Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Chloroplast characterization and phylogenetic relationship of Cymbidium aloifolium (Orchidaceae).

ABSTRACT: Cymbidium aloifolium is an epiphytic orchid with high medicinal and ornamental value. In order to get a deeper understanding of C. aloifolium, we determined the complete chloroplast genome of C. aloifolium by Illumina sequencing data. The length of this genome is 157,328 bp, including a couple of inverted repeat (IR) regions of 26,829 bp, a large single-copy (LSC) region of 85,793 bp, and a small single-copy (SSC) region of 17,877 bp. The chloroplast genome comprised of 139 genes, including 78 protein-coding genes, 38 tRNA genes, and 8 rRNA genes. In addition, the phylogenetic analysis based on 17 chloroplast genomes of Orchidaceae indicated that C. mannii was closely related to C. aloifolium. This study will provide more valuable information for the classification and phylogenetic research of Cymbidium genus.

SUBMITTER: Chen J

PROVIDER: S-EPMC7748541 | biostudies-literature | 2020 Jan

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Chloroplast characterization and phylogenetic relationship of Cymbidium aloifolium (Orchidaceae).

Chen Juan J Chen Ming-Kun MK Zheng Qing-Dong QD Ma Shan-Hu SH Liu Zhong-Jian ZJ Ai Ye Y

Mitochondrial DNA. Part B, Resources 20200110 1

Cymbidium aloifolium is an epiphytic orchid with high medicinal and ornamental value. In order to get a deeper understanding of C. aloifolium, we determined the complete chloroplast genome of C. aloifolium by Illumina sequencing data. The length of this genome is 157,328 bp, including a couple of inverted repeat (IR) regions of 26,829 bp, a large single-copy (LSC) region of 85,793 bp, and a small single-copy (SSC) region of 17,877 bp. The chloroplast genome comprised of 139 ...[more]

PMID: 33366610

Similar Datasets

The complete chloroplast genome of Cymbidium longibracteatum (Orchidaceae) and phylogenetic analysis.

Project description:Cymbidium longibracteatum is a common cultivated species in the genus Cymbidium due to its elegant appearance, rich flower colors and strong fragrance, but its classification is quite controversial. In this study, the complete chloroplast genome of C. longibracteatum was obtained by Illumina sequencing. The chloroplast genome of C. longibracteatum is 150,070 bp in length with an overall GC content of 37.12%, which contains a large single-copy (LSC;84,949 bp) region, a small single-copy (SSC;13,745bp) region, and a pair of inverted repeats (IRs; 25,688 bp) regions. The genome contains 130 genes, namely 84 protein-coding genes, 38 tRNA genes and 8 rRNA genes. The maximum-likelihood phylogenetic tree has proved that C. longibracteatum should exist as an independent species in the genus Cymbidium, and it is most closely related to C. tortisepalum. This study provides valuable sequence resources for further study of C. longibracteatum.

| S-EPMC7782654 | biostudies-literature

Complete chloroplast genome of Cymbidium ensifolium（Orchidaceae）.

Project description:Cymbidium ensifolium is one of the most economical and ornamental significant orchids. It's facing serious genetic resources loss and habitat fragmentation. A conservation strategy is therefore imperative for this endangered orchid. Here, we report on the first complete chloroplast (cp) genome of C. ensifolium. Its full-length of 150,257 bp include large single-copy (LSC) region of 85,110 bp, small single-copy (SSC) region of 13,761 bp, and a pair of invert repeats (IR) regions of 25,692 bp. Plastid genome contain 137 genes, 78 protein-coding genes, 38 tRNA genes, and 8 rRNA genes. Cymbidium ensifolium was sister to C. sinense, Cy. Tortisepalum, and C. kanran. The cp genome will help for further research and conservation of C. ensifolium.

| S-EPMC7687436 | 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 of Cymbidium changningense (Orchidaceae).

