Browse
Submit Data
Databases
API
Help

Dataset Information

25 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

The chloroplast genome of an Endangered orchid species, Gastrochilus calceolaris (Orchidaceae: Aeridinae).

ABSTRACT: This study reported the complete chloroplast genome of a critically Endangered Orchidaceae species Gastrochilus calceolaris and its phylogenetic position in subtribe Aeridinae based on 12 orchid species plastomes. The plastome of G. calceolaris, with a 148,428?bp size, consisted of a pair of inverted repeat regions of 25,950?bp, a small single copy region of 11,139?bp, and a large single copy region of 85,389?bp. G?+?C content was 36.8%. The phylogenetic analysis highly supported the sisterhood between Gastrochilus and Pelatantheria and a monophyletic Gastrochilus group comprising of G. calceolaris, G. fuscopunctatus, and G. japonicus.

SUBMITTER: Tang F

PROVIDER: S-EPMC7800495 | biostudies-literature | 2018 Oct

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

The chloroplast genome of an Endangered orchid species, Gastrochilus calceolaris (Orchidaceae: Aeridinae).

Tang Fengxia F Song Yu Y Liu Qiang Q

Mitochondrial DNA. Part B, Resources 20181003 2

This study reported the complete chloroplast genome of a critically Endangered Orchidaceae species Gastrochilus calceolaris and its phylogenetic position in subtribe Aeridinae based on 12 orchid species plastomes. The plastome of G. calceolaris, with a 148,428 bp size, consisted of a pair of inverted repeat regions of 25,950 bp, a small single copy region of 11,139 bp, and a large single copy region of 85,389 bp. G + C content was 36.8%. The phylogenetic analysis highly supported t ...[more]

PMID: 33474389

Similar Datasets

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.

| S-EPMC7800090 | 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

Two complete chloroplast genomes of an endangered orchid species, Pelatantheria scolopendrifolia (Orchidaceae), in Korea.

Project description:We determined the complete chloroplast genome sequence of two individuals of Pelatantheria scolopendrifolia, an endangered orchid species in Korea. The total chloroplast genome size of Mokpo (MG752972) and Naju (MG752973) population was 146,971?bp and 146,848?bp, respectively. The chloroplast genome contained 106 genes, including 72 protein-coding genes, 30 tRNA genes, and four rRNA genes. Variation in gene contents and structures was not found between two individuals. We found truncated or deleted ndh genes in P. scolopendrifolia. Phylogenetic analysis, based on the whole chloroplast genome sequences of 25 species of Orchidaceae, showed that P. scolopendrifolia was most closely related to Gastrochilus fuscopunctatus.

| S-EPMC7872586 | biostudies-literature

The complete chloroplast genome sequence of Thrixspermum amplexicaule (Orchidaceae, Aeridinae).

Project description:The complete chloroplast genome sequence of Thrixspermum amplexicaule was assembled and analyzed in this work. The total chloroplast genome size of T. amplexicaule was 148,124 bp in length, containing a large single-copy (LSC) region of 86,079 bp, a small single-copy (SSC) region of 10,799 bp, and a pair of inverted repeat (IR) regions of 25,623 bp. The GC content of T. amplexicaule was 36.4%. It encoded a total of 120 unique genes, including 75 protein-coding genes, 37 tRNA genes, and eight rRNA genes. The results of phylogenetic analysis strongly supported that all four samples of Thrixspermum are monophyletic and T. amplexicaule was closely related to T. centipeda.

| S-EPMC8475115 | 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 complete chloroplast genome of an Endangered species Cymbidium Nanulum (Orchidaceae).

Project description:Cymbidium nanulum Y.S.Wu & S.C.Chen is an IUCN Red listed Endangered species and distributes in South-Central China and Hainan. Here, we report the complete chloroplast (cp) genome sequence and the cp genome features of C. nanulum. The complete chloroplast (cp) genome sequence of C. nanulum was 149,776?bp in length. It presented a typical quadripartite structure including one large single-copy region (LSC, 85,392?bp), one small single-copy region (SSC, 14,210?bp), and two inverted repeat regions (IRs, 25,087?bp). The cp genome encoded 133 genes, of which 104 were unique genes (77 protein-coding genes, 23 tRNAs, and 4 rRNAs). The maximum-likelihood phylogenetic analysis showed that C. nanulum was closely related to other species of genus Cymbidium.

| S-EPMC7687592 | biostudies-literature

The complete chloroplast genome of an endangered species Cymbidium mastersii (Orchidaceae).

Project description:Cymbidium mastersii Griff. & Lindl. is an endangered orchid. In this study, we report the complete chloroplast (cp) genome sequence and the cp genome features of C. mastersii. The cp genome sequence of C. mastersii was 155,362?bp in length. It included one large single-copy region (LSC, 84,465?bp), one small single-copy region (SSC, 20,647?bp), and two inverted repeat regions (IRs, 25,125?bp). The cp genome encoded 130 genes, of which 107 were unique genes (80 protein-coding genes, 23 tRNAs, and 4 rRNAs). The maximum-likelihood phylogenetic analysis showed that C. mastersii was a sister of C. erythraeum and C. nanulum.

| S-EPMC7706812 | biostudies-literature

The complete chloroplast genome of an endangered species Apostasia ramifera (Orchidaceae).

Project description:Apostasia ramifera S. C. Chen & K. Y. Lang 1986 is a Chinese endemic and endangered orchid. Here, we report the complete chloroplast (cp) genome sequence and the cp genome features of A. ramifera. The cp genome was 157,518 bp in length with a typical quadripartite structure, which was comprised of one large single-copy region (LSC, 86,353 bp) and one small single-copy region (SSC, 16,445 bp) separated by two inverted repeat regions (IRs, 27,360 bp). The cp genome encoded 133 genes, which included 87 protein-coding genes, 38 tRNAs and eight rRNAs. The average GC content of the genome is 35.8%. The phylogenetic analysis showed that A. ramifera was sister with A. wallichii and then nested in the other Apostasia species.

| S-EPMC7889234 | biostudies-literature

Chloroplast characterizations and phylogenetic position of an endangered orchid, Vanda coerulea (Orchidaceae).

Project description:Vanda coerulea possess a high ornamental value and medical effect against glaucoma and cataract. The whole complete chloroplast (cp) genome of V. coerulea and the phylogenetic position based on the cp sequences remain unclear. Herein, we report the complete chloroplast genome of V. coerulea. The chloroplast genome was 149,376 bp in length, including a large single-copy (LSC) region of 86,100 bp, a small single-copy (SSC) region of 11,702 bp, and two inverted repeat (IRs) regions of 25,787 bp. A total of 129 genes were characterized, including 74 protein-coding genes, 36 tRNA genes, and 8 rRNA genes. The overall GC content was 36.6%, and GC percentages range from 27.9% to 43.2% throughout LSC, IRs, and SSC regions. Phylogenetic analysis based on 20 chloroplast genomes of Orchidaceae indicated that V. coerulea is closely related to V. brunnea. Our study provides a valuable resource for the identification and distinction of Vanda genus, and will lay a foundation for further research and conservation measures of V. coerulea.

| S-EPMC7748861 | 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