The complete chloroplast genome sequence of Calanthe sieboldii (orchidaceae)
Ontology highlight
ABSTRACT:
SUBMITTER: Peng C
PROVIDER: S-EPMC10913714 | biostudies-literature | 2024 Mar
REPOSITORIES: biostudies-literature
Similar Datasets
Project description:The orchid Calanthe discolor, which has high ornamental and medicinal value, is mainly distributed in Zhejiang, Jiangsu, and southeast Hubei Provinces of China, as well as in Japan and the southern Korean peninsula. In this study, the whole chloroplast genome sequence of C. discolor was first assembled using high-throughput Illumina paired-end technology, providing data to evaluate the evolution of this species. The C. discolor chloroplast genome was158,286 bp long, including a large single-copy region of 87,095 bp, a small single-copy region of 18,407 bp, and two copies of a repeat region (26,392-bp each). The overall G + C content was 41.2%. A total of 133 genes were predicted from the genome, including 87 protein-coding genes, eight ribosomal RNAs, 38 transfer RNAs. Phylogenetic analysis indicated a close relationship between C. discolor and C. bicolor.
| S-EPMC11457340 | biostudies-literature
Project description:The first complete chloroplast (cp) genome sequences of an endemic and endangered species in China, Calanthe henryi, were reported in this study. The cp genome of C. henryi was 158,256 bp long, with two inverted repeat (IR) regions of 26,348 bp, a large single copy (LSC) region of 87,137 bp, and a small single copy (SSC) region of 18,423 bp. The cp genome of this species contained 113 genes, including 79 protein-coding genes, 4 ribosomal RNA genes, and 30 transfer RNA genes. The overall GC content was 36.7%. Phylogenetic analysis of 60 cp genomes within the subfamily of Epidendroideae suggests that C. henryi is closely related to C. bicolor.
| S-EPMC7510761 | biostudies-literature
Project description:Paphiopedilum henryanum Braem 1987 is a critically Endangered terrestrial orchid mainly occurred around the southern China and northern Vietnamese borders. Recently, the population size of this species has been sharply declined due to many threats such as climate change, habitat loss, and narrow distribution. In this study, the complete chloroplast genome sequence of P. henryanum was determined from Illumina pair-end sequencing data. The chloroplast genome was 155,886 bp in length, including a large single copy region (LSC) of 87,573 bp, a small single-copy region (SSC) of 2,831 bp, and a pair of inverted repeated regions (IRa and IRb) of 32,741 bp each. The chloroplast genome contained 121 genes corresponding to 76 protein-coding genes, 8 ribosomal RNA (rRNA) genes and 37 transfer RNA (tRNA) genes, respectively. The results of phylogenetic analysis indicated that P. henryanum was closely related to P. violascens and P. venustum in the genus Paphiopedilum based on sixteen whole chloroplast genome sequences. The results would provide a valuable resource for future genetic studies of Paphiopedilum.
| S-EPMC9354640 | biostudies-literature
Project description:Dendrobium wangliangii is a rare orchid species with extremely small populations, endemic to China. In this study, the complete chloroplast (cp) genome sequence and the genome features of D. wangliangii were analyzed. The whole cp genome sequence of D. wangliangii is 160,052 including a large single-copy region (LSC, 87,525 bp), a small single-copy region (SSC, 18,373 bp), and a pair of repeat regions (IRs, 27,077 bp, each). The contents of four bases in cpDNA were A (30.9%), C (18.9%), G (18.3%) and T (31.9%), respectively. The total content of GC is 37.1%. The cp genome contains 129 genes, consisting of 124 unique genes (78 protein-coding genes, 38 tRNAs, and 8 rRNAs). Phylogenetic analysis showed that D. wangliangii nested with other Dendrobium spp. and was closely related to D. ellipsophyllum, D. wattii and D. longicornu.
| S-EPMC7783038 | biostudies-literature
Project description:In this paper, we obtained and characterized the complete chloroplast genome sequence of a unique moth orchid, Phalaenopsis lowii. The total plastid genome size is 146,834 bp, containing a large single copy (LSC) region (84,469 bp) and a small single-copy region (10,477 bp) that were separated by two inverted repeats (IRs) regions (25,944 bp). We annotated 110 unique genes, within which there are 76 protein-coding genes, 30 tRNA genes, and 4 rRNA genes. Phylogenetic analysis indicated the P. lowii showed a sister relationship with subgenus Phalaenopsis clade.