Project description:Cymbidium changningense is an ornamental orchid and endemic specie in China. Here, we report the complete chloroplast (cp) genome sequence and the cp genome features of C. changningense. The cp genome was 155,388 bp in length with a typical quadripartite structure, which was comprised of one large single copy (LSC, 84,522 bp) region and one small single copy (SSC, 20,622 bp) region separated by two inverted repeat (IR, 25,122 bp) regions. The cp genome encoded 132 genes, of which 108 were unique genes (80 protein-coding genes, 24 tRNAs, and four rRNAs). The phylogenetic analysis showed that C. changningense was sister with C. erythraeum.

| S-EPMC7707721 | biostudies-literature

The complete chloroplast genome of Cymbidium eburneum (Orchidaceae).

Project description:Cymbidium eburneum Lindl. is an endangered species of Orchidaceae and distributed in Guangxi, Yunnan and Hainan of China, and India, Myanmar, Nepal, Vietnam. Here, we report the complete chloroplast (cp) genome sequence and the cp genome features of C. eburneum. The complete chloroplast (cp) genome sequence of C. eburneum is 156,520 bp in length and presented a typical quadripartite structure including one large single-copy region (LSC, 85,518 bp), one small single-copy region (SSC, 20,014 bp), and two inverted repeat regions (IRs, 25,471 bp). The cp genome encoded 135 genes, of which 106 were unique genes (78 protein-coding genes, 24 tRNAs, and 4 rRNAs). The phylogenetic relationships show that C. eburneum is closely related to other species in the genus Cymbidium, and is sister with C. tracyanum.

| S-EPMC7687489 | biostudies-literature

The complete chloroplast genome of Cymbidium dayanum (Orchidaceae).

Project description:Cymbidium dayanum, a wild orchid species in the Orchid family (Orchidaceae), is considered highly valuable because of its long flowering period and beautiful plant shape. We sequenced the complete chloroplast genome of C. dayanum using the Illumina Hiseq platform (Illumina, San Diego, CA). The size of the C. dayanum chloroplast genome is 155,408 bp, with an average GC content of 36.76%. This chloroplast genome has containing a large single-copy (LSC) region of 84,189 bp, a small single-copy (SSC) region of 17,991 bp, and two inverted (IRa and IRb) repeat regions of two 26,614 bp. A total of 118 unique genes were annotated, including 76 protein-coding genes, 38 tRNA genes, and 4 rRNA genes. A maximum-likelihood phylogenetic tree indicated that C. dayanum is closely related to C. tracyanum in the genus Cymbidium based on 9 whole chloroplast genome sequences.

| S-EPMC8189086 | 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 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 a Cymbidium Tortisepalum (Orchidaceae) male mutant.

Project description:The chloroplast (cp) genome of natural male mutant Cymbidium tortisepalum 'Guanshihe' has been characterized using Illumina pair-end sequencing technology. The complete cp genome was 149,830 bp in length, containing a large single-copy region (LSC) of 85,131 bp and a small single-copy region (SSC) of 13,275 bp, which were separated by a pair of 25,712 bp inverted repeat regions (IRs). The genome contained 130 genes, with 111 unique genes, including 77 protein-coding genes, 30 tRNA genes, and 4 rRNA genes. The overall GC content is 37.09% with the values of the LSC, SSC, and IR regions are 34.40%, 29.63%, and 43.45%, respectively. Further, phylogenetic analysis suggested that the plastome of C. tortisepalum male mutant 'Guanshihe' is close to sequenced C. sinense, C. kanran, C. tortisepalum, and C. ensifolium plastomes.

| S-EPMC7707707 | biostudies-literature

The complete chloroplast genome of Cymbidium hookerianum (Orchidaceae): genome structure and basic analysis.

Project description:Cymbidium hookerianum Rchb.f. is an ornamental orchid with large flowers and delicate aroma. Here, we reported the complete chloroplast genome sequence of C. hookerianum. The total chloroplast genome cycle was 155,447 bp. It displayed a typical structure including one large single-copy (LSC, 84,186 bp) region, one small single-copy (SSC, 17,839 bp) region, and two inverted repeat (IRs, 26,711 bp). 124 genes (78 CDSs, 38 tRNAs, 8 rRNAs) were encoded by the cp genome. The average GC content of this sequence was 36.8%. The phylogenetic analysis revealed C. hookerianum and C. changningense are sisters. The groundwork of chloroplast genome would provide available reference for molecular taxonomy and breeding.

| S-EPMC7801036 | biostudies-literature