found that most SSRs were A/T rich and located in the intergenic spacer, and the nucleotide divergence exhibited higher levels in the non-coding region than in the coding region. The Ka/Ks ratio of cemA gene was > 1 for species collected in America, while it was < 1 for other species in China, which dedicated that the Rhus species from North America and East Asia have different evolutionary pressure. The phylogenetic analysis of the complete chloroplast genome clarified the Rhus placement and relationship. The results obtained in this study are expected to provide valuable genetic resources to perform species identification, molecular breeding, and intraspecific diversity of the Rhus species.

Unveiling the chloroplast genomes of Capsella bursa-pastoris, Descurainia sophia, and Lepidium apetalum (Brassicaceae)

We de novo assembled and analysed the chloroplast genomes of Capsella bursa-pastoris, Descurainia sophia, and Lepidium apetalum of the plant family Brassicaceae. These chloroplast genomes exhibited a quadripartite structure characterised by inverted repeat regions (26,268–26,460 bp) separating large single copy (83,771–83,870 bp) and small single copy (17,570–18,014 bp) regions. Genetic analysis revealed 112 unique genes, comprising 78 protein-coding genes, 30 transfer RNA (tRNA) genes, and 4 ribosomal RNA (rRNA) genes. Notably, phylogenetic analysis of 21 species revealed close relationships between C. bursa-pastoris and C. orientalis, D. sophia and D. erodiifolia, and L. apetalum and L. cordatum, with 100% bootstrap support. In conclusion, the analysis of these genomes will contribute to the growing knowledge of chloroplast genomes in the Brassicaceae family and of the specific genera Capsella, Descurainia, and Lepidium.

Comparative and phylogenetic analyses based on the complete chloroplast genome of Cornus subg. Syncarpea (Cornaceae) species.

This study presents a comprehensive analysis of the chloroplast (cp) genomes of Cornus species, including comparative and phylogenetic evaluations, as well as examinations of their genomic structure and composition. The cp genomes exhibit a typical circular quadripartite structure and demonstrate highly similar gene order and genomic structure. The complete cp genome size of the 10 taxa in this study is 156,965 bp to 157,383 bp, where the length of the large single-copy (LSC) region is 86,296 bp to 86,691 bp, small single-copy (SSC) region is 18,386 bp to 18,454 bp, and inverted repeat (IR) region is 23,143 bp to 26,112 bp. A total of 131 genes were found, including 86 protein-coding genes (PCGs), eight rRNA genes, and 37 tRNA genes. The mean GC content of the 10 taxa is 38.145%, where the LSC region is 36.396%, the SSC region is 32.372%, and the IR region is 43.076%. Despite the relatively conserved nature of the cp genome within the species of Cornus, 25-31 simple sequence repeats (SSRs) were identified in the 10 taxa in our study. The SSRs were found to be distributed in the LSC, SSC, and IR regions in Cornus hongkongensis subsp. hongkongensis, C. hongkongensis subsp. elegans, C. hongkongensis subsp. gigantea, and C. hongkongensis subsp. tonkinensis, while the SSR was not found in the IR region of the other six taxa. Thus, whole cp genomics is a valuable tool for species identification, taxonomic clarification, and genomic evolutionary analysis. Furthermore, our findings reveal that C. hongkongensis and C. hongkongensis subsp. gigantea, along with Cornus kousa and Cornus elliptica, form sister groups. Notably, C. hongkongensis subsp. ferruginea and C. hongkongensis subsp. melanotricha did not exhibit affinity with C. hongkongensis subsp. hongkongensis. Our study furnishes essential data for further research on their classification and provides novel insights into the relationship within Cornus subg. Syncarpea.

