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 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.

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 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.

The complete sequence of chloroplast genome of Baeckea frutescens Linaeus 1753 (Myrtoideae), a traditional folk medicinal plant.

Baeckea frutescens Linaeus 1753, as a traditional folk medicine in South East Asia, possesses sesquiterpenes, phloroglucinols, chromones, and essential oil, and is utilized for traditional Chinese medicinal purposes. The genetic diversity of the plant must be better understood, considering its significance. The complete chloroplast (cp) genome of B. frutescens was sequenced and assembled by using Illumina paired-end data, marking a significant advancement toward comprehending its genetic composition. The complete cp genome is 158,939 bp in length and contains 128 genes, consisting of 83 protein-coding genes, 8 ribosomal RNA genes, and 37 transfer RNA genes. Phylogenetic analyses indicated that B. frutescens and other the 13 were clustered to the family of Myrtaceae. These findings are crucial for the conservation and utilization of this important plant species. Additionally, they underscore the potential for future research on the evolution and preservation of B. frutescens, which could be advantageous in pharmaceutical applications.

The complete chloroplast genome of Tabebuia rosea (Bignoniaceae).

Tabebuia rosea is a world-renowned woody plant with colorful flowers in full bloom. In addition to its high ornamental value, it also has ecological and medicinal value. In this study, the complete circular chloroplast genome of T. rosea was reconstructed and annotated using Illumina sequencing. The chloroplast genome was 158,919 bp in size with GC content of 38.21%, including a large single-copy region of 85,823 bp, a small single-copy region of 12,816 bp, and a pair of inverted repeats of 30,140 bp. It encoded 132 genes, including 87 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. Based on current available chloroplast genome sequences, the phylogenetic analysis indicated that T. rosea was clustered with T. nodosa and H. chrysanthus. This study provided insights into the evolutionary relationships among different species of Bignoniaceae.

Whole chloroplast genome sequence and phylogenetic analysis of Calanthe discolor (Orchidaceae).

The orchid Calanthe discolor, which has high ornamental and medicinal value, is mainly distributed in Zhejiang, Jiangsu, and southeast Hubei Provinces of China, as well as in Japan and the southern Korean peninsula. In this study, the whole chloroplast genome sequence of C. discolor was first assembled using high-throughput Illumina paired-end technology, providing data to evaluate the evolution of this species. The C. discolor chloroplast genome was158,286 bp long, including a large single-copy region of 87,095 bp, a small single-copy region of 18,407 bp, and two copies of a repeat region (26,392-bp each). The overall G + C content was 41.2%. A total of 133 genes were predicted from the genome, including 87 protein-coding genes, eight ribosomal RNAs, 38 transfer RNAs. Phylogenetic analysis indicated a close relationship between C. discolor and C. bicolor.

Comparative study on chloroplast genome of Tamarix species.

Tamaricaceae comprises about 120 species and has a long evolutionary history, Tamarix Linn accounts for approximately 75% of the total species in this family. It is the most widely distributed and diverse genus in the family. They have important ecological significance for transforming deserts and improving climate conditions. However, Tamarix is the most poorly classified genera among flowering plants owing to its large variability and high susceptibility to interspecific hybridization. In this study, the complete chloroplast genomes of three Tamarix species and one draft chloroplast genome were obtained in this study. Combined with eight chloroplast genomes deposited in GenBank, complete chloroplast sequences of 12 Tamarix species were used for further analysis. There are 176 non-SSR-related indels and 681 non-indel-related SSRs in the 12 Tamarix chloroplast genomes. The mononucleotide SSRs are the most prevalent among all types of SSRs. The mVISTA results indicate high sequence similarities across the chloroplast genome, suggesting that the chloroplast genomes are highly conserved, except for sample Tamarix androssowii (ENC850343). The IR regions and the coding regions are more conserved than the single-copy and noncoding regions. The trnF-ndhJ, ndhC-trnM-CAU, ycf1, and trnL-UAG-ndhF regions are the most variable and have higher variability than those of the universal DNA markers. Finally, the first phylogenetic tree of Tamaricaceae was constructed which confirmed the monophyly of Tamarix in Tamaricaceae. The first phylogenetic tree of Tamarix was based on the complete chloroplast genome to date, the changes in branch length and support rate can potentially help us clarify the phylogenetic relationships of Tamarix. All the obtained genetic resources will facilitate future studies in population genetics, species identification, and conservation biology of Tamarix.

Characterization of the complete chloroplast genome sequence of Schisandra propinqua subsp. sinensis (Oliv.) R.M.K.Saunders 1997 (Schisandraceae).

