Small Single-copy Region Research Articles

The chloroplast genome sequence and phylogenetic analysis of Rubia alata Wall and Rubia ovatifolia Z. Ying Zhang. (Rubiaceae).

Rubia alata Wall (R. alata) and Rubia ovatifolia Z. Ying Zhang (R. ovatifolia) are unique medicinal plants native to China. Sequencing their chloroplast genomes is important for understanding species differentiation and establishing phylogenetic relationships. The chloroplast genomes of R. alata and R. ovatifolia were sequenced using the Illumina HiSeq platform. The chloroplast genome of R. alata is 154,973 base pairs (bp) in length, containing a large single-copy region (LSC) of 84,801bp, a small single-copy region (SSC) of 17,138bp, and a pair of inverted repeats (IRs) of the same length. The length of the chloroplast genome, LSC, SSC, and IR regions of R. ovatifolia is 26,517bp, 84,716bp, 17,116bp and 26,517bp, respectively. Codon usag e analysis revealed that R. alata had the highest frequency of Aspartic acid (Asp) (1650 occurrences) in protein-coding sequences (CDS), while R. ovatifolia showed the highest frequency of Tyrosine (Try) (1479 occurrences). Comparative analysis of chloroplast genomes across seven species from the genus Rubia identified the most divergent coding regions, including rps16, psbI-trns-CGA, and petN, while plastid rRNAs were the most conserved. Phylogenetic analysis showed R. alata clustering with R. cordifolia (66.3% support), and R. ovatifolia clustering with Rubia podantha (100% support). These findings enhance our understanding of the chloroplast genome structure in Rubia species and provide molecular information for the future development and utilization of R. alata and R. ovatifolia resources.

Comparative analysis of chloroplast genome of Lonicera japonica cv. Damaohua.

Lonicera japonica is a well-known medicinal plant, and the Damaohua cultivar is one of the oldest known honeysuckle cultivars in China. The 155,151 bp chloroplast genome of this cultivar was obtained through Illumina sequencing. The genome includes a pair of inverted repeats (IRa and IRb; 23,789 bp each), a large single-copy region (88,924 bp), and a small single-copy (SSC) region (18,649 bp). In total, 127 unique genes were identified: 80 protein-coding, 39 tRNA, and 8 rRNA genes. Only ycf3 contained two introns. Eighty-nine large repetitive sequences and 54 simple sequence repeats were detected. Fifty potential RNA editing sites were predicted. Adaptive evolution analysis revealed that infA, matK, petB, petD, rbcL, rpl16, rpl2, rps3, ycf1, and ycf2 were positively selected, possibly reflecting the specific environmental adaptations of this cultivar. Sequence alignment and analysis revealed several candidate fragments for Lonicera species identification, such as the intergenic regions rpoB-petN, rbcL-accD, and psaA-ycf3. The IR region boundary and phylogenetic analysis revealed that the L. japonica cv. Damaohua chloroplast genome was most closely related to the L. japonica genome, but there were five distinct differences between the two. There are four sites with high variability between L. japonica and L. japonica cv. Damaohua with nucleotide variability (Pi) greater than 0.002, including rps2-rpoC2, atpB-rbcL, ycf1, and ycf1-trnN GUU. The differences between L. japonica and L. japonica cv. Damaohua were further confirmed by the single nucleotide polymorphism sites between these two species. Therefore, this study revealed that the chloroplast genome can serve as a universal super barcode for plant identification, which can identify differences and help distinguish Lonicera japonica from related species. An understanding of Lonicera japonica cv. Damaohua chloroplast genomics and a comparative analysis of Lonicera species will provide a scientific basis for breeding, species identification, systematic evolution analysis, and chloroplast genetic engineering research on medicinal honeysuckle plants.

De Novo Sequencing of Drymaria villosa and Comparative Analysis of Plastome in Caryophyllaceae Across 23 Species.

