Complete Chloroplast Genome Sequence Research Articles

The complete chloroplast genome sequence of <i>Dracocephalum rupestre</i> (Lamiaceae)

<i>Dracocephalum rupestre</i> Hance is a perennial herb distributed across China, Mongolia, and Korea. This study reports the first complete chloroplast genome sequence of <i>D. rupestre</i>. The plastome is 151,230 bp long and exhibits a typical quadripartite structure comprising a large single-copy region of 82,536 bp, a small single-copy region of 17,408 bp, and a pair of identical inverted repeat regions of 25,643 bp each. It contains 130 genes, comprising 85 protein-coding genes, 37 tRNA genes, and eight rRNA genes. Phylogenetic analysis of <i>D. rupestre</i> and related species of Lamiaceae showed that the genus <i>Dracocephalum</i> is a monophyletic group, and <i>D. rupestre</i> is most closely related to <i>D. psammophilum</i>.

The Complete Chloroplast Genomes of Two Physalis Species, Physalis macrophysa and P. ixocarpa: Comparative Genomics, Evolutionary Dynamics and Phylogenetic Relationships

Physalis macrophysa (PMA) and Physalis ixocarpa (PIX) have significant economic, medicinal, and ornamental value and are often used in the fields of edible fruits, medicinal herbs, and ornamental plants. In the present study, we obtained the complete chloroplast (cp) genome sequences of PMA and PIX, compared to the cp genome sequences of 10 Physalis species, and constructed the phylogenetic tree among the tribe Physaleae. The results showed that the cp genomes of PMA and PIX consisted of a large single copy (LSC) region (87,115 bp and 87,103 bp, respectively), a small single copy (SSC) region (18,412 bp and 18,420 bp, respectively), and a pair of same-length inverted-repeat (IRa and IRb) regions (25,604 bp and 25,674 bp, respectively). The two species contained 132 genes, including 87 encoding proteins, eight encoding ribosomal RNAs (rRNAs), and 37 encoding transfer RNAs (tRNAs), which indicated that the two species have strong similarities with respect to genome structure and gene content. PMA and PIX contained repeat sequences (35 and 40, respectively) and simple-sequence repeats (SSRs) (61 and 60, respectively). Nine regions with considerable nucleotide divergence were found, most of which were located in the LSC and SSC regions. The gene selective pressure analysis indicated that eight genes were affected by positive selection, the Ka/Ks values of which were greater than one. Our phylogenetic results indicated that PMA and PIX had the closest genetic relationship and are closely adjacent to Physalis philadelphica (PPH) in the subtribe Physalinae. Our analysis of the cp genomes in both Physalis species will be beneficial for further research into species identification, phylogeny, evolution, and the potential for germplasm resource exploitation in Physalis.

The Complete Chloroplast Genome Sequence of Eupatorium fortunei: Genome Organization and Comparison with Related Species.

Eupatorium fortunei Turcz, a perennial herb of the Asteraceae family, is one of the horticultural and medicinal plants used for curing various diseases and is widely distributed in China and other Asian countries. It possesses antibacterial, antimetastatic, antiangiogenic, and antioxidant properties along with anticancer potential. However, the intrageneric classification and phylogenetic relationships within Eupatorium have long been controversial due to the lack of high-resolution molecular markers, and the complete chloroplast (cp) genome sequencing has not been reported with new evolutionary insights. In the present study, E. fortunei was used as an experimental material, and its genome was sequenced using high-throughput sequencing technology. We assembled the complete cp genome, and a systematic analysis was conducted for E. fortunei, acquiring the correspondence of its NCBI accession number (OK545755). The results showed that the cp genome of E. fortunei is a typical tetrad structure with a total length of 152,401 bp, and the genome encodes 133 genes. Analysis of the complete cp genomes of 20 Eupatorieae shows that the number of simple sequence repeats (SSRs) ranged from 19 to 36 while the number of long sequence repeats was 50 in all cases. Eleven highly divergent regions were identified and are potentially useful for the DNA barcoding of Eupatorieae. Phylogenetic analysis among 22 species based on protein-coding genes strongly supported that E. fortunei is more closely related to Praxelis clematidea and belongs to the same branch. The genome assembly and analysis of the cp genome of E. fortunei will facilitate the identification, taxonomy, and utilization of E. fortunei as well as provide more accurate evidence for the taxonomic identification and localization of Asteraceae plants.

