Large Single-copy Region Research Articles

Characterization of the complete chloroplast genome of the rare medicinal plant: Mandragora caulescens (Solanaceae)

In this study, we assembled high-quality chloroplast genomes of Mandragora caulescens through a reference-guided approach using high-throughput Illumina sequencing reads. The resulting chloroplast genome assembly displayed a typical quadripartite structural organization, comprising a large single-copy (LSC) region of 85,233 bp, two inverted repeat (IR) regions of 25,685 bp each, and a small single-copy (SSC) region of 18,207 bp. The chloroplast genome harbored 141 complete genes, and its overall GC content was 38.0%. In maximum-likelihood (ML) and Bayesian inference (BI) trees, the 19 Solanaceae species formed a monophyletic group, dividing into two main clades. M. caulescens and Nicandra physalodes formed a monophyletic group, suggesting a close relationship between the two species. The M. caulescens cp genome presented in this study lays a good foundation for further genetic and genomic studies of the Solanaceae.

Characterization of the complete chloroplast genome sequence of Bassia scoparia (L.) A. J. Scott 1978 (Amaranthaceae) and its phylogenetic analysis

Bassia scoparia, an annual potherb belonging to the family Amaranthaceae, has been widely used in traditional Chinese and Japanese medicine for over 2000 years. Herein, we presented its complete chloroplast. The chloroplast genome sequence was 151,278 bp in length with a 36.6% content of GC. The genome showed the typical quadripartite structure, comprising a pair of inverted repeat (IR) regions (24,353 bp) separated by a large single-copy (LSC) region (84,067 bp) and a small single-copy (SSC) region (18,505 bp). This chloroplast genome harbored 133 predicted genes, including 88 protein-coding genes, 37 transfer RNA (tRNA) genes, and eight ribosomal RNA (rRNA) genes. The phylogenetic analysis indicated that B. scoparia was closely related to B. littorea. This newly sequenced chloroplast genome not only enhances our understanding of the genome of Bassia but also provides valuable insights for the evolutionary study of the family Amaranthaceae.

The complete chloroplast genome of Meconopsis torquata (Papaveraceae), a traditional Tibetan medicine

Meconopsis torquata Prain 1906, a national second-class rare and endangered plant, is reported here for the first time for its complete chloroplast genome. The genome is 153,290 bp in length, comprising a large single-copy region (LSC, 83,918 bp), a small single-copy region (SSC, 17,740 bp), and two inverted repeat sequences (IRa and IRb, each 25,816 bp). The overall GC content is 38.7%, with the IR region having the highest content (43.1%). The genome is annotated with 112 unique genes, including 4 rRNA genes, 29 tRNA genes, and 79 protein-coding genes. Analysis of codon usage bias reveals that codons ending in A/T account for 96.7% of those with a Relative Synonymous Codon Usage (RSCU) value above 1. This predominance of A/T-ending codons might be indicative of M. torquata adaptation to high-altitude environments. Phylogenetic analysis reveals a close kinship between M. torquata and M. pinnatifolia and M. paniculata, indicating that the ancestral groups of these species might have a complex evolutionary history. This study uncovers the genetic characteristics and adaptive evolution of M. torquata, offering a new perspective in understanding the phylogenetic relationships within the genus. The findings not only provide a solid theoretical foundation for the conservation and sustainable use of this rare and endangered species but also offer significant scientific support for the conservation of biodiversity.

Complete chloroplast genome of Saxifraga fortunei var. pilosissima (Saxifragaceae) endemic to Ulleung-do island, Korea

The Saxifraga fortunei var. pilosissima Nakai is an endemic species to Ulleung-do island. Here we report the complete chloroplast genome sequence of S. fortunei var. pilosissima, which was 151,186 bp in total length with the large single copy (LSC) region of 83,536 bp, the small single copy (SSC) region of 17,644 bp, and two inverted repeat (IR) regions of 25,003 bp. The chloroplast genome contained 131 genes, including 86 protein-coding, 37 tRNA, 8 rRNA genes, and GC (guanine-cytosine) content was 37.8%. Additionally, we found that the chloroplast genome of S. fortunei var. pilosissima exhibited intron loss in the rpl2 gene. Within the IR region, six protein-coding genes, seven tRNA genes, and four rRNA genes were duplicated. In the chloroplast genome of S. fortunei var. pilosissima, there are a total of 17 genes containing introns. Among them, 15 genes contain one intron each, while two genes contain two introns. Phylogenetic analysis based on 37 representative chloroplast genomes of the Saxifragaceae suggested that genus Saxifraga is monophyletic and S. fortunei var. pilosissima is placed in sect. Irregulares Haw. and grouped with S. fortunei, S. rufescens, and S. stolonifera with a strong maximum likelihood bootstrap support value.

