Browse
Submit Data
Databases
API
Help

Dataset Information

14 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Next-generation sequencing yields the complete chloroplast genome of Pleione chunii, a vulnerable orchid in China.

ABSTRACT: Pleione chunii is a vulnerable epiphytic orchid with significant ornamental value. Here, we report the first complete chloroplast genome of P. chunii. The circular genome was 158,880?bp in length and consisted of a pair of inverted repeats (IR 26,465?bp), which were separated by a large single copy region (LSC 87,259?bp) and a small single copy region (SSC 18,691?bp). It contained 115 unique genes, including 87 protein-coding genes, 38 tRNAs, and eight rRNAs. The maximum-likelihood phylogenetic analysis indicated that P. chunii was sister to P. bulbocodioides and P. formosana.

SUBMITTER: Wu SS

PROVIDER: S-EPMC7706524 | biostudies-literature | 2019 Jul

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Next-generation sequencing yields the complete chloroplast genome of Pleione chunii, a vulnerable orchid in China.

Wu Sha-Sha SS Shen Li-Ming LM Ling Rui R Dai Zhong-Wu ZW Liu Zhong-Jian ZJ Lan Si-Ren SR

Mitochondrial DNA. Part B, Resources 20190716 2

Pleione chunii is a vulnerable epiphytic orchid with significant ornamental value. Here, we report the first complete chloroplast genome of P. chunii. The circular genome was 158,880 bp in length and consisted of a pair of inverted repeats (IR 26,465 bp), which were separated by a large single copy region (LSC 87,259 bp) and a small single copy region (SSC 18,691 bp). It contained 115 unique genes, including 87 protein-coding genes, 38 tRNAs, and eight rRNAs. The maximum-likelihood ...[more]

PMID: 33365633

Similar Datasets

Next-generation sequencing yields the complete chloroplast genome of Pleione forrestii (Orchidaceae).

Project description:Pleione forrestii is an endangered terrestrial orchid with significant ornamental values. Here, we report the first complete chloroplast genome of P. forrestii. The circular genome was 158,759?bp in length and consisted of a pair of inverted repeats (IR 26,429?bp), which were separated by a large single-copy region (LSC 87,236?bp) and a small single copy-region (SSC 18,665?bp). It contained 135 genes (115 unique), including 87 protein-coding genes, 38 tRNAs, and 8 rRNAs. The maximum likelihood phylogenetic analysis indicated that P. forrestii was sister to P. bulbocodioides and P. formosana.

| S-EPMC7687623 | biostudies-literature

Next-generation sequencing yields the complete chloroplast genome of Abies kawakamii.

Project description:Abies kawakamii is endemic to the island of Taiwan and has been listed as a threatened species in the Red List. In present study, we reported the complete chloroplast genome of A. kawakamii. The chloroplast genome is 121,290?bp in size. It was composed of 114 genes and they were 68 peptide-encoding genes, 35 tRNA genes, four rRNA genes, six open reading frames and one pseudogene. Loss of ndh genes was identified in the genome of A. kawakamii. Inverted repeat sequences include trnS-psaM-ycf12-trnG and trnG-ycf12-psaM-trnS were recognized in 52-kb inversion points. The phylogenetic analysis confirms that the Abies species are strongly supported as monophyletic. The complete plastome of A. kawakamii will provide potential genetic resources for further conservation and management strategies.

| S-EPMC7510649 | biostudies-literature

Next-generation sequencing yields the complete chloroplast genome of C. goeringii acc. smg222 and phylogenetic analysis.

Project description:Spring orchid (Cymbidium goeringii) is one of the most important species belonging to Orchidaceae owing to its aesthetic appeal, fragrant flowers and ideal characteristics for using as a houseplant. In this study, the complete chloroplast genome of Korean C. goeringii acc. smg222 was determined by Illumina sequencing. The circular double-stranded DNA of 148,441 bp consisted of two inverted repeat regions of 25,610 bp each, a large single copy region of 83,311 bp, and a small single copy region of 13,910 bp. The genome contained 122 genes, of which 104 were unique and 18 were duplicated within the IRs. The 104 unique genes included 70 protein-coding genes, 30 distinct tRNA genes, and four rRNA genes. Phylogenetic tree analysis revealed that C. goeringii acc. smg222 was clustered with Cymbidium kanran, a cymbidium species native to Korea.

| S-EPMC7800249 | biostudies-literature

The complete chloroplast genome of Pleione maculata, an orchid with important ornamental value and medicinal value.