Characterization of the complete chloroplast genome of Wolffia arrhiza and comparative genomic analysis with relative Wolffia species

Lemnoideae, commonly referred to as the duckweed, are aquatic plants found worldwide. Wolffia species are known for their extreme reduction in size and complexity, lacking both roots and leaves, and they hold the distinction of being the smallest plants among angiosperms. Interestingly, it belongs to the Araceae family, despite its apparent morphological differences from land plants in the same family. Traditional morphological methods have limitations in classifying these plants, making molecular-level information essential. The chloroplast genome of Wolffia arrhiza is revealed that a total length of 169,602 bp and a total GC content of 35.78%. It follows the typical quadripartite structure, which includes a large single copy (LSC, 92,172 bp) region, a small single copy (SSC, 13,686 bp) region, and a pair of inverted repeat (IR, 31,872 bp each) regions. There are 131 genes characterized, comprising 86 Protein-Coding Genes, 37 Transfer RNA (tRNA) genes, and 8 ribosomal RNA (rRNA) genes. Moreover, 48 simple sequence repeats and 32 long repeat sequences were detected. Comparative analysis between W. arrhiza and six other Lemnoideae species identified 12 hotspots of high nucleotide diversity. In addition, a phylogenetic analysis was performed using 14 species belonging to the Araceae family and one external species as an outgroup. This analysis unveiled W. arrhiza and Wolffia globosa as closely related sister species. Therefore, this research has revealed the complete chloroplast genome data of W. arrhiza, offering a more detailed understanding of its evolutionary position and phylogenetic categorization within the Lemnoideae subfamily.

Complete chloroplast genomes of three copal trees (Bursera: Bullockia): comparative analysis and phylogenetic relationships.

Bursera trees are conspicuous elements of the tropical dry forests in the Neotropics that have significant cultural value due to their fragrant resins (incense), wood sources (handcrafts), and ecological benefits. Despite their relevance, genetic resources developed for the genus are scarce. We obtained the complete chloroplast (Cp) genome sequence, analyzed the genome structure, and performed functional annotation of three Bursera species of the Bullockia section: Bursera cuneata, B. palmeri, and B. bipinnata. The Cp genome sizes ranged from 159,824 to 159,872bp in length, including a large single-copy (LSC) region from 87,668 to 87,656bp, a small single-copy (SSC) from 18,581 to 18,571bp, and two inverted repeats regions (IRa and IRb) of 26,814bp each. The three Cp genomes consisted of 135 genes, of which 90 were protein-coding, 37 tRNAs, and 8 rRNAs. The Cp genomes were relatively conserved, with the LSC region exhibiting the greatest nucleotide divergence (psbJ, trnQ-UCC, trnG-UCC, and petL genes), whereas few changes were observed in the IR border regions. Between 589 and 591 simple sequence repeats were identified. Analysis of phylogenetic relationships using our data for each Cp region (LSC, SSC, IRa, and IRb) and of seven species within Burseraceae confirmed that Commiphora is the sister genus of Bursera. Only the phylogenetic trees based on the SSC and LSC regions resolved the close relationship between B. bipinnata and B. palmeri. Our work contributes to the development of Bursera's genomic resources for taxonomic, evolutionary, and ecological-genetic studies.

Chloroplast Genome-Wide Analysis Reveals New Single-Nucleotide Polymorphism Resources for the ARMS-qPCR Identification of Dendrobium brymerianum

Dendrobium brymerianum Rchb. f. is a species of orchid with pharmacological interest for its potential to inhibit the growth of human lung cancer cells. The identification of the Dendrobium species is a notable problem due to morphological similarities and the limitations of universal DNA barcodes. To overcome these difficulties, this study employed complete chloroplast (cp) genome sequences as useful resources for the identification of D. brymerianum. Based on Illumina sequencing, the complete cp genomes of five D. brymerianum individuals were assembled. These genomes were in the quadripartite structure, diverse in length between 151,832 and 152,189 bp, and comprised 126 genes. Moreover, significant differences were found in the Small Single-Copy (SSC) and Large Single-Copy (LSC) regions in comparison to the Inverted Repeat (IR) regions. This study recognized hotspot regions and simple sequence repeat (SSR) loci, providing valuable insights into genetic markers. The phylogenetic relationship of Dendrobium species was discovered, highlighting the need for more precise differentiation practices. To address this, ARMS-specific primers, mainly AAob1/AAob2, confirmed strong specificity, permitting the accurate identification of D. brymerianum from other species through ARMS-qPCR. Overall, this study of D. brymerianum chloroplast genomes has generated valuable data about sequence variations, phylogenetics, and mutation dynamics. These perceptions will be valuable in future research on population genetics, taxonomy, and species identification within the Dendrobium genus.