Characterization of the plastid and mitochondrial genomes of Aeschynomene indica (Fabaceae)

The current study undertook a detailed analysis of both the plastid and mitochondrial genomes (plastome and mitogenome) of Aeschynomene indica (Fabaceae), a plant notable both as a problematic weed in global rice cultivation and for its medicinal properties. The primary goal was to furnish comprehensive organelle genome resources and explore genomic characteristics. A sample of A. indica was collected and sequenced using a next-generation sequencing technique. The resulting plastome is 160,502 base pairs (bp) long and includes 128 genes—comprising 83 protein-coding genes, 37 transfer RNA (tRNA) genes, and eight ribosomal RNA (rRNA) genes. The plastome displays a typical quadripartite structure consisting of a large single-copy region (89,347 bp), a small single-copy region (19,803 bp), and two inverted repeat regions (each 25,676 bp). The mitogenome spans 388,249 bp and contains 57 genes, which include 34 protein-coding genes, 20 tRNA genes, and four rRNA genes. Phylogenetic analyses leveraging these organelle genome sequences produced well-resolved trees, elucidating the phylogenetic position of A. indica within the Fabaceae. The organelle genomes of A. indica presented in this study offer valuable genomic resources that will facilitate further research in plant systematics and biotechnology.

The complete chloroplast genome of Arachis lutescens Krapov. & Rigoni (Fabaceae)

Arachis lutescens Krapov. & Rigoni 1958 is an important species due to their potentially extensive applications for cultivated peanut breeding. The whole chloroplast genome of A. lutescens was successfully assembled and annotated for the first time. The complete chloroplast genome of A. lutescens is a typically circular structure of 156,398 bp with a GC content of 36.3%. It comprises a large single-copy (LSC) region of 85,950 bp, a small single-copy (SSC) region of 18,800 bp, and two inverted repeat regions (IRs) of 25,824 bp, each. The plastome of A. lutescens contains a total of 125 genes, including 81 protein-coding genes, 36 tRNAs, and eight rRNAs. The phylogenetic analysis strongly supports the close relationship between A. lutescens and cultivated peanut clades. This study contributes to our understanding of the molecular characteristics and evolutionary relationships of this plant species.

Comparative Analysis of Complete Chloroplast Genomes of Rubus in China: Hypervariable Regions and Phylogenetic Relationships.

With more than 200 species of native Rubus, China is considered a center of diversity for this genus. Due to a paucity of molecular markers, the phylogenetic relationships for this genus are poorly understood. In this study, we sequenced and assembled the plastomes of 22 out of 204 Chinese Rubus species (including varieties) from three of the eight sections reported in China, i.e., the sections Chamaebatus, Idaeobatus, and Malachobatus. Plastomes were annotated and comparatively analyzed with the inclusion of two published plastomes. The plastomes of all 24 Rubus species were composed of a large single-copy region (LSC), a small single-copy region (SSC), and a pair of inverted repeat regions (IRs), and ranged in length from 155,464 to 156,506 bp. We identified 112 unique genes, including 79 protein-coding genes, 29 transfer RNAs, and four ribosomal RNAs. With highly consistent gene order, these Rubus plastomes showed strong collinearity, and no significant changes in IR boundaries were noted. Nine divergent hotspots were identified based on nucleotide polymorphism analysis: trnH-psbA, trnK-rps16, rps16-trnQ-psbK, petN-psbM, trnT-trnL, petA-psbJ, rpl16 intron, ndhF-trnL, and ycf1. Based on whole plastome sequences, we obtained a clearer phylogenetic understanding of these Rubus species. All sampled Rubus species formed a monophyletic group; however, sections Idaeobatus and Malachobatus were polyphyletic. These data and analyses demonstrate the phylogenetic utility of plastomes for systematic research within Rubus.

Re-sequencing of the complete chloroplast genome of Cinnamomum burmanni (Nees & T.Nees) Blume (Lauraceae) from Indonesia using MinION Oxford Nanopore Technologies

Cinnamomum burmanni (Nees & T.Nees) Blume (Lauraceae) belongs to the Magnoliids group and is mainly distributed in Indonesia and Southeast Asia. The complete chloroplast (cp) genome of C. burmanni sampled from Indonesia was assembled and annotated for the first time in this study. The length of the cp genome is 152,765 bp with a GC content of 39%, and it consists of four subregions: a large single-copy (LSC) region of 93,636 bp, a small single-copy (SSC) region of 18,893 bp and two inverted repeats (IR) regions (IRA 20,121 bp; IRB 20,115 bp) . The cp genome of C. burmanni encodes a total of 173 unique genes, which are 96 protein-coding genes, 19 rRNA genes, and 68 tRNA genes that can be utilized for advanced genetic and genomic studies of the species.