| S-EPMC7707205 | biostudies-literature
Project description:Here, we report the first complete chloroplast genome of Platanthera chlorantha (Orchidaceae: Orchidoideae). The circular genome with the length of 154,260 bp possesses the typical structure consisting of a large single copy region (LSC) of 83,279 bp and a small single copy region (SSC) of 17,759 bp, separated from each other by two copies of inverted repeats (IRs) of 26,611 bp. The plastome encodes 134 genes, of which 88 were protein-coding, eight encoded ribosomal RNA, and 38 transfer RNAs. The overall GC content was 36.74%. The plastome sequence provided here constitutes a valuable resource for analyzing genetic diversity of the Orchidaceae family.
| S-EPMC7706912 | biostudies-literature
Project description:Habenaria dentata is a rare species with high ornamental value in China. In this study, we report the complete chloroplast (cp) genome of H. dentata using the Illumina sequencing data. The total genome of H. dentata is 153,682 bp in length and the GC content is 36.62%, with a pair of inverted repeats (IRs) regions of 26,339 bp each, a large single-copy (LSC) region of 83,963 bp and a small single-copy (SSC) region of 17,041 bp. The cp genome encoded 133 genes, including 87 protein-coding genes (PCG), eight rRNA genes, and 38 tRNA genes. The maximum-likelihood phylogenetic analysis based on 12 cp genomes showed that H. dentata was sister to Habenaria chejuensis and Habenaria ciliolaris. This work will be valuable for genetic and phylogenetic studies on H. dentata.
| S-EPMC9196706 | biostudies-literature
Project description:Paphiopedilum purpuratum, an endangered terrestrial orchid distributed in southwestern and south of China. In this study, the complete chloroplast genome (cpDNA) sequence of P. purpuratum was determined from Illumina pair-end sequencing data. With a total length of 158,459 bp in length and includes two inverted repeat regions (IRs) of 34,484 bp each, which were separated by a large single-copy region (LSC) 88,022 bp and a small single-copy region (SSC) 1,469 bp. The chloroplast genome contained 126 genes, including 74 protein conding genes,38 tRNA genes, and 8 rRNA genes. Phylogenetic analysis indicated that P. purpuratum, P. dianthum, P. niveum, P. delenatii, and P. armeniacum cluster together, placed them within genus Paphiopedilum. The complete chloroplast genome sequence of P. purpuratum will provide a useful resource for the evolutionary biology study of phylogenetic studies in Orchidaceae.
| S-EPMC7707658 | biostudies-literature
Project description:Liparis bootanensis is an epiphytic orchid distributed in tropical and subtropical regions of Asia, and has been listed as an endangered species in the Wildlife Conservation List. In this study, the complete chloroplast genome of L. bootanensis was assembled using Illumina sequencing data. The complete chloroplast (cp) genome is 158,325 bp in length, including a pair of invert repeats (IRA and IRB) regions of 26,700 bp, large single-copy (LSC) region of 86,584 bp, and small single-copy (SSC) region of 18,341 bp. The chloroplast genome contains 133 genes, including 83 protein-coding genes, 38 tRNA genes, and 8 rRNA genes. The phylogenetic analysis indicated that Oberonia japonica was closely related to L. bootanensis based on 17chloroplast genomes matrix of Orchidaceae.
| S-EPMC7782275 | biostudies-literature
Project description:In the present study, we reported and characterized the complete chloroplast genome of a moth orchid, Phalaenopsis wilsonii, which is endemic to South China. Its plastid genome size is 145,373 bp, consisting of a large single copy (LSC) region (84,996 bp), a small single-copy region (10,668 bp), and two inverted repeats (IRs) regions (24,855 bp). A total of 122 plastid genes were annotated, comprising 76 protein-coding genes, 38 tRNA genes, and 8 rRNA genes. The phylogenetic tree further revealed that P. wilsonii showed a sister relationship with P. lowii within subgenus Parishianae.
| S-EPMC8555540 | biostudies-literature