Browse
Submit Data
Databases
API
Help

Dataset Information

33 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

The complete chloroplast genome sequence of Taxus yunnanensis.

ABSTRACT: The first complete chloroplast genome (cpDNA) sequence of Taxus yunnanensis was determined from Illumina HiSeq pair-end sequencing data in this study. The cpDNA is 129,190 bp in length. Like other species of taxus genus, the chloroplast genome of T. yunnanensis has lost one of the large inverted repeats (IRs). The genome contains 116 genes, including 82 protein-coding genes, 4 ribosomal RNA genes, and 30 transfer RNA genes. Further phylogenomic analysis showed that T. yunnanensis closed to T. brevifolia in Lauraceae family.

SUBMITTER: Geng Y

PROVIDER: S-EPMC7782282 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

The complete chloroplast genome sequence of Altingia yunnanensis.

Project description:The first complete chloroplast genome (cpDNA) sequence of Altingia yunnanensis was determined from Illumina HiSeq pair-end sequencing data in this study. The cpDNA is 160,860 bp in length, contains a large single-copy region (LSC) of 89,162 bp and a small single-copy region (SSC) of 19,008 bp, which were separated by a pair of inverted repeat (IR) regions of 26,325 bp each. The genome contains 130 genes, including 85 protein-coding genes, 8 ribosomal RNA genes, and 37 transfer RNA genes. Further, the phylogenomic analysis showed that A. yunnanensis and Altingia excelsa clustered in a clade in Saxifragales order.

| S-EPMC7748700 | biostudies-literature

The complete chloroplast genome sequence of Amentotaxus yunnanensis (Taxaceae).

Project description:The complete chloroplast genome sequence of Amentotaxus yunnanensis has been defined in this study. The genome is 138,604 bp in length and one of the large inverted repeats found till date. The overall GC content of the genome is 35.1%. The A. yunnanensis chloroplast genome contains 118 unique genes, including 81 protein-coding genes, 31 tRNA genes, and 4 rRNA genes. Nine protein-coding genes and 6 tRNA contain a single intron, while another species (ycf3) has a couple of introns. A neighbor-joining phylogenetic analysis suggested that A. yunnanensis is closely related to A. argotaenia and A. formosana within the Taxaceae family.

| S-EPMC7687433 | biostudies-literature

Complete chloroplast genome of Angiopteris yunnanensis (Marattiaceae).

Project description:The complete chloroplast genome of Angiopteris yunnanensis has been sequenced and assembled to provide genomic resources to reconstruct the phylogenetic relationship among species of Angiopteris as required to support conservation management of these ancient ferns. The chloroplast genome is 152,962 bp in length with the large single copy (LSC), the small single copy (SSC), and two inverted repeat (IR) regions of length 89,717bp, 20,585bp, and 21,330bp, respectively. We annotated 136 genes in total, including 89 coding genes, 39 tRNAs and 8 rRNAs. Comparative analyses confirmed the conservatism of plastid genome sequences among the species of Angiopteris and the distant related genus Christensenia.

| S-EPMC7707810 | biostudies-literature

The complete chloroplast genome sequence of Pellacalyx yunnanensis: an endangered species in China.

Project description:Pellacalyx yunnanensis is an endangered plant species occurring in Yunnan province of China. The first complete chloroplast genome (cpDNA) sequence of P. yunnanensis was determined from Illumina HiSeq pair-end sequencing data in this study. The cpDNA is 163,743 bp in length, contains a large single-copy region (LSC) of 91,075 bp and a small single-copy region (SSC) of 18,668 bp, which were separated by a pair of inverted repeats (IR) regions of 27,000 bp. The genome contains 128 genes, including 83 protein-coding genes, 8 ribosomal RNA genes, and 37 transfer RNA genes. The overall GC content of the whole genome is 35.7%, and the corresponding values of the LSC, SSC, and IR regions are 33.0%, 29.6%, and 42.3%, respectively. Further phylogenomic analysis showed that P. yunnanensis clustered in a unique clade in family Rhizophoraceae.

| S-EPMC7707691 | biostudies-literature

The complete chloroplast genome of Goodyera yunnanensis Schltr.

Project description:The family Orchidaceae is renowned for its extensive diversity. Within this family, the genus Goodyera R. Br. is classified under the subtribe Goodyerinae, comprising approximately 99 species. In this study, a species Goodyera yunnanensis Schltr., its plastid genome was characterized. The plastid genome of G. yunnanensis is 146,197 bp in size and exhibits a typical quadripartite structure with a pair of inverted repeat regions (IRs) of 25,611 bp, a large single-copy region (LSC) of 81,300 bp and a small single-copy region (SSC) of 13,675 bp. A total of 126 genes were identified, containing 80 protein-coding genes, 38 tRNA genes and 8 rRNA genes. The overall GC content is 37.2%, with corresponding values of 43.3%, 34.7% and 29.1% in IR, LSC and SSC regions, respectively. Forty-seven simple sequence repeats (SSRs