The complete chloroplast genome sequence of Vitis vinifera ‘Krasnostop Zolotovskiy’, an autochthonous variety of the Don Valley

DNA sequence data from complete chloroplast genomes expand our understanding of plant diversity and contributes to our understanding of evolutionary relationships among species. De novo assembly and annotation of plant chloroplast genomes are difficult due to the high number of repeats and low number of plant chloroplast genomes in international databases. The development of long-read sequencing platforms such as PacBio and Oxford Nanopore, as well as specialized assemblers, is simplifying the process of assembling and annotating large circular molecules. In this work, we report the complete chloroplast genome of the autochthonous Vitis vinifera variety ‘Krasnostop Zolotovskiy’, obtained de novo by the hybrid assembly method using short and long DNA reads. The circular genome of the chloroplast is 160,927 bp long with a GC ratio of 37.38 %. It has four subregions: large single-copy (LSC) region of 71,946 bp, a small single-copy (SSC) region of 36,273 bp, and two inverted repeat regions (IRs) of 26,354 bp each. The chloroplast genome of V. vinifera ‘Krasnostop Zolotovskiy’ harbours 129 genes, comprising 84 protein-coding genes, 8 rRNA genes, and 37 tRNA genes. We also carry out a phylogenetic analysis based on all the complete sequences of grape chloroplast genomes available in the databases, which shows that the V. vinifera ‘Krasnostop Zolotovskiy’ does not have a direct origin with any European variety.

The complete chloroplast genome of Illicium simonsii Maxim. (Illiciaceae), a species with important medicinal properties

Illicium simonsii Maxim (1888) is a medicinal species of the genus Illicium in the Illiciaceae family. It is commonly used to cure gastro-frigid vomiting, cystic hernia, gas pains in the chest, and scabies as folk medicine. To utilize its resources efficiently, the complete chloroplast genome of I. simonsii was sequenced, assembled, and annotated by using high-throughput sequencing data. The complete chloroplast genome was 143,038 bp in length, with a large single-copy region (LSC) of 101,094 bp, a short single-copy region (SSC) of 20,070 bp, and a pair of inverted repeats (IRs) of 21,874 bp. A total of 113 genes were annotated, including 79 protein-coding genes, 30 tRNA genes, and four rRNA genes. The phylogenetic tree exhibited that I. simonsii and Illicium burmanicum form a sister group, and were nested in the monophyletic clade of the Illicium genus.

The complete chloroplast genome sequence and phylogenetic analysis of the Bichetii grass Chlorophytum laxum (Asparagaceae)

Chlorophytum laxum of Asparagaceae is a valuable ornamental plant native to the tropical regions of Asia, Africa, and Australia. The plant also has medicinal properties and is used as source for folk medicine. Despite being commercially important, genetic studies of C. laxum are still limited. To expand the genomic information of this plant species, we sequenced, assembled, and characterized its complete chloroplast genome. The chloroplast genome was 153,678 bp in length, with a large single-copy region (83,225 bp) and a small single-copy region (18,031 bp) separated by a pair of inverted repeat regions (26,211 bp each). A total of 127 genes were predicted, including 81 protein-coding, 38 tRNA, and eight rRNA genes. The overall GC content was 37.3%. Based on current sampling size, phylogenetic analysis using the maximum likelihood based on the complete chloroplast genome sequence revealed that the relationship in Chlorophytum is well resolved; C. laxum was closely related to C. rhizopendulum.

Characteristics and phylogenetic analysis of the complete chloroplast genome of Cornus hongkongensis Hemsl. 1888 (Cornaceae)

Cornus hongkongensis Hemsl. 1888, native to Hong Kong, belongs to the subgenus Syncarpea within the Cornus genus of the Cornaceae family. The complete chloroplast genome of C. hongkongensis spans 156,954 bp, comprising four subregions: a large single-copy region (86,290 bp), a small single-copy region (18,394 bp), and a pair of inverted repeats (26,135 bp). Within the chloroplast genome of C. hongkongensis, we identified 113 unique genes, including 80 protein-encoding genes, four ribosomal RNA (rRNA) genes, and 30 transfer RNA (tRNA) genes. Phylogenetic analysis based on the complete chloroplast genome of 30 related taxa of the Cornus genus indicates that C. hongkongensis has not formed a monophyletic lineage. Analyses of sequence divergence found three intergenic regions including rps19-rpl22, ccsA-ndhD, and atpH-atpI, exhibiting a high degree of variations. The first chloroplast genome of C. hongkongensis was reported in this work contributes to the enrichment of genomic data for the genus Cornus.