Plant plastome are well studied due to their essential roles in photosynthesis and plant development. Comparative studies among plastome of closely related genera or families are limited, hindering our understanding of evolutionary changes and adaptation. This study presents a comparative analysis of 23 Caryophyllaceae plastome revealing a dynamic interplay of conserved and variable features. The genome size exhibited a moderate coefficient of variation (CV) of 2.58%. The large single-copy (LSC) and small single-copy (SSC) regions were highly conserved, with CVs of 2.55% and 2.00%, respectively. In contrast, the inverted repeat (IR) regions displayed greater variability, with a CV of 4.23%, indicating dynamic evolutionary processes. Exon counts varied significantly (CV 17.20%), while intron counts showed some variability (CV 7.79%), reflecting diverse gene structures. Coding sequences had moderate variability (CV 3.67%), while non-coding sequences varied more (CV 5.05%). tRNA counts were slightly variable (CV 2.67%), and GC content was notably consistent (CV 0.40%). This study includes the newly sequenced plastome of Drymaria villosa (GenBank accession OR790517), confirming its placement within Caryophyllaceae with significant diversification through phylogenetic analysis. Correlations (> 0.6) among plastome components and genome size reflect their tight evolutionary linkage, enhancing our understanding of plastome evolution in Caryophyllaceae and aiding future investigations into the ecological and medicinal potential of D. villosa and related species.

Complete chloroplast genome and phylogenetic analysis of Lonicera microphylla Willd. ex Roem. & Schult. 1819 Caprifoliaceae

Lonicera microphylla Willd. ex Roem. & Schult. 1819 is a medicinal plant species, especially for treating chronic fever and dysentery. This study aimed to characterize the chloroplast genome of L. microphylla and reconstruct the phylogenetic relationships among Lonicera Linn. 1753. The circular complete chloroplast genome is 154,945 bp in length, with two inverted repeat regions (IRs; 23,841 bp), separated by a small single-copy region (SSC; 18,789 bp) and a large single-copy region (LSC; 88,474 bp). The overall GC content of L. microphylla plastome was 38.36%. The chloroplast genome encoded a total of 131 genes, including 84 protein-coding genes, 39 tRNA genes, and eight rRNA genes. Phylogenetic analysis reveals that L. microphylla was more closely related to Lonicera tangutica Maxim. 1878. Our result can provide reference for the phylogenetic relationship, resource development, and utilization of Lonicera.

Characterization and phylogenetic analysis of the complete chloroplast genome sequence of Phalaenopsis deliciosa (Rchb. f. 1854)

Phalaenopsis deliciosa (Rchb. f.), an ornamental orchid known for vibrant flowers, has a 148,090 bp chloroplast genome with 36.78% GC content. It includes an 85,241 bp large single-copy (LSC) region, an 11,649 bp small single-copy (SSC) region, and two 13,800 bp inverted repeats (IRs), encoding 122 genes (76 protein-coding, 38 tRNA, and 8 rRNA). This genome data refines the Phalaenopsis gene database and supports research on phylogeny and molecular breeding.

Comparison of the Complete Chloroplast Genomes of Astilbe: Two Korean Endemic Plant Species

Background: Astilbe, consisting of about 18 species, is distributed throughout East Asia and Northeastern America, and most Astilbe species are widely cultivated as ornamental plants. A total of four species of Astilbe have been confirmed to be distributed throughout Korea, two of which are endemic to Korea. Methods: In this study, we sequenced and assembled the complete chloroplast genomes of two endemic Korean plants using Illumina sequencing technology, identified simple sequence repeats (SSRs) and repetitive sequences, and compared them with three previously reported chloroplast genomes. Results: The chloroplast genomes of the two species were 156,968 and 57,142 bp in length and had a four-part circular structure. They consisted of a large single-copy region of 87,223 and 87,272 bp and a small single-copy region of 18,167 and 18,138 bp, separated by a pair of inverted repeats (IRa and IRb, 25,789 and 25,866 bp). The genomes contained 130 genes, 49 SSRs, and 49 long repetitive sequences. Comparative analysis with the chloroplast genomes of five Astilbe species indicated that A. uljinensis was closely related to A. chinensis and A. taquetii to A. koreana. Conclusions: This study provides valuable references for the identification of two endemic Korean Astilbe species and contributes to a deeper understanding of the phylogeny and evolution of the genus Astilbe.