Complete Chloroplast Genome Sequence of Endangered Species in the Genus Opisthopappus C. Shih: Characterization, Species Identification, and Phylogenetic Relationships.

Opisthopappus C. Shih is a rare genus of the Asteraceae family native to the Taihang Mountains in China. Due to the narrow distribution area, poor reproduction ability and human harvesting, Opisthopappus is threatened by extinction. However, the limited genetic information within Opisthopappus impede understanding of the conservation efforts and bioprospecting. Therefore, in this study, we reported the complete chloroplast (cp) genome sequences of two Opisthopappus species, including Opisthopappus taihangensis and Opisthopappus longilobus. The cp genomes of O. taihangensis and O. longilobus were 151,117 and 151,123 bp, which contained 88 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. The repeat sequences, codon usage, RNA-editing sites, and comparative analyses revealed a high degree of conservation between the two species. The ycf1 gene was identified as a potential molecular marker. The phylogenetic tree demonstrated that O. longilobus was a separate species and not a synonym or variety of O. taihangensis. The molecular clock showed that two species diverge over a large time span, O. longilobus diverged at 15.24 Mya (Million years ago), whereas O. taihangensis diverged at 5.40 Mya We found that Opisthopappus and Ajania are closely related, which provides new ideas for the development of Opisthopappus. These results provide biological information and an essential basis to understand the evolutionary history of the Opisthopappus species, which will aid in the future the bioprospecting and conservation of endangered species.

A reappraisal of the phylogeny and historical biogeography of Sparganium (Typhaceae) using complete chloroplast genomes

BackgroundSparganium (Typhaceae) is a widespread temperate genus of ecologically important aquatic plants. Previous reconstructions of the phylogenetic relationships among Sparganium species are incompletely resolved partly because they were based on molecular markers comprising < 7,000 bp. Here, we sequenced and assembled the complete chloroplast genomes from 19 Sparganium samples representing 15 putative species and three putative subspecies in order to explore chloroplast genome evolution in this genus, clarify taxonomic lineages, estimate the divergence times of Sparganium species, and reconstruct aspects of the biogeographic history of the genus.ResultsThe 19 chloroplast genomes shared a conserved genome structure, gene content, and gene order. Our phylogenomic analysis presented a well-resolved phylogeny with robust support for most clades. Non-monophyly was revealed in three species: S. erectum, S. eurycarpum, and S. stoloniferum. Divergence time estimates suggest that the two subgenera of Sparganium split from each other ca. 30.67 Ma in the middle Oligocene. The subgenus Xanthosparganium diversified in the late Oligocene and Miocene, while the subgenus Sparganium diversified in the late Pliocene and Pleistocene. Ancestral area reconstruction suggested that the two subgenera may have originated in East Eurasia and North America.ConclusionThe non-monophyletic nature of three putative species underscores the necessity of taxonomic revision for Sparganium: S. stoloniferum subsp. choui may be more appropriately identified as S. choui, and subspecies of S. erectum may be in fact distinct species. The estimated diversification times of the two subgenera correspond to their species and nucleotide diversities. The likely ancestral area for most of subgenus Xanthosparganium was East Eurasia and North America from where it dispersed into West Eurasia and Australia. Most of subgenus Sparganium likely originated in North America and then dispersed into Eurasia. Our study demonstrates some of the ways in which complete chloroplast genome sequences can provide new insights into the evolution, phylogeny, and biogeography of the genus Sparganium.

