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The complete chloroplast genome sequence of a medicinal orchid species Coelogyne fimbriata (Orchidaceae).

ABSTRACT: Coelogyne fimbriata is an important orchid species with high medicinal value. Its complete chloroplast genome is 158,935 bp in length, which possesses the typical structure consising of a small single-copy region (SSC) of 18,743 bp, two inverted repeats (IRs) of 26,374 bp, and a large-single copy region (LSC) of 87,444 bp. The genome encodes 137 genes, including 91 protein-coding genes (PCGs), 38 tRNA genes and 8 rRNA genes. And the overall GC content is 37.40%. In addition, our phylogenetic analysis based on cp genome revealed the phylogenetic relationship between C. fimbriata and other 22 species in Orchidaceae.

SUBMITTER: Yue Z

PROVIDER: S-EPMC7782944 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Characterization of the complete chloroplast genome of Coelogyne fimbriata (Orchidaceae).

Project description:Coelogyne fimbriata has been classified as a national second-class protected orchid species in China. In this study, we report and characterize the complete chloroplast (cp) genome sequence of C. fimbriata in an effort to provide genomic resources useful for promoting its conservation and systematic research. The complete genome is 159,010 bp in length and the overall GC content is 43.3%. The cp genome sequence has a typical quadripartite structure, comprising two inverted repeats (IRA and IRB) regions, which are separated by a small single-copy (SSC) region and a large single-copy (LSC) region. Moreover, a total of 135 functional genes were annotated, including 89 protein-coding genes, 38 tRNA genes, and 8 rRNA genes. The phylogenetic analysis recovered a close relationship between C. fimbriata and Pleione formosana, and both species are placed within the tribe Arethuseae (Orchidaceae).

| S-EPMC7782987 | biostudies-literature

The complete chloroplast genome of Coelogyne barbata (Orchidaceae), a rare and ornamental orchid.

Project description:The genus of Coelogyne Lindl. comprised about 200 species while its generic relationship has been uncertain. The whole chloroplast genome of C. barbata was reported in order to provide new data on the molecular phylogeny of Coelogyne. The cp genome of C. barbata was 1,600,93 bp in total length, including a pair of inverted repeat regions (IR, 26,710 bp), one large single-copy region (LSC, 87,868 bp), and one small single-copy region (SSC, 188,05 bp). The complete chloroplast DNA encoded 132 genes, containing 86 protein-coding genes, 38 tRNA genes, and eight rRNA genes. Phylogenetic analysis showed that C. barbata was related to Pholidota imbricata.

| S-EPMC7671590 | biostudies-literature

The complete chloroplast genome sequence of Pholidota articulata (Orchidaceae), a rarely medicinal orchid.

Project description:Pholidota Lindl. ex Hook. was placed in tribe Arethuseae Lindl. (Epidendroideae, Orchidaceae), while its generic relationship has been unclear. Since the plastid genome could play a key role in plant systematics, the complete chloroplast (cp) genome of P. articulata was reported in this paper. The cp genome was 160,114 bp in length with four typical quadripartite structures, which was consisted of a large single copy (LSC) region of 87,756 bp, a small single copy (SSC) region of 18,872 bp, and two inverted repeats (IR) of 26,734 bp. In addition, the cp genome encoded 132 genes in total, of which were 113 unique genes, including 79 protein-coding genes, 30 tRNAs, and 4 rRNAs. The phylogenetic analysis indicated that P. articulata was closely clustered with other two species of Pholidota and that they appeared to be related to Pleione in Arethuseae Lindl.

| S-EPMC7759241 | biostudies-literature

The complete chloroplast genome sequence of an Endangered orchid species Dendrobium bellatulum (Orchidaceae).

Project description:Dendrobium bellatulum Rolfe is an Endangered orchid species that is distributed in the subtropical regions of Yunnan Province, China. It was listed in the category of the Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES). Here, we reported the complete chloroplast (cp) genome sequence and the cp genomic features of D. bellatulum. The genome was 152,107?bp long with 129 genes comprising 83 protein-coding genes, 40 tRNA genes, and 6 rRNA genes. Phylogenetic analysis of a data set of cp genomes indicated that D. bellatulum is clustered with other species in Dendrobium.

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The complete chloroplast genome sequence of Phalaenopsis wilsonii Rolfe, a vulnerable wild moth orchid species (Orchidaceae).

Project description:Phalaenopsis wilsonii Rolfe is a vulnerable wild moth orchid species with important horticultural value. The complete chloroplast genome sequence of P. wilsonii was generated by de novo assembly using whole genome next-generation sequencing to provide genomic data for further conservation genetics, phylogeny and molecular breeding in Phalaenopsis. The complete plastome of P. wilsonii is 145,096 bp in length, containing two inverted repeats (IR) regions (24,787 bp), a large single-copy (LSC) region (84,688 bp), and a small single-copy (SSC) region (10,834 bp). The chloroplast genome encoded 119 unique genes, including 73 protein-coding genes, 38 tRNA genes, and 8 rRNA genes. The overall GC content of the whole genome is 36.9%. Phylogenetic analysis indicated P. wilsonii was closely related to P. lowii.

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Chloroplast Genome Analysis of Two Medicinal Coelogyne spp. (Orchidaceae) Shed Light on the Genetic Information, Comparative Genomics, and Species Identification.

