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The complete plastome genome and its inference on the phylogenetic position of Bletilla formosana (Orchidaceae).

ABSTRACT: Bletilla formosana is a traditional Chinese medicinal herb and recently threatened by overexploitation owing to the increasing demand. In present study, we sequenced and assembled the complete chloroplast (cp) genomes of this species. The plastome genome is a typical quadripartite circle molecule with the total lenth of 158,968 bp and overall GC content of 37.3%. We predicted 104 genes in the cp genome, including 80 protein coding gens, 20 tRNA and 4 rRNA. Phylogenetic analysis shows that B. formosana is sister to B. striata.

SUBMITTER: Wu X

PROVIDER: S-EPMC7707696 | biostudies-literature |

REPOSITORIES: biostudies-literature

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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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Characterization of the complete chloroplast genome of Bletilla striata (Orchidaceae: Bletilla), the herb in China.

Project description:Chloroplast (cp) genome sequences have been become a useful tool for phylogenetic and evolutionary studies in the herb. In this study, the complete cp genome of Bletilla striata was assembled. The complete cp genome is circular of 157,016 base pairs (bp) in length, which harbours a large single-copy region (85,821 bp), a small single-copy region (17,743 bp), and two inverted-repeat regions (each one of 26,726 bp). The cp genome of B. striata contains 139 genes, including 94 protein-coding genes (PCGs), 37 transfer RNA (tRNAs), and 8 ribosome RNA (rRNAs). The overall nucleotide content of the cp genome is A of 31.0%, T of 31.8%, C of 18.9%, and G of 18.3%, with a total AT content of 62.8% and GC content of 37.2%. However, the phylogenetic relationship analysis using maximum-likelihood (ML) method, which the result showed that the position of B. striata was situated as Bletilla ochracea in Orchidaceae. This study will be helpful for studies on the cp genetic engineering and medicinal herb value of Orchidaceae species in further.

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Plastomes of Bletilla (Orchidaceae) and Phylogenetic Implications.

Project description:The genus Bletilla is a small genus of only five species distributed across Asia, including B. chartacea, B. foliosa, B. formosana, B. ochracea and B. striata, which is of great medicinal importance. Furthermore, this genus is a member of the key tribe Arethuseae (Orchidaceae), harboring an extremely complicated taxonomic history. Recently, the monophyletic status of Bletilla has been challenged, and the phylogenetic relationships within this genus are still unclear. The plastome, which is rich in both sequence and structural variation, has emerged as a powerful tool for understanding plant evolution. Along with four new plastomes, this work is committed to exploring plastomic markers to elucidate the phylogeny of Bletilla. Our results reveal considerable plastomic differences between B. sinensis and the other three taxa in many aspects. Most importantly, the specific features of the IR junction patterns, novel pttRNA structures and codon aversion motifs can serve as useful molecular markers for Bletilla phylogeny. Moreover, based on maximum likelihood and Bayesian inference methods, our phylogenetic analyses based on two datasets of Arethuseae strongly imply that Bletilla is non-monophyletic. Accordingly, our findings from this study provide novel potential markers for species identification, and shed light on the evolution of Bletilla and Arethuseae.

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The first complete chloroplast genome of Liparis nervosa and its phylogenetic position within Orchidaceae.

Project description:Liparis nervosa is a plant of the family Orchidaceae and mainly distributed in subtropical and tropical regions of the world. In Chinese traditional medicine, it has been used for the treatment of hemostasis, carbuncle, and furuncle for centuries. The chloroplast (cp) genome of L. nervosa, sequenced based on next-generation platform (NEOSAT), is 157,274?bp in size. The cp genome encodes 130 genes, including eight rRNA genes, 85 protein-coding genes (PCGs), and 37 tRNA genes. Phylogenetic relationship analysis based on complete cp genome sequences exhibited that both of L. nervosa and L. loeselii were phylogenetically closer to Dendrobium officinale.

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The complete plastid genome of Jeffersonia diphylla and its phylogenetic position inference.