Comparative and phylogenetic analysis of the complete chloroplast genome sequences of Allium mongolicum

Allium mongolicum Regel is a wild and sandy vegetable with unique flavours. In this study, a complete chloroplast (cp) genome of A. mongolicum was obtained (Genbank accession number: OM630416), and contained 153,609 base pairs with the GC ratio as 36.8%. 130 genes were annotated including 84 protein-coding genes, 38 tRNA, and 8 rRNA genes. The large single-copy (LSC) region was 82,644 bp, and a small single-copy (SSC) region was 18,049 bp, which were separated by two inverted repeats (IRs, including IRa and IRb) of 26,458 bp. Comparative genome analyses of 55 Allium species suggested that genomic structure of genus Allium was conserved, and LSC and SSC regions were outstanding with high variability. Among them, more divergent loci were in the SSC region covering ycf1-rrn4.5 and ndhF-ccsA. Phylogenetic analysis on cp genomes of 55 Allium determined that all members were clustered into 13 clades, and A. mongolicum had close relationship with A. senescens. Corresponding analyses of four protein-coding genes (ycf1, ndhF, rpl32, and ccsA) in aforementioned divergent loci confirmed that ycf1 was finally chosen as the candidate gene for species identification and evolutionary classification of genus Allium. These data provide valuable genetic resources for future research on Allium.

Characterization and molecular evolution analysis of Periploca forrestii inferred from its complete chloroplast genome sequence

Periploca forrestii, a medicinal plant of the family Apocynaceae, is known as an effective and widely used clinical prescription for the treatment of rheumatoid diseases. In this study, we de novo sequenced and assembled the completement chloroplast (cp) genome of P. forrestii based on combined Oxford Nanopore PromethION and Illumina data. The cp genome was 153 724bp in length and had four subregions. Moreover, an 84 433 bp large single-copy and a 17 731 bp small single-copy were separated by 25 780 bp inverted repeats (IRs). The cp genome included 132 genes with 18 duplicates in the IRs. A total of 45 repeat structures and 183 simple sequence repeats were detected. Codon usage showed a bias toward A/T-ending codons. A comparative study of Apocynaceae revealed that an IR expansion occurred on P. forrestii. The Ka/Ks values of eight species of Apocynaceae suggested that positive selection was exerted on the psaI and ycf2 genes, which might reflect specific adaptions to the P. forrestii particular growth environment. Phylogenetic analysis indicated that Periplocoideae was a sister to Asclepiadoideae, forming a monophyletic group in the family Apocynaceae. This study provided an important P. forrestii genomic resource for future evolutionary studies and the phylogenetic reconstruction of the family Apocynaceae.

Complete organellar genomes of six Sargassum species and development of species-specific markers

Sargassum is one of the most important brown algal genera that can be used as food and raw material for medicinal purpose, and has various beneficial effects. As the classification of Sargassum species is currently based on their morphological characteristics, organellar genome sequences of Sargassum would provide important information for accurate identification of species and developing species-specific markers. We sequenced the complete organellar genomes of six Sargassum species, including the first complete chloroplast genome sequences of S. fulvellum, S. serratifolium, S. macrocarpum, and S. siliquastrum, and the first complete mitochondrial genome sequences of S. fulvellum, S. serratifolium, and S. macrocarpum. The chloroplast genomes of the 6 Sargassum species contained 139 protein-coding genes (PCGs), and the mitochondrial genomes possessed 37 PCGs. A comparative study was performed between the newly sequenced organellar genomes and 44 other species belonging to class Phaeophyceae. Phylogenetic relationships using PCGs shared by Phaeophyceae species were constructed with IQ-TREE 2 using the maximum likelihood method. In addition, we developed real-time PCR markers based on SNPs to distinguish the 6 Sargassum species. Our results provide useful information for establishing phylogenetic relationships between brown algae.

Application value of Fagopyrum tataricum extracts in postpartum depression and phylogenetic analysis

Fagopyrum tataricum combines seven nutrients in one body. It is neither a medicine, nor a health care product, but a food that can part of a meal. F. tataricum has drawn the attention of most researchers because of the pharmacological activity of plant extracts. After the extraction of new compound from Fagopyrum tataricum, its preventive effect combined with psychological intervention on postpartum depression was evaluated, and the related mechanism was explored. The 5-HT content in the brain was first measured by ELISA. The relative expression of the 5-HT receptor on the neurons was determined with real-time RT-PCR assay. The complete chloroplast genome sequence of Fagopyrum tataricum was characterized through Illumina pair-end sequencing, and the neighbor-joining phylogenetic analysis of the F. tataricum was conducted.

Comparative and phylogenetic analyses of the chloroplast genome reveal the taxonomy of the Morus genus.