Complete Chloroplast Genome of Crassula aquatica: Comparative Genomic Analysis and Phylogenetic Relationships

Background/Objectives: Crassula aquatica (L.) Schonl. is a very small annual plant growing along riverbanks. Chloroplast (cp) genomes, crucial for photosynthesis, are highly conserved and play a key role in understanding plant evolution. In this study, we conducted cp genome analysis of C. aquatica, aiming to elucidate its phylogenetic position and structural variations. We analyzed and described the features of the complete cp genome of C. aquatica and conducted comparative analysis with the cp genomes of closely related taxa. Rsults: The cp genome was 144,503 bp in length and exhibited the typical quadripartite structure, consisting of a large single-copy region (LSC; 77,993 bp), a small single-copy region (SSC; 16,784 bp), and two inverted repeats (24,863 bp). The cp genome of C. aquatica comprised 113 unique genes, including 79 protein-coding genes (PCGs), 30 tRNAs, and 4 rRNA genes. Comparative genomic analysis of 13 other Crassula species and six outgroups demonstrated highly conserved gene content and order among Crassula species. However, notable differences were observed, including the complete loss of the rpoC1 intron in C. aquatica and several closely related species, which may serve as a synapomorphic trait supporting the monophyly of the subgenus Disporocarpa. We analyzed the nucleotide diversity among 14 Crassula cp genomes and identified five highly variable regions (pi > 0.08) in the IGS regions. Phylogenetic analysis based on 78 PCGs confirmed the monophyly of Crassula and its division into two subgenera: Crassula and Disporocarpa. Although the phylogenetic tree supported the subgeneric classification system, the sectional classification system requires reassessment. Conclusions: In this study, we conducted a comparative analysis of the cp genome of the genus Crassula. We inferred evolutionary trends within the Crassula cp genome and provided molecular evidence supporting the integration of the genus Tillaea into the genus Crassula. However, as this study does not represent all species within the genus Tillaea, further comprehensive phylogenetic analyses are requrired.

Comparative plastomes sheds light on phylogeny of Weigela.

Weigela Thunb. is a genus in the family Caprifoliaceae. All species in this genus have high ornamental and medicinal value. However, the genetic divergence between species and the phylogeny within Weigela is still unclear. Therefore, we sequenced and analyzed four plastomes from four different Weigela species to reveal the genetic divergence among species of this genus, and the phylogeny within Weigela. The four plastomes from Weigela ranged from 156,909 bp to 157,739 bp in size, and presented a typical circular quadripartite structure. Each complete plastome contained a pair of inverted repeat regions (23,592~24,957 bp), a larger single-copy (LSC) region (89,922~90,229 bp), and a small single-copy (SSC) region (17,668~20,429 bp). We identified three types of repeats, corresponding to 268 forward repeats, 128 palindromic repeats, and 867 tandem repeats, for a total of 1,263 long repeats. A total of 352 SSRs were identified from the four plastomes, and most of them were concentrated in the LSC region and the noncoding regions. Mononucleotide repeat units were the most frequently detected types of repeats, of which A/T repeat units were the most abundant. Three mutational hotspots (trnH-psbA, trnR-ndhF, and trnN-ndhF) were identified as candidate barcodes for Weigela species. Weigela belongs to Diervilloideae located at an early diverging position in the Caprifoliaceae. Within Weigela, W. japonica and W. floribunda were sister with W. subsessilis and W. florida. This study revealed the plastome structure and variation of four well-known Weigela species, and found three candidate barcodes for further study of four well-known Weigela species. In addition, the phylogenetic location of Weigela within the Caprifoliaceae was identified.