The complete chloroplast genome of Dianella ensifolia (Asphodelaceae)

Dianella ensifolia (L.) Redouté 1802 is a plant known for its significant medicinal values. In this study, we presented its chloroplast genome. The length of the chloroplast genome was found to be 156,571 bp, with a GC content of 37.86%. It consisted of a large single-copy (LSC) of 85,318 bp and a small single-copy (SSC) of 18,307 bp, a pair of inverted repeats (IRs) of 26,473 bp each that separated the LSC and SSC regions. The chloroplast genome of D. ensifolia consisted of 114 unique genes, including 80 protein-coding genes, four rRNA genes, and 30 tRNA genes. Through phylogenetic analysis, we identified a close relationship between D. ensifolia and D. nigra. This newly sequenced chloroplast genome not only enhances our understanding of the genome of Dianella, but also provides valuable insights for the evolutionary study of the family Asphodelaceae.

The complete chloroplast genome sequence of Myricaria wardii Marquand 1929 (Tamaricaceae): a shrub species endemic to the Tibet Plateau

Myricaria wardii Marquand 1929, endemic to the Tibet Plateau, is a perennial shrub with important medicinal and ecological values. In this study, the complete chloroplast (cp) genome of M. wardii was assembled, and the phylogenetic tree was reconstructed to evaluate the phylogenetic location of the species. The results showed that the cp genome size of the M. wardii was 155,299 bp, which contained a pair of inverted repeat (IR) regions (26,150 bp), a large single copy (LSC) region (84,715 bp), and a small single copy (SSC) region (18,284 bp). The total GC content of the cp genome was 36.30%. A total of 128 genes were annotated, consisting of 83 protein-coding genes, 37 tRNA genes and 8 rRNA genes. The phylogenetic analysis showed that M. wardii was closely related to M. prostrata. This study provides useful information for the conservation of this species and the phylogenetic analysis of Tamaricaceae.

The complete chloroplast genome of Hemiboea pterocaulis (Gesneriaceae) exclusively distributed in Guilin, Guangxi, China

Hemiboea pterocaulis is a unique species only found in Guilin, Guangxi, China. In this study, we sequenced and assembled the complete chloroplast genome of H. pterocaulis and revealed its phylogenetic relationship with other Hemiboea species. The chloroplast genome sequence of H. pterocaulis is 153,159 bp in length and comprises a large single-copy (LSC) region of 84,178 bp, a small single-copy (SSC) region of 18,087 bp, and a pair of inverted repeat (IR) regions, each with a length of 25,447 bp. It has a total GC content of 37.6% and encodes 132 genes, including 87 protein-coding genes, 37 tRNA genes, and eight rRNA genes. The phylogenetic relationships based on the complete chloroplast genome sequences of Hemiboea taxa indicate that H. pterocaulis is most closely related to H. suiyangensis, indicating that H. pterocaulis is an independent species and is separated from the H. subcapitata complex. These results provide valuable insights into the phylogeny, species divergence, and delimitation of the Hemiboea genus.

Complete chloroplast genome of sageretia thea (rhamnaceae), an ornamental fruit and medicinal tree

Sageretia thea (Osbeck) M.C. Johnst (1968) is an important fruit and medicinal species of Rhamnaceae family. The complete chloroplast genome (cp) of Sageretia genus was sequenced and reported for the first time in this study. The cp genome had a total length of 161,352 bp, consisting of a largesingle-copy (LSC) region of 89,802 bp, a small single-copy (SSC) region of 18,914 bp, and a pair of inverted repeat (IR) regions totaling 26,318 bp. The plastid genome contained 129 genes, including 84 protein-coding genes, 37 tRNA genes, 8 rRNA genes. The overall GC content of the genome was found to be 37.10%. Phylogenetic analysis based on comparison with 27 chloroplast genomes revealed that S. thea is closely related to genera Rhamnus and Berchemia. The findings of this study can provide fundamental insights for the conservation, exploitation, and systematic genomic investigation of Rhamnus plants.