Project description:Jeffersonia diphylla, which belongs to Berberidaceae, is a perennial herb native to North America. In the present study, we determined the first plastome of J. diphylla using genome skimming approach. The pastome of J. diphylla is 152,842 bp in length, with a large single copy region (LSC) of 82,266 bp and a small single copy region (SSC) of 19,284 bp separated by a pair of inverted repeats (IRs) of 25,646 bp. It encodes 113 unique genes, consisting of 79 protein-coding genes, 30 tRNA genes, and four rRNA genes, with 19 duplicated genes in the IR regions. Phylogenetic analysis indicates that J. diphylla is sister to Plagiorhegma dubium, subsequently is sister to a clade including Diphylleia, Sinopodophyllum, Podophyllum, Dysosma, Achlys, and Epimedium.

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Complete Chloroplast Genome of Paphiopedilum delenatii and Phylogenetic Relationships among Orchidaceae.

Project description:Paphiopedilum delenatii is a native orchid of Vietnam with highly attractive floral traits. Unfortunately, it is now listed as a critically endangered species with a few hundred individuals remaining in nature. In this study, we performed next-generation sequencing of P. delenatii and assembled its complete chloroplast genome. The whole chloroplast genome of P. delenatii was 160,955 bp in size, 35.6% of which was GC content, and exhibited typical quadripartite structure of plastid genomes with four distinct regions, including the large and small single-copy regions and a pair of inverted repeat regions. There were, in total, 130 genes annotated in the genome: 77 coding genes, 39 tRNA genes, 8 rRNA genes, and 6 pseudogenes. The loss of ndh genes and variation in inverted repeat (IR) boundaries as well as data of simple sequence repeats (SSRs) and divergent hotspots provided useful information for identification applications and phylogenetic studies of Paphiopedilum species. Whole chloroplast genomes could be used as an effective super barcode for species identification or for developing other identification markers, which subsequently serves the conservation of Paphiopedilum species.

| S-EPMC7020410 | biostudies-literature

The complete plastome of Bulbophyllum pingnanense (Orchidaceae: Dendrobiinae).

Project description:The complete plastid genome of Bulbophyllum pingnanense, a critically endangered species, was determined and analyzed in this study. The complete genome was 151,224 bp in length, consisting of a large single-copy region (LSC) of 86,017 bp, a small single-copy region (SSC) of 13,497 bp, and two inverted repeat (IR) regions of 25,855 bp. The genome contained 127 genes, including 81 protein-coding genes, 38 transfer RNA (tRNA) genes, and eight ribosomal RNA (rRNA) genes. Phylogenetic analysis indicated that B. pingnanense is sister to B. inconspicuum.

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Chloroplast genome structure and phylogenetic position of Calanthe sylvatica (Thou.) Lindl. (Orchidaceae).

Project description:Calanthe sylvatica plays an important role in horticulture and is undergoing the pressure of population decline. In this study, its complete chloroplast genome sequence was successfully obtained by the technology of Illumina sequencing. The whole chloroplast genome length was 158,828 bp with a typical quadripartite structure: one large single copy (LSC) region (87,277 bp), one small single copy (SSC) region (18,535 bp) and a pair of inverted repeats (IR) regions (26,508 bp). The GC content of this genome was 36.7%. The genome contained 118 genes consisting of 84 protein-coding genes, 30 tRNA genes, and 4 rRNA genes. The phylogenetic analysis indicated a close relationship between C. sylvatica and Calanthe triplicata.

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Complete plastome sequence of Phalaenopsis cornu-cervi (Vandeae, Orchidaceae).

Project description:Phalaenopsis cornu-cervi is a taxonomically and horticulturally important moth orchid. In this study, we report and characterize the complete plastid genome sequence of P. cornu-cervi for the first genomic resources in section Polychilos. Its complete plastome is 147,241?bp in length and contains two inverted repeat (IR) regions of 25,005bp, a large single-copy (LSC) region of 85,714?bp, and a small single-copy (SSC) region of 11,517?bp. The plastome contains 110 genes, consisting of 76 unique protein-coding genes, 30 unique tRNA genes, and 4 unique rRNA genes. It also shows the typical characteristics of Phalaenopsis chloroplast genome, while all ndh genes are non-functional. The complete plastome sequence of P. cornu-cervi will provide a useful resource for future phylogenetic study of Phalaenopsis and its garden utilization.

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Complete mitochondrial genome of Neotoxoptera formosana (Takahashi, 1921) (Hemiptera: Aphididae), with the phylogenetic analysis.

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