Project description:Pleione maculata is an epiphytic orchid with significant ornamental value and medicinal value. Here, we report the first complete chloroplast genome of P. maculata. The circular genome was 158,394 bp in length and consisted of a pair of inverted repeats (IR 26,646 bp), which were separated by a large single copy region (LSC 86,603 bp) and a small single copy region (SSC 18,499 bp). It contained 135 genes, including 89 protein-coding genes, 38 tRNAs and 8 rRNAs. Phylogenetic analysis of cp genomes from 41 species of Orchidaceae revealed that all species of Pleione formed one monophyletic clade and P. maculata was located at the base of the genus with high bootstrap values (≥99.1%).

| S-EPMC8274512 | biostudies-literature

Next-generation sequencing yields a nearly complete mitochondrial genome of Plestiodon liui (Reptilia, Squamata, Scincidae) endemic to China.

Project description:The Liu's skink, Plestiodon liui, is endemic to China. In this study, a nearly complete mitochondrial genome (mitogenome) (17,643 bp in length) of P. liui from Junzhang Mountain, Wuxi, Jiangsu province, China, was determined by next-generation sequencing. Similar to the typical mtDNA of vertebrates, it contained two ribosomal RNA genes, 13 protein-coding genes (PCGs), 22 transfer RNA genes, and one control region (CR). With exception to the CR, all of the 37 genes were completely recovered. The PCGs were used to perform Bayesian phylogenetic analyses together with other scincid lizards with mitogenome data in GenBank. The resulting phylogenetic tree supported the monophyly of the P. capito group, and suggested that P. liui is the sister taxon to P. capito plus P. tunganus. The mitogenome of P. liui will provide fundamental data for the exploration of the mitogenome evolution in skinks.

| S-EPMC7646586 | biostudies-literature

Next-generation sequencing yields the complete mitogenome of the Shaw's sea-snake (Squamata: Elapidae).

Project description:We report the complete mitogenome of Hydrophis curtus, which is 17,702?bp in size and includes 13 protein-coding (PCGs), two rRNA genes, 22 tRNA genes, and two control regions. PCGs, with 13 genes, are 11,261?bp in length. All PCGs use as the start codon ATN except ND1 (CTA) and COX1 (GTG); ATP8, ATP6, ND4L, ND5, and Cytb use the typical stop codon TAA; but COX2 and ND4 with a single T-. Phylogeny recon-structed using the Bayesian inference (BI) method with 13 PCGs indicates that H. curtus at the root of Laticaudinae.

| S-EPMC7707276 | biostudies-literature

Next-generation sequencing yields the complete mitogenome of stony coral (Favites abdita).

Project description:In this study, the complete mitogenome sequence of stony coral, Favites abdita (Scleractinia), has been decoded for the first time by next-generation sequencing and genome assembly. The assembled mitogenome, consisting of 17,825?bp, has unique 13 protein-coding genes (PCGs), 2 transfer RNAs and 3 ribosomal RNAs genes. The complete mitogenome provides essential and important DNA molecular data for further phylogenetic and evolutionary analysis for stony coral phylogeny.

| S-EPMC7800620 | biostudies-literature

Next-generation sequencing yields the complete mitogenome of wattled crane (Bugeranus carunculatus).

Project description:In this study, the complete mitogenome sequence of wattled crane (Bugeranus carunculatus) has been decoded by next-generation sequencing and genome assembly. The assembled mitogenome, consisting of 16,679?bp, has unique 14 protein-coding genes (PCGs), 22 transfer RNAs and 2 ribosomal RNAs genes. The complete mitogenome provides essential and important DNA molecular data for further phylogenetic and evolutionary analysis for wattled crane phylogeny.

| S-EPMC7799669 | biostudies-literature

Next generation sequencing yields the complete mitogenome of Smith's zokor (Eospalax smithii).

Project description:Sequencing analysis of mitochondrial genomes is useful for understanding the genome structures. In this study, complete mitochondrial genomes of the Eospalax smithii was obtained by using next generation sequencing method. The complete mitogenome of E. smithii was 16,350 bp long, containing 13 protein-coding genes (PCGs), 2 ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA) genes, and 1 non-coding control region (D-loop). The overall base composition of the heavy strand is A (33.65%), C (23.80%), T (30.31%), and G (12.24%). The base compositions present highly biased toward A + T nucleotides. The result of phylogenetic analysis showed the five Eospalax species formed a monophyly with the high bootstrap value and as a sister group of the genus Myospalax. This is the first report of the complete mitochondrial genomes of E. smithii and the mitogenome is potentially important for evolutionary biology, population genetics, and species diagnosis studies of the Mysopalacinae.

| S-EPMC7510577 | biostudies-literature

Next-generation sequencing yields the complete mitogenome of Niya chicken (Gallus gallus).

Project description:In this study, the complete mitochondrial genome sequence of Niya chicken (Gallus gallus) was obtained by using the next-generation sequencing technology for the first time. The complete mitogenome sequence of Niya chicken is 16,784 bp in length, containing 2 ribosomal RNAs, 13 protein-coding genes, 22 transfer RNA genes and a D-loop region. Our work provides a valuable source of data for phylogenetic studies and helps us to understand the maternal origins of the native chickens.

| S-EPMC7782777 | biostudies-literature