Comparative analysis of complete chloroplast genomes of 14 Asteraceae species.

The Asteraceae family, the largest and one of the most diverse families of angiosperms, presents significant challenges in taxonomic classification and systematic research due to its vast species diversity and morphological complexity. A comprehensive understanding of the chloroplast genomes within this family is essential for refining taxonomic classifications and advancing phylogenetic studies. In this study, we sequenced the complete chloroplast genomes of 14 Asteraceae species and conducted a thorough bioinformatic analysis of their characteristics. The chloroplast genomes, ranging from 150,907bp to 152,858bp, exhibit a typical quadripartite structure: a large single-copy (LSC) region (83,044bp to 84,625bp), a small single-copy (SSC) region (18,223bp to 18,673bp), and a pair of inverted repeats (IRs) (24,806bp to 25,201bp). These genomes encode 87 to 89 protein-coding genes (PCGs), 36 to 37 tRNA genes, and 8 rRNA genes, with high conservation in size, structure, gene content, and order. Comparative analysis with other Asteraceae species' chloroplast genomes revealed notable similarities and structural variations, particularly in the IR regions. Nucleotide polymorphism analysis identified four genes-trnY-GUA, trnE-UUC, ycf1, and rrn23-with higher Pi values, suggesting potential hotspots for evolutionary studies. Phylogenetic analysis using maximum likelihood (ML) and Bayesian inference (BI) approaches provided new insights, proposing the reclassification of Himalaiella auriculata and Jacobaea raphanifolia as independent genera, distinct from Saussurea and Senecio. This study presents a comprehensive analysis of the chloroplast genome structures and phylogenetic relationships of 14 Asteraceae species, offering critical data for future molecular identification, evolutionary biology, and population genetics research. The findings hold significant implications for the ongoing refinement of Asteraceae taxonomic classifications and enhance our understanding of the evolutionary dynamics within this complex family.

Conserved Plastid Genomes of Pourthiaea Trees: Comparative Analyses and Phylogenetic Relationship

The genus Pourthiaea Decne., a deciduous woody group with high ornamental value, belongs to the family Rosaceae. Here, we reported newly sequenced plastid genome sequences of Pourthiaea beauverdiana (C. K. Schneid.) Hatus., Pourthiaea parvifolia E. Pritz., Pourthiaea villosa (Thunb.) Decne., and Photinia glomerata Rehder & E. H. Wilson. The plastomes of these three Pourthiaea species shared the typical quadripartite structures, ranging in size from 159,903 bp (P. parvifolia) to 160,090 bp (P. beauverdiana). The three Pourthiaea plastomes contained a pair of inverted repeat regions (26,394–26,399 bp), separated by a small single-copy region (19,304–19,322 bp) and a large single-copy region (87,811–87,973 bp). A total of 113 unique genes were predicted for the three Pourthiaea plastomes, including four ribosomal RNA genes, 30 transfer RNA genes, and 79 protein-coding genes. Analyses of inverted repeat/single-copy boundary, mVISTA, nucleotide diversity, and genetic distance showed that the plastomes of 13 Pourthiaea species (including 10 published plastomes) are highly conserved. The number of simple sequence repeats and long repeat sequences is similar among 13 Pourthiaea species. The three non-coding regions (trnT-GGU-psbD, trnR-UCU-atpA, and trnH-GUG-psbA) were the most divergent. Only one plastid protein-coding gene, rbcL, was under positive selection. Phylogenetic analyses based on 78 shared plastid protein-coding sequences and 29 nrDNA sequences strongly supported the monophyly of Pourthiaea. As for the relationship with other genera in our phylogenies, Pourthiaea was sister to Malus in plastome phylogenies, while it was sister to the remaining genera in nrDNA phylogenies. Furthermore, significant cytonuclear discordance likely stems from hybridization events within Pourthiaea, reflecting complex evolutionary dynamics within the genus. Our study provides valuable genetic insights for further phylogenetic, taxonomic, and species delimitation studies in Pourthiaea, as well as essential support for horticultural improvement and conservation of the germplasm resources.