The complete chloroplast genome sequence of Isoetes baodongii (Isoetaceae)

Isoetes baodongii is a diploid species of Isoetaceae distributed in low altitude area, its megaspore ornamentation is similar to tetraploid species I. sinensis. We collected leaf material of I. baodongii and sequenced it for low depth whole genome sequence, then, a complete chloroplast genome of I. baodongii was assembled and annotated. This chloroplast genome has a circular structure of 145,494 bp in length with a GC content of 38.0%, comprising a large single copy (LSC) region of 91,860 bp, a pair of inverted repeat (IR) regions of 13,207 bp each, and a small single copy (SSC) region of 27,220 bp. 136 genes were annotated, including 84 protein-coding genes, 38 tRNA genes, and 8 rRNA genes. A maximum likelihood phylogeny tree was reconstructed after the sequences alignment, the result showed that I. baodongii formed a sister clade to the one clustered by I. sinensis, I. taiwanensis and I. orientalis. Although the chloroplast genome structure of I. baodongii is extremely similar to other species distributed in China, a well-supported phylogenetic relationship was reconstructed here, these results may provide new messages for further studies on phylogeny and evolution of vascular plant on the earth.

The complete plastome and phylogenetic analysis of Commelina benghalensis L.1753 (Commelinaceae)

Commelina benghalensis L. 1753, a member of the Commelinaceae family, holds significant medicinal and culinary value. This study represents the first documentation of the sequencing and assembly of the entire plastome of C. benghalensis. The genome spans a total length of 160,663 bp, exhibiting a conventional quadripartite architecture that comprises a large single-copy (LSC) region (87,750 bp), a small single-copy (SSC) region (18,417 bp), and two inverted repeats (IR) regions (both 27,248 bp). In its entirety, the C. benghalensis plastome encompasses 129 genes (with 108 being unique), incorporating 77 individual protein-coding genes, 37 unique tRNA genes, and four unique rRNA genes. Phylogenetic analysis revealed a close resemblance between C. benghalensis and C. communis. The sequencing of this plastome stands to expedite the development of molecular markers and significantly contribute to genetic assays involving this distinctive plant.

The complete chloroplast genome sequence of Hydrocotyle vulgaris L. (Araliaceae)

Hydrocotyle vulgaris is a perennial wetland clonal plant in the Araliaceae family, which was introduced to China as an ornamental plant in the 1990s. Although H. vulgaris is now considered a potential invasiveness species in China, it also plays a significant role in the remediation of water pollution. Here, we reported its complete chloroplast genome and analyzed the basic characteristics. The chloroplast genome was 153,165 bp in length, including a pair of inverted repeat (IR) regions of 25,072 bp separated by a large single-copy (LSC) region of 84,291 bp and a small single-copy (SSC) region of 18,730 bp. The H. vulgaris chloroplast genome contained 132 predicted genes, and its overall GC content was 37.60%. Phylogenetic analysis revealed that H. vulgaris was closely related to H. verticillata. The H. vulgaris chloroplast genome presented in this study will lay a foundation for further genetic and genomic studies of the genus Hydrocotyle.

The complete chloroplast genome sequence of Calystegia hederacea Wall. in Roxb. 1824 (Convolvulaceae) in Enshi, Hubei

Calystegia hederacea Wall. in Roxb. 1824 is a perennial herbaceous vine in the family Convolvulaceae and has several biological effects. Herein, we reported the first complete chloroplast genome of C. hederacea. The chloroplast genome sequence was 152,057 bp in length, comparing a large single-copy (LSC) region of 87,891 bp, a small single-copy (SSC) region of 19,866 bp, and a pair of inverted repeat (IR) regions of 22,150 bp. This sequenced chloroplast genome contained 126 predicted genes, including 81 protein-coding genes, 37 tRNA genes, and eight rRNA genes, and the total GC content of the chloroplast genome was 37.79%. Phylogenetic analysis revealed that C. hederacea was closely related to C. soldanella. The chloroplast genome presented in this study will enrich the genome information of the genus Calystegia and provide deeper insights into the evolution study of the family Convolvulaceae.