Schisandra propinqua subsp. sinensis (Oliv.) R.M.K. Saunders 1997, a woody vine plant esteemed for its medicinal properties, has garnered attention in botanical research. In this study, we elucidated the complete chloroplast genome sequence of S. propinqua. The genome spans 145,562 bp and comprises a large single-copy (LSC) region of 94,164 bp, a small single-copy region of 18,294 bp (SSC), and a pair of inverted repeats (IR) of 16,552 bp. Notably, S. propinqua exhibits an overall GC content of 36.2%. Annotation revealed a total of 116 genes, encompassing 81 protein-coding genes, 27 transfer RNA (tRNA) genes, and 8 ribosomal RNA (rRNA) genes. Phylogenetic analysis unveiled a close relationship among Schisandraceae, indicating the evolutionary proximity. This comprehensive genomic dataset provides valuable insights into the genetic makeup and evolutionary dynamics within the Schisandra genus.

Comparative analysis of complete chloroplast genomes of 14 Asteraceae species.

BACKGROUND: 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. METHODS AND RESULTS: 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 150,907 bp to 152,858 bp, exhibit a typical quadripartite structure: a large single-copy (LSC) region (83,044 bp to 84,625 bp), a small single-copy (SSC) region (18,223 bp to 18,673 bp), and a pair of inverted repeats (IRs) (24,806 bp to 25,201 bp). 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. CONCLUSIONS: 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.

The complete chloroplast genome sequence of Arytera littoralis (Sapindoideae, Sapindaceae).

Arytera littoralis Blume 1847 is an evergreen small tree belonging to the Sapindaceae family. It is distributed in South China to SE Asia and the Solomon Islands. However, the chloroplast genome of A. littoralis has yet to be reported. In this study, the complete chloroplast genome of Arytera littoralis was determined. The total genome size was 161,091 bp in length, consisting of two inverted repeats (IRs) (28,432 bp) separated by the large single-copy (LSC) (85,737 bp) and small single-copy (SSC) (18,490 bp) regions. The genome contained 133 genes, including 87 protein-coding genes, 37 tRNA genes, and eight rRNA genes. The GC content of the complete chloroplast genome was 37.8%. A maximum-likelihood (ML) phylogenetic tree of A. littoralis and 13 related species from the family Sapindaceae indicated that A. littoralis was close to a clade composed of Sapindus, Nephelium, Litchi, and Dimocarpus. This study will offer essential genetic resources of A. littoralis and provide insights into the phylogeny and evolution of Sapindaceae.

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 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.

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.

Comparative Analysis of the Codon Usage Pattern in the Chloroplast Genomes of Gnetales Species.

Codon usage bias refers to the preferential use of synonymous codons, a widespread phenomenon found in bacteria, plants, and animals. Codon bias varies among species, families, and groups within kingdoms and between genes within an organism. Codon usage bias (CUB) analysis sheds light on the evolutionary dynamics of various species and optimizes targeted gene expression in heterologous host plants. As a significant order of gymnosperms, species within Gnetales possess extremely high ecological and pharmaceutical values. However, comprehensive analyses of CUB within the chloroplast genomes of Gnetales species remain unexplored. A systematic analysis was conducted to elucidate the codon usage patterns in 13 diverse Gnetales species based on the chloroplast genomes. Our results revealed that chloroplast coding sequences (cp CDSs) in 13 Gnetales species display a marked preference for AT bases and A/T-ending codons. A total of 20 predominantly high-frequency codons and between 2 and 7 optimal codons were identified across these species. The findings from the ENC-plot, PR2-plot, and neutrality analyses suggested that both mutation pressure and natural selection exert influence on the codon bias in these 13 Gnetales species, with natural selection emerging as the predominant influence. Correspondence analysis (COA) demonstrated variation in the codon usage patterns among the Gnetales species and indicated mutation pressure is another factor that could impact CUB. Additionally, our research identified a positive correlation between the measure of idiosyncratic codon usage level of conservatism (MILC) and synonymous codon usage order (SCUO) values, indicative of CUB's potential influence on gene expression. The comparative analysis concerning codon usage frequencies among the 13 Gnetales species and 4 model organisms revealed that Saccharomyces cerevisiae and Nicotiana tabacum were the optimal exogenous expression hosts. Furthermore, the cluster and phylogenetic analyses illustrated distinct patterns of differentiation, implying that codons, even with weak or neutral preferences, could affect the evolutionary trajectories of these species. Our results reveal the characteristics of codon usage patterns and contribute to an enhanced comprehension of evolutionary mechanisms in Gnetales species.

New Chloroplast Microsatellites in Helichrysum italicum (Roth) G. Don: Their Characterization and Application for the Evaluation of Genetic Resources.

Helichrysum italicum (Roth) G. Don is a Mediterranean medicinal plant with great potential in the cosmetics, culinary and pharmaceutical fields due to its unique bioactive compounds. Its recent introduction into agroecosystems has enhanced the exploitation of genetic diversity in natural populations, although limited molecular markers have made this challenging. In the present study, primers were designed for all 43 SSRs (72.1% mononucleotide, 21% dinucleotide and 6.9% trinucleotide repeats) identified in the chloroplast genome. Populations from Cape Kamenjak (Croatia) and Corsica (France) were analyzed with ten carefully selected cpSSR markers. From the initial set of 16 cpSSRs amplified in all samples, 6 cpSSR markers were removed due to low-length polymorphisms, size homoplasy and nucleotide polymorphisms that could not be detected with allele length. Of the 38 haplotypes detected, 32 were unique to their geographic origin. The highest number of private haplotypes was observed in the Cape Kamenjak population (seven out of nine detected). Based on clustering analyses, the Kamenjak population was the most similar to the Capo Pertusato (south Corsica) population, although only one sub-haplotype was shared. Other Corsican populations were more similar to each other. A cross-species transferability test with Helichrysum litoreum Guss. and Helichrysum arenarium (L.) Moench was successfully conducted and private alleles were identified.