Complete chloroplast genomes of Desmidorchis penicillata (Deflers) plowes and Desmidorchis retrospiciens Ehrenb.: comparative and phylogenetic analyses among subtribe Stapeliinae (Ceropegieae, Asclepiadoideae, Apocynaceae)

The succulent shrubs Desmidorchis penicillata and D. retrospiciens, part of the taxonomically challenging genus Desmidorchis, are well‐known for their ecological resilience and medicinal significance. This study sequences the first complete chloroplast genomes of these species, shedding light on their genomic characteristics and evolutionary relationships. The circular genomes of D. penicillata (161 776 bp) and D. retrospiciens (162 277 bp) display a quadripartite structure typical of Angiosperms. Gene content, order, and GC content are consistent, featuring 114 unique genes, including 80 protein‐coding, 30 transfer RNAs, and four ribosomal RNAs genes. Codon usage analysis underscores A/U‐rich preferences, while RNA editing sites, predominantly in ndhB and ndhD genes, suggest post‐transcriptional modifications. Analysis of long repeated sequences reveals a predominance of forward and palindromic repeats. Simple sequence repeats (SSRs), particularly A/T motifs, are abundant, with high presence of mononucleotide, offering potential molecular markers. Comparative analysis with their relatives in subtribe Stapeliinae identifies mutational hotspots such as ycf1, ndhF, trnG(GCC)‐trnfM(CGA) and ndhG‐ndhI that could be potential DNA barcoding markers. The inverted repeat (IR) boundaries analysis revealed an expansion of IR on the small single copy region, leading to the formation of a pseudogene. Overall, substitution rate analysis indicated purifying selection, with a few genes (rpl22, clpP and rps11) showing signatures of positive selection. Additionally, the phylogenetic analysis positioned Desmidorchis within the Stapeliinae clade and strongly supported the sister relationship between D. penicillata and D. retrospiciens. This study provides comprehensive molecular data for future research in Desmidorchis.

The Complete Chloroplast Genome of Meconopsis simplicifolia and Its Genetic Comparison to Other Meconopsis Species.

Background: Chloroplasts, due to their high conservation and lack of recombination, serve as important genetic resources for the classification and evolutionary analysis of closely related species that are difficult to distinguish based on their morphological features. Meconopsis simplicifolia (M. simplicifolia), an endangered herb within the Meconopsis genus, has demonstrated therapeutic potential in treating various diseases. However, the highly polymorphic morphology of this species poses a challenge for accurate identification. Methods: In this study, the complete chloroplast genome of M. simplicifolia was sequenced and assembled using Illumina sequencing technology. Simple sequence repeats (SSRs) and repetitive sequences were characterized. In addition, a comparative analysis was conducted with the chloroplast genomes of six other Meconopsis species. Results: The chloroplast genome of M. simplicifolia has a quadripartite circular structure with a total length of 152,772 bp. It consists of a large single-copy region of 83,824 bp and a small single-copy region of 17,646 bp, separated by a pair of inverted repeat sequences (IRa and IRb, 25,651 bp). The genome contains 131 genes, 33 SSRs, and 27 long repetitive sequences. Comparative analysis with six other chloroplast genomes of Meconopsis revealed that M. simplicifolia is closely related to M. betonicifolia and that the rpl2 (ribosomal protein L2) gene in the IRb region has been deleted. This deletion is of significant importance for future taxonomic studies of M. simplicifolia. Conclusions: This study provides a valuable reference for the identification of M. simplicifolia and contributes to a deeper understanding of the phylogeny and evolution of the Meconopsis genus.