Mulberry (genus Morus) is an economically important woody plant with an altered ploidy level. The variable number of Morus species recognized by different studies indicates that the genus is in need of revision. In this study, the chloroplast (CP) genomes of 123 Morus varieties were de novo assembled and systematically analyzed. The 123 varieties represented six Morus species, namely, Morus alba, Morus nigra, Morus notabilis, Morus rubra, Morus celtidifolia, and Morus serrata. The Morus CP genome was found to be 158,969~159,548 bp in size with 125 genes, including 81 protein coding, 36 tRNA, and 8 rRNA genes. The 87 out of 123 mulberry accessions were assigned to 14 diverse groups with identical CP genome, which indicated that they are maternally inherited and share 14 common ancestors. Then 50 diverse CP genomes occurred in 123 mulberry accessions for further study. The CP genomes of the Morus genus with a quadripartite structure have two inverted repeat (IR) regions (25,654~25,702 bp) dividing the circular genome into a large single-copy (LSC) region (87,873~88,243 bp) and small single-copy (SSC) region (19,740~19,994 bp). Analysis of the phylogenetic tree constructed using the complete CP genome sequences of Morus revealed a monophyletic genus and that M. alba consisted of two clades, M. alba var. alba and M. alba var. multicaulis. The Japanese cultivated germplasms were derived from M. alba var. multicaulis. We propose that the Morus genus be classified into six species, M. nigra, M. notabilis, M. serrata, M. celtidifolia, M. rubra, and M. alba with two subspecies, M. alba var. alba and M. alba var. multicaulis. Our findings provide a valuable resource for the classification, domestication, and breeding improvement of mulberry.

The complete chloroplast genome sequences of eight Orostachys species: Comparative analysis and assessment of phylogenetic relationships.

We analyzed the complete chloroplast genomes of eight Orostachys species and compared the sequences to those of published chloroplast genomes of the congeneric and closely related genera, Meterostachys and Hylotelephium. The total chloroplast genome length of thirteen species, including the eight species analyzed in this study and the five species analyzed in previous studies, ranged from 149,860 (M. sikokianus) to 151,707 bp (H. verticillatum). The overall GC contents of the genomes were almost identical (37.6 to 37.8%). The thirteen chloroplast genomes each contained 113 unique genes comprising 79 protein-coding genes, 30 tRNA genes, and four rRNA genes. Among the annotated genes, sixteen genes contained one or two introns. Although the genome structures of all Orostachys and Hylotelephium species were identical, Meterostachys differed in structure due to a relatively large gene block (trnS-GCU-trnS-GGA) inversion. The nucleotide diversity among the subsect. Orostachys chloroplast genomes was extremely low in all regions, and among the subsect. Appendiculatae, genus Orostachys, and all thirteen chloroplast genomes showed high values of Pi (&gt;0.03) in one, five, or three regions. The phylogenetic analysis showed that Orostachys formed polyphyly, and subsect. Orostachys and Appendiculatae were clustered with Hylotelephium and Meterostachys, respectively, supporting the conclusion that each subsection should be considered as an independent genus. Furthermore, the data supported the taxonomic position of O. margaritifolia and O. iwarenge f. magnus, which were treated as synonyms for O. iwarenge in a previous study, as independent taxa. Our results suggested that O. ramosa and O. japonica f. polycephala were individual variations of O. malacophylla and O. japonica, respectively. The exact taxonomic position of O. latielliptica and the phylogenetic relationship among the three species, O. chongsunensis, O. malacophylla and O. ramosa, should be a topic of future study.

The complete chloroplast genome of ‘biasong’ (Citrus micrantha Wester), a native species from the Southern Philippines

‘Biasong’ (Citrus micrantha), native to the Southern Philippine Islands, is an important cultivated fruit tree but has no published plastome sequence. We assembled and characterized the C. micrantha chloroplast genome from accession in the germplasm collection of the Institute of Crop Science, University of the Philippines Los Baños. The complete chloroplast (cp) genome sequence is 159,928-bp long with 128 coding genes comprising 83 mRNA genes, 37 tRNA genes, and eight rRNA genes. Out of the mRNA genes, 45 genes code for photosynthesis, 30 genes code for self-replication, and five genes code for other functions. A phylogenetic analysis of the assembled genome, along with 24 Citrus species and three other Rutaceae species, identified Citrus aurantiifolia as its closest relative with available complete cpDNA sequence.

The complete chloroplast genome sequences of an endangered orchid species Paphiopedilum wenshanense (Orchidaceae)

Paphiopedilum wenshanense, a species of the family Orchidaceae, is endangered in the world with highly ornamental and biological value, the morphology of P. wenshanense is very similar to its relative species, P. bellatulum and P. concolor. However, there are few studies on the molecular biology and phylogeny of this species currently. Therefore, we report its complete chloroplast (cp) genome sequence at the first time, hoping to provide a foundation for its future phylogenetic analysis. The complete chloroplast genome of P. wenshanense was 161,750 bp in size, which contained a large single-copy (LSC) region of 90,656 bp, a small single-copy (SSC) region of 1886 bp, and two inverted repeat (IR) regions of 34,604 bp each. The total GC content was 35.66%. The genome encodes 38 transfer RNA genes, eight ribosomal RNA genes, and 80 protein-coding genes. The phylogenetic analysis indicated that the genetic relationship between P. wenshanense and P. concolor was very close.

Characterization of the complete chloroplast genome sequence of Stipa bungeana (Poaceae), an important forage grass in the temperate steppe of Northern China

Stipa bungeana Trin. 1833 is an important forage grass in Poaceae, widely distributed in the temperate steppe of Northern China, with strong grazing tolerance and feeding value. In this study, we performed the complete chloroplast (cp) genome sequence of S. bungeana to explore its phylogenetic position with other Stipa. The results showed that the circular complete cp genome of S. bungeana was 137,759 bp in length, including a large single copy (LSC) of 81,652 bp, a small single copy (SSC) of 12,817 bp, and two inverted repeats (IR) of 21,645 bp. The GC content accounts for 43.71% and annotated 134 single genes, which include 87 protein-coding genes, eight rRNA genes, and 39 tRNA genes. Maximum-likelihood (ML) phylogenetic tree suggested that the S. bungeana was closely related to other Stipa except for S. purpurea.

Complete chloroplast genome sequence of a bulbous flowering plant, Allium triquetrum Linnaeus, 1753 (Amaryllidaceae)

Allium triquetrum (Linnaeus, 1753) is a bulbous flowering plant of the genus Allium (Amaryllidaceae), native to the Mediterranean basin, and is now widespread and invasive in different parts of the world via ornamental horticultural trade. However, to date, the genomic study of A. triquetrum has lagged, which impedes the development of appropriate utilization and management practices for this species. Here, we report the complete chloroplast genome sequence of A. triquetrum. The chloroplast genome size of A. triquetrum was 153,298 bp, consisting of a pair of inverted repeat regions (26,547 bp), separated by a large single-copy (82,875 bp) region and a small single-copy (17,329 bp) region. Genome annotation predicted 133 genes, including 87 protein-coding genes, 38 tRNA genes, and eight rRNA genes. Phylogenetic analysis based on 60 whole chloroplast genome sequences of Allium species suggested that A. triquetrum and A. moly are sister to each other along with the clade of A. fasciculatum, A. hookeri, and A. macranthum.

The complete chloroplast genome sequence of Thunbergia erecta (Benth.) T. Anders. (Acanthaceae)

Thunbergia erecta (Benth.) T. Anders. is an upright shrub species of Acanthaceae with great ecological and economical values. In this paper, we explored the complete chloroplast genome sequence of T. erecta using next generation sequencing to provide genomic resources that could help to promote its conservation. The genome of T. erecta is 152,202 bp in length, containing a large single-copy region of 84,232 bp, and a small single-copy region of 17,656 bp. It encodes a total of 131 genes, including 8 rRNA genes, 37 tRNA genes, 84 protein-coding genes and 2 pseudo genes. The GC content of T. erecta genome is 38.47%. The phylogenetic analysis suggests that it was closely related to Avicennia marina in Acanthaceae. In addition, we found that T. erecta appeared late clade in the whole family while outgroups plants appeared even later. T. erecta is morphologically similar to other plants in Acanthaceae, but is genetically closed to the outgroup species.

The complete chloroplast genome sequence of the water fern Ceratopteris thalictroides (Pteridaceae)

This work determined and analyzed the complete chloroplast genome sequence of Ceratopteris thalictroides (Linnaeus) Brongniart 1822 (Pteridaceae). The results indicate that the total chloroplast genome size of C. thalictroides is 149,399 bp in length, and the genome contains a large single-copy (LSC) region of 83,580 bp, a small single-copy (SSC) region of 21,241 bp, and a pair of inverted repeat (IR) regions of 22,289 bp. The GC content of C. thalictroides is 36.7%. The genome encodes a total of 131 unique genes, including 82 protein-coding genes, 38 tRNA genes, and 8 rRNA genes. The phylogenetic analysis results strongly suggest that C. thalictroides is closely related to C. cornuta.

The complete chloroplast genome sequence of Persicaria perfoliata (L.) H. Gross: a medicinal plant

Persicaria perfoliata (L.) H. Gross is an herbal medicine with a long history of common use in China. In this study, we sequenced and assembled the complete chloroplast genome sequence of P. perfoliata and investigated its phylogenetic relationship in the family Polygonaceae. The total genome size is 160,585 bp in length with 37.96% GC content, consisting of a small single-copy (SSC) of 12,876 bp, a large single-copy (LSC) of 85,439 bp, and two inverted repeats (IRs) of 31,135 bp. The cp genome contains 128 genes, including 35 tRNA genes, eight rRNA genes, and 85 protein-coding genes. The phylogenetic tree showed that P. perfoliata was closely related to P. maackiana, and Persicaria exhibited a closer relationship with Bistorta in the family Polygonaceae. This work provides a molecular basis for investigating the evolutionary status, phylogenetic relationships, and population genetics of this species.

The complete chloroplast genome sequence of Michelia macclurei (Dandy, 1928) (Magnoliaceae), an important fire-resistant tree species

Michelia macclurei (Dandy, 1928) is an evergreen broad-leaved tree species native to South China. This species has great ecological and economic importance. However, the genomic study of M. macclurei has lagged far behind. Here, we reported the complete chloroplast genome sequence of M. macclurei. The chloroplast genome size of M. macclurei was 160,139 bp, consisting of a pair of inverted repeat (IR) regions (26,575 bp), which was separated by a large single copy (LSC) region (88,167 bp) and a small single copy (SSC) region (18,822 bp). A total of 113 unique genes were annotated, including 79 protein-coding genes, 30 tRNA genes, and four rRNA genes. The overall GC content was 39.2%. Phylogenetic analysis based on 16 whole chloroplast genome sequences of Michelia species suggested that M. macclurei and M. maudiae are sister to each other, and jointly sister to M. chapensis.

Comparative chloroplast genome analysis of 10 Ilex species and the development of species-specific identification markers

The genus Ilex L. (Aquifoliaceae) includes economically important species of ornamental and medicinal value. However, germplasm identification and phylogenetic analysis of Ilex are limited due to morphological similarities and insufficient genomic resources. In this study, the complete chloroplast genome sequences of I. intermedia, I. dabieshanensis 2, and I. vomitoria were described, and along with seven published chloroplast genomes of Ilex—all of which are widely used in mid-southern China—for comparative genomics analysis. The 10 chloroplast genomes were 157,216–157,988 bp in length and displayed a typical quadripartite structure. A total of 133 genes were annotated, including 88 protein-coding genes, 37 tRNA genes, and eight rRNA genes. Genome structure, gene content, and genome arrangement were conserved, with some variations in the IR/SC (inverted repeats/single-copy) boundary regions and divergent hotspot regions. Phylogenetic analysis among 39 genus members clarified evolutionary relationships within Ilex based on complete chloroplast genome sequences. I. intermedia, I. dabieshanensis 2, and I. vomitoria were clustered in section Aquifolium in clade C. This study also developed 11 molecular markers as DNA barcodes for discriminating among the 10 Ilex species based on hypervariable regions and validated successfully. This study provides resources for further investigations on the identification, genetic engineering, evolution, and phylogeny of Ilex species.