The complete chloroplast genome sequence and phylogenetic analysis of Asplenium antiquum Makino 1929, an Endangered species in Korea

Asplenium antiquum Makino 1929 is one of the Endangered endemic species on the Korean Peninsula. The complete chloroplast of A. antiquum is 150,690 bp in length with typical quadripartite structure comprised of large single-copy region of (83,166 bp), a small single copy region (21,932 bp), and two inverted repeat regions, each 22,796 bp in length. 114 genes were detected in the chloroplast genome of A. antiquum, comprising 84 protein-encoding genes, 26 tRNA genes, and 4 rRNA genes. The phylogenetic analysis revealed a monophyletic relationship, placing A. antiquum as a sister to voth A. Prolongatum and A. nidus, forming a subclade of Asplenium species within the Aspleniaceae family. The genomic data obtained from this study will serve as valuable information for the species’ genetic classification of Asplenium.

The complete chloroplast genome assembly of Amorphophallus tonkinensis Engler and Gehrmann 1911 from southwestern China

Species in the Amorphophallus genus are important cash crops in many tropical and subtropical Asian countries. Although several molecular markers have been employed to determine relationships and assess genetic variation in the Amorphophallus genus, some conflicts remain in infrageneric classification and evolution. To aid in the phylogenetic research of the Amorphophallus genus, we collected one sample of Amorphophallus tonkinensis Engler and Gehrmann 1911 from southwestern China. We assembled the first chloroplast genome of this species using high-throughput sequencing. The assembled genome was 169,341 bp long with a typical quadripartite structure (GenBank accession number: PP234804). The lengths of the large single-copy region, small single-copy region, and two inverted repeats were 90,705 bp, 15,640 bp, 31,498 bp, and 31,498 bp, respectively. We annotated 129 genes across the chloroplast genome of A. tonkinensis. The phylogenetic trees suggested that the Amorphophallus species distributed in continental Asia split into two main clades. The chloroplast genome reported in our study provided valuable genomic resources for the future phylogenetic research of the Amorphophallus genus.

Comparative analysis of sipeimine content, metabolome and chloroplast genome in cultivated and wild varieties of Fritillaria taipaiensis.

The wild variety Fritillaria taipaiensis E.B (EB) is known for its superior therapeutic effects, but its limited production cannot meet demand. As a result, the cultivated variety F. taipaiensis P. Y. Li (PY) has been widely grown. In this study, we conducted a comprehensive analysis comparing EB and PY in terms of external features, sipeimine content, metabolome and chloroplast genome to differentiate these two varieties. Our research revealed that the petals and pods of EB are green, while those of PY have purple markings. The bulbs of EB contain significantly higher levels of sipeimine compared to those of PY. Metabolomic analysis identified 56 differentially expressed metabolites (DMs), with 23 upregulated and 33 downregulated in EB bulbs. Particularly, 3-hydroxycinnamic acid and secoxyloganin may serve as distinctive DMs. These DMs were associated with 17 KEGG pathways, including pyrimidine metabolism, alanine, aspartate and glutamate metabolism, and galactose metabolism. Differences in the length of the chloroplast genome were primarily observed in the large single-copy (LSC) region, with the largest variation in the trnH-GUC-psbA region. The placement of the trnH gene and the rps gene in proximity to the LSC/IRb boundary differs between EB and PY. The results of this study provide valuable insights for the introduction and comprehensive development of wild F. taipaiensis from a scientific perspective. © 2024 Society of Chemical Industry.

The complete chloroplast genome sequence of leibnitzia anandria (linnaeus) turczaninow

Leibnitzia anandria is a perennial herbaceous plant with medicinal properties, and the entire plant can be used in traditional medicine. Leibnitzia anandria was once classified under the genus Gerbera Cass., but was reclassified under Leibnitzia Cass. recently. In this study, using the GeneLab M sequencing technology of the Genemind platform, we have sequenced, assembled, and analyzed the complete chloroplast genome of Leibnitzia anandria for the first time. The genome is 154168 bp in length, consisting of a large single-copy region(LSC, 80166 bp), a small single-copy region(SSC, 18202 bp), and a pair of inverted repeat sequences(IR, 27900 bp). We have predicted and annotated a total of 133 genes, including 88 protein-coding genes, 37 tRNA-coding genes, and 8 rRNA-coding genes. The results of the phylogenetic analysis indicate that Leibnitzia anandria and Leibnitzia nepalensis, as well as the closely related Gerbera plant, clustered into a separate clade, rather than grouping together with the other plants belonging to the tribe Mutisieae. This study provides new information for the phylogeny research of Leibnitzia anandria, contributing to a better understanding of its taxonomy and evolution.