The complete chloroplast genome sequence of Primula medogensis (Primulaceae) and its phylogeny

Primula medogensis W.B Ju, B. Xu & X.F. Gao 2023, a new species categorized under P. sect. Cordifoliae, was officially described in 2023. Given its recent classification, the genetic resources for this species are currently very limited. Here, we sequenced and assembled the first complete chloroplast genome of P. medogensis using Illumina sequencing technology. The complete chloroplast genome of P. medogensis is 151,486 bp in length, exhibiting a typical quadripartite structure. It consists of a large single-copy region (LSC; 83,407 bp) and a small single-copy region (SSC;17675 bp), separated by a pair of inverted repeat regions (IRs; 25202 bp). A total of 131 genes were annotated, including 86 protein-coding, 37 tRNA, and eight rRNA genes. The overall GC content was 37.1%. Phylogenetic analysis of 59 Primula species revealed a close relationship between P. medogensis and P. calliantha subsp. bryophila.

The complete chloroplast genome sequence and phylogenetic analysis of Hordeum pusillum Nutt., 1818 (Poaceae)

Hordeum pusillum (Hordeum pusillum Nutt., 1818) is an annual barley that is native to the west of the North America and widespread in southern United States and tropical America. In this study, we have provided the first complete characterization of the chloroplast genome of H. pusillum. Our research revealed that the circular chloroplast genome of H. pusillum consists of a large single-copy region (LSC: 80,853 bp), a small single-copy region (SSC: 12,745 bp), and a pair of inverted repeat regions (IRs: 21,587 bp), totaling 136,772 bp in length. Within the chloroplast genome of H. pusillum, 91 protein-coding genes, 38 tRNA genes, and ten rRNA genes were identified. To determine the evolutionary relationship of Hordeum species with reported chloroplast genome sequences, we constructed a phylogenetic tree using the entire chloroplast genome sequences. The evolutionary position of H. pusillum corresponds to its geographical location. The chloroplast genome of H. pusillum provided in this study may have significant implications for the phylogenetic study of Poaceae species.

The complete chloroplast genome of Camellia huulungensis Rosmann et Ninh, a golden Camellia species endemic to Vietnam

Camellia huulungensis Rosmann & Ninh 1997, belonging to the sect. Chrysantha, holds important ornamental value and medicinal value. In this study, the complete chloroplast genome sequence of C. huulungensis was assembled using high-throughput sequencing technology. The entire length of chloroplast genome is 156,546 bp and contains a small single-copy region (18,257 bp), a large single-copy region (86,219 bp), and a pair of inverted repeat regions (26,035 bp). A total of 133 genes were annotated, including 88 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. The overall GC content is 37.33%. The phylogenetic analysis showed that C. huulungensis is sister to C. aurea. The results can provide genetic data for further phylogenetic studies of Camellia.

The complete chloroplast genome and phylogenetic analysis of Garcinia esculenta Y. H. Li. 1981 (Clusiaceae)

Garcinia esculenta Y. H. Li. 1981 (Clusiaceae) is an endemic tree species in China, primarily found in western and northwestern Yunnan Province. In this research, the complete chloroplast genome of G. esculenta was sequenced using the Illumina NovaSeq6000 platform. The result showed that the length of the complete chloroplast genome was 155,853 bp, which was composed of a large single-copy region (LSC) of 84,534 bp, a small single-copy region (SSC) of 17,175 bp, and a pair of inverted repeat (IR) regions of 27,072 bp. The overall GC content was 36.1%. The complete chloroplast genome encompassed 128 genes, comprising 83 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. Phylogenetic analysis of the complete chloroplast genome sequences of 22 species revealed that G. esculenta is most closely related to G. oblongifolia.