The complete chloroplast genome and phylogenetic analysis of Bauhinia glauca subsp. hupehana (Craib) T. C. Chen 1988

Bauhinia glauca subsp. hupehana (Craib) T. C. Chen 1988, a member of the Leguminosae family, Cercidoideae subfamily, and Bauhinia genus, has a rich history of traditional usage in Chinese medicine. Renowned for its analgesic properties, it is commonly employed for managing inflammation and pain. This study aimed to sequence the complete chloroplast genome of B. glauca subsp. hupehana using Illumina paired-end sequencing data. The chloroplast genome spans 156,967 bp and consists of four main regions: the large single-copy (LSC) region (89,185 bp), the small single-copy (SSC) region (19,146 bp), and a pair of inverted repeats (IRs) (24,318 bp). The overall GC content of the chloroplast genome is 36.19%, with specific values of 33.99%, 29.79%, and 42.76% for the LSC, SSC, and IR regions, respectively. A total of 128 genes were annotated in the chloroplast genome, including 83 protein-coding genes, 37 tRNA genes, and eight rRNA genes. Phylogenetic analysis revealed that B. glauca subsp. hupehana is closely related to Bauhinia racemose, indicating a sister taxon relationship between the two species. This study significantly contributes to the chloroplast genomic resource for Bauhinia, laying the groundwork for future phylogenetic investigations within the genus.

Comparative analysis of plastomes of Rubus chingii and R. chingii var. suavissimus

Rubus chingii and R. chingii var. suavissimus are unique dual-purpose plant resources, with significant nutraceutical, pharmaceutical, and economic value, as well as promising prospects for further development. To investigate the genetic structure and evolutionary characteristics of these two varieties, this study conducted plastome sequencing using the Illumina HiSeq XTen sequencing platform. Subsequently, the study performed assembly, annotation, and characterization of the genomes, followed by a comparative plastome and phylogenetic analysis using bioinformatics techniques. The results revealed that the plastomes of R. chingii and R. chingii var. suavissimus exhibited a tetrad structure, comprising a large single-copy region(LSC), a small single-copy region(SSC), and two inverted repeat regions(IRs). The study identified a total of 56 simple sequence repeats(SSRs) after comparative analysis, predominantly consisting of A and T. Furthermore, the structure of the IR boundary genes in both varieties was found to be highly conserved, with only minor nucleotide variations. Additionally, the study identified three highly variable regions: rps16-trnQ-psbK, trnR-atpA, and trnT-trnL, which held promise as potential identification marks for further development and utilization. Phylogenetic analysis results obtained by the maximum likelihood and Bayesian inference methods demonstrated a close clustering of R. chingii and R. chingii var. suavissimus(100% support), with their closest relatives being R. trianthus. This study, focusing on plastome-level genetic distinctions between these two varieties, lays a foundation for future species protection, development, and utilization.

Comparative analyses of complete plastid genomes of representative species of subfamily Convallarioideae (Asparagaceae)

Convallarioideae are a subfamily of Asparagaceae, a morphologically diverse group comprising seven tribes, i.e., Eriospermeae, Rusceae, Dracaeneae, Nolineae, Convallarieae, Ophiopogoneae and Polygonateae, and two genera unclassified to tribe. In this study, we conducted comparative plastid genome (plastome) analyses of seven species representing seven clades of the subfamily. The results showed that all plastomes exhibited standard conserved quadripartite structures with inverted repeats (26,261–26,522 bp) separated by a large single-copy region (83,007–85,692 bp) and a small single-copy region (18,205–18,707 bp). Each plastome has 137 genes, including 87 protein-coding genes, 38 transfer RNAs and 8 ribosomal RNA genes. Furthermore, we detected 33–61 simple sequence repeats in six categories and 39–57 long repeats in four categories. We selected eleven hotspots as primer sites for potential molecular markers. Phylogenetic analysis of the subfamily revealed that all the tribes are strongly supported except for Polygonateae, but weak support was observed among the main clades in the subfamily.