The complete chloroplast genome of Erodium cicutarium (Linnaeus) l' Héritier ex Aiton 1789 (Geraniaceae): genome characterization and phylogenetic consideration.

Erodium cicutarium is an annual herbaceous plant valued for its applications in traditional medicine. However, the chloroplast genome of E. cicutarium has yet to be reported. In this study, we assembled chloroplast genomes of Erodium cicutarium using Illumina sequencing reads. The chloroplast genome was 114,652 bp long, harbored 111 complete genes, and its overall GC content was 39.1%. In Maximum Likelihood (ML) and Bayesian inference (BI) trees, the 13 Erodium species divided into three main clades, with E. cicutarium and E. carvifolium forming a monophyletic group, suggesting a close relationship between the two species. The E. cicutarium cp genome presented in this study lays a good foundation for the Erodium.

Complete chloroplast genome sequence of Artemisia littoricola (Asteraceae) from Dokdo Island Korea: genome structure, phylogenetic analysis, and biogeography study.

The Asteraceae family, particularly the Artemisia genus, presents taxonomic challenges due to limited morphological characteristics and frequent natural hybridization. Molecular tools, such as chloroplast genome analysis, offer solutions for accurate species identification. In this study, we sequenced and annotated the chloroplast genome of Artemisia littoricola sourced from Dokdo Island, employing comparative analyses across six diverse Artemisia species. Our findings reveal conserved genome structures with variations in repeat sequences and junction boundaries. Notably, the chloroplast genome of A. littoricola spans 150,985 bp, consistent with other Artemisia species, and comprises 131 genes, including 86 protein-coding, 37 tRNA, and 8 rRNA genes. Among these genes, 16 possess a single intron, while clpP and ycf3 exhibit two introns each. Furthermore, 18 genes display duplicated copies within the IR regions. Moreover, the genome possesses 42 Simple Sequence Repeats (SSRs), predominantly abundant in A/T content and located within intergenic spacer regions. The analysis of codon usage revealed that the codons for leucine were the most frequent, with a preference for ending with A/U. While the chloroplast genome exhibited conservation overall, non-coding regions showed lower conservation compared to coding regions, with the Inverted Repeat (IR) region displaying higher conservation than single-copy regions. Phylogenetic analyses position A. littoricola within subgenus Dracunculus, indicating a close relationship with A. scoparia and A. desertorum. Additionally, biogeographic reconstructions suggest ancestral origins in East Asia, emphasizing Mongolia, China (North East and North Central and South Central China), and Korea. This study underscores the importance of chloroplast genomics in understanding Artemisia diversity and evolution, offering valuable insights into taxonomy, evolutionary patterns, and biogeographic history. These findings not only enhance our understanding of Artemisia's intricate biology but also contribute to conservation efforts and facilitate the development of molecular markers for further research and applications in medicine and agriculture.

Assessing Genetic Diversity in Endangered Plant Orchidantha chinensis: Chloroplast Genome Assembly and Simple Sequence Repeat Marker-Based Evaluation.

Orchidantha chinensis T. L. Wu, an endemic species in China, is listed as a key protected wild plant in Guangdong Province. However, the lack of reports on the chloroplast genome and simple sequence repeat (SSR) markers has hindered the assessment of its genetic diversity and conservation strategies. The limited number of molecular markers to assess the genetic diversity of this species, and thus develop proper conservation strategies, highlighted the urgent need to develop new ones. This study developed new SSR markers and investigated genetic variation using 96 samples of O. chinensis from seven populations. Through high-throughput sequencing, a complete chloroplast genome of 134,407 bp was assembled. A maximum-likelihood phylogenetic tree, based on the chloroplast genome, showed that O. chinensis is closely related to Ravenala madagascariensis. The study identified 52 chloroplast SSRs (cpSSRs) and 5094 expressed sequence tag SSRs (EST-SSRs) loci from the chloroplast genome and leaf transcriptome, respectively. Twenty-one polymorphic SSRs (seven cpSSRs and fourteen EST-SSRs) were selected to evaluate the genetic variation in 96 accessions across seven populations. Among these markers, one cpSSR and 11 EST-SSRs had high polymorphism information content (>0.5). Cluster, principal coordinate, and genetic structure analyses indicated that groups G1 and G6 were distinct from the other five groups. However, an analysis of molecular variance showed greater variation within groups than among groups. The genetic distance among the populations was significantly positively correlated with geographical distance. These findings provide new markers for studying the genetic variability of O. chinensis and offer a theoretical foundation for its conservation strategies.

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.