The complete chloroplast genome of Fuchsia standishii J. Harrison, 1840 (Onagraceae) from Yunnan, China

Fuchsia standishii J. Harrison, 1840, a perennial shrub, is renowned for its vividly colored and uniquely shaped blooms, which have an extended flowering season. Commonly cultivated as an ornamental potted plant, it is utilized in traditional Chinese medicine. In this study, we successfully sequenced and assembled the complete chloroplast genome of F. standishii using high-throughput Illumina sequencing technology. The assembled chloroplast genome displays a typical quadripartite structure, with a total length of 156,391 bp. It consists of a pair of inverted repeat regions (IRs), each measuring 25,069 bp, separated by a large single-copy region (LSC) of 87,754 bp and a small single-copy region (SSC) of 18,499 bp. The overall GC content of the genome is 37.60%. The genome includes a total of 129 genes, comprising 84 protein-coding genes, 37 tRNA genes, and eight rRNA genes. Phylogenetic analysis of 17 complete chloroplast genomes revealed that F. standishii forms a monophyletic group with the entire Circaea. This study provides a molecular foundation for future phylogenetic research on Fuchsia.

Characterization of the complete chloroplast genome of Liparis gigantea (Orchidaceae)

Liparis gigantea is a Chinese traditional medicinal herb in the Orchidaceae family. It is a rare and special Liparis species that exhibits relatively large flowers. To illuminate its phylogenetic status and augment genomic resources, the complete chloroplast (cp) genome of L. gigantea was first sequenced and assembled using whole genome next-generation sequencing in this study. The cp genome size is 158,462 bp with a total GC content of 36.9%. Characterized by a quadripartite structure, the genome consists of a large single-copy (LSC) region of 86,032 bp, a small single-copy (SSC) region of 18,322 bp, which is separated by a pair of 27,054 bp inverted repeat regions (IRs). A total of 133 genes were annotated, including 87 protein-coding genes, 38 tRNA genes, and 8 rRNA genes. Phylogenetic analysis strongly supported L. gigantea as the sister to two closely related terrestrial species, Liparis nervosa and L. vivipara. The results of this study provide genomic information for future research and application of this medicinal herb.

The complete chloroplast genome of Calyptothecium philippinense Broth. (Pterobryaceae, Hypnales)

The genus Calyptothecium, currently comprising ca. 30 species worldwide, is the largest genus within the family Pterobryaceae. However, a comprehensive taxonomic revision of this genus is lacking. Calyptothecium philippinense Broth. 1899, a moss species widely found in the tropical regions of Asia, is characterized by the unique rugose leaves and large auriculate leaf bases. In this study, we sequenced the complete chloroplast genome (CPG) of C. philippinense using the Illumina NovaSeq 6000 platform. The length of the CPG of C. philippinense was determined to be 124,513 bp, with an AT content of 74%. The CPG of C. philippinense exhibited a standard quadripartite structure, consisting of one small single-copy (SSC) region (18,541 bp), one large single-copy region (LSC) (87,222 bp), and two inverted repeat (IR) regions (9375 bp each). A total of 126 genes from the CPG of C. philippinense were annotated, including 82 protein-coding genes, eight ribosomal RNA genes, and 36 transfer RNA genes. Phylogenetic analysis based on the CPGs of 25 bryophyte taxa revealed that the three Pterobryaceae species C. philippinense, Calyptothecium hookeri (Mitt.) Broth. and Pterobryopsis orientalis (Müll. Hal.) M. Fleisch. formed a robust clade. The findings could facilitate more accurate classification and help elucidate evolutionary relationships within Calyptothecium.

Characterization of the complete chloroplast genome sequence of Artemisia sylvatica Maximowicz 1859 (Asteraceae)

Artemisia sylvatica Maximowicz 1859 is one of the medicinal herbs in Artemisia. This study presents the complete chloroplast genome of A. sylvatica, sequenced using the Illumina NovaSeq platform. The genome is 151,161 bp in length, featuring a GC content of 38%. It consists of a large single-copy (LSC) region of 82,892 bp, a small single-copy (SSC) region of 18,353 bp, and two inverted repeat (IR) regions of 24,958 bp each. In total, the genome contains 132 genes, including 87 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. Phylogenetic analysis positions A. sylvatica within the subgenus Artemisia, highlighting its evolutionary relationships within this diverse genus. The first chloroplast genome of A. sylvatica was reported in this work contributes to the enrichment of genomic data for the genus Artemisia.