Project description:Although the medicinal properties of Coelogyne spp. have been previously studied, there is little genomic information providing a valuable tool for the plant taxonomy, conservation, and utilization of this genus. This study used the next-generation MiSeq sequencing platform to characterize the chloroplast (cp) genomes of Coelogyne fimbriata and Coelogyne ovalis. The Maximum Likelihood (ML) and Bayesian (BI) methods were employed to confirm the phylogenetic position of two Coelogyne species based on the whole chloroplast genome sequences. Additionally, we developed eight new primers based on the two cp genomes' medium variable regions and evaluated the transferability to another 16 Coelogyne species. We constructed phylogenetic trees including 18 Coelogyne species and four outgroup species using the chloroplast fragments with the ML method. Our results showed that the cp genomes of C. fimbriata and C. ovalis contained a small single-copy region (18,839 and 18,851 bp, respectively) and a large single-copy region (87,606 and 87,759 bp, respectively), separated by two same-length inverted-repeat regions (26,675 bp in C. fimbriata and 26,715 bp C. ovalis, respectively). They all contained 86 protein-coding genes, 38 tRNA genes, and eight rRNA genes, revealing strong structure and gene content similarities. The phylogenetic analysis indicated a close relationship between the genera Coelogyne and Pleione. The newly developed primers revealed good transferability among the Coelogyne taxa and provided enough variable sites to distinguish C. fimbriata and C. ovalis. The two complete cp genomes and the eight new primers of Coelogyne provide new genomic data for further studies on phylogenomics, population genetics, and evolutionary history of Coelogyne taxa.

| S-EPMC7601144 | biostudies-literature

Characterization of the complete chloroplast genome of orchid family species Cymbidium bicolor (Orchidaceae).

Project description:Cymbidium bicolor belongs to Orchid family (Orchidaceae), it has high ornamental and traditional medicinal value. The complete chloroplast genome of C. bicolor was sequenced using the Illumina Hiseq platform. The size of the C. bicolor chloroplast genome is 156,528 bp, with an average GC content of 36.8%. This chloroplast genome has containing a large single copy (LSC) region of 85,907 bp, a small single copy (SSC) region of 17,215 bp, and two inverted (IRa and IRb) repeat regions of two 26,703 bp. A total of 124 genes were annotated, including 78 protein-coding genes, 38 tRNA genes, and 8 rRNA genes. A maximum likelihood phylogenetic tree indicated that C. bicolor is closely related to C. mannii in the genus Cymbidium based on 16 whole chloroplast genome sequences.

| S-EPMC7748745 | biostudies-literature

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

Project description:Paphiopedilum parishii (Rchb. f.) Stein is an endangered and rare species with highly ornamental value. In this study, we report the complete chloroplast genome of P. parishii using the Illumina sequencing data. The total genome of P. parishii is 154,689 bp in length and the GC content is 35.9%, with a pair of inverted repeats (IRs) regions of 32,690 bp each, a large single-copy region (LSC) of 86,863 bp and a small single-copy region (SSC) of 2,446 bp. The chloroplast genome encoded 127 genes, including 82 protein-coding genes (CDS), 8 rRNA genes and 37 tRNA genes. The phylogenetic tree showed that P. parishii was clustered with other species in Paphiopedilum with strong support based on the complete chloroplast genome.

| S-EPMC8330699 | biostudies-literature

Chloroplast Genome Sequence Annotation of Dendrobium nobile (Asparagales: Orchidaceae), an Endangered Medicinal Orchid from Northeast India.

Project description:Orchidaceae constitutes one of the largest families of angiosperms. Owing to the significance of orchids in plant biology, market needs and current sustainable technology levels, basic research on the biology of orchids and their applications in the orchid industry is increasing. Although chloroplast (cp) genomes continue to be evolutionarily informative, there is very limited information available on orchid chloroplast genomes in public repositories. Here, we report the complete cp genome sequence of Dendrobium nobile from Northeast India (Orchidaceae, Asparagales), bearing the GenBank accession number KX377961, which will provide valuable information for future research on orchid genomics and evolution, as well as the medicinal value of orchids. Phylogenetic analyses using Bayesian methods recovered a monophyletic grouping of all Dendrobium species (D. nobile, D. huoshanense, D. officinale, D. pendulum, D. strongylanthum and D. chrysotoxum). The relationships recovered among the representative orchid species from the four subfamilies, i.e., Cypripedioideae, Epidendroideae, Orchidoideae and Vanilloideae, were consistent within the family Orchidaceae.

| S-EPMC5501700 | biostudies-literature

The first complete chloroplast genome sequence of the medicinal plant Bletilla formosana (Orchidaceae).

Project description:Bletilla formosana is a medicinal plant commonly used in southwest of China. In this study, we sequenced the complete chloroplast (cp) genome sequence of B. formosana to investigate its phylogenetic relationship in the family Orchidaceae. The chloroplast genome of B. formosana was 159,112 bp in length with 37.3% overall GC content, including a large single-copy (LSC) region of 86,838 bp, a small single-copy (SSC) region of 18,672 bp and a pair of inverted repeats (IRs) of 26,801 bp. The cp genome contained 116 genes, including 83 protein-coding genes, 29 tRNA genes, and 4 rRNA genes. The phylogenetic analysis indicated the genus Bletilla was closely related to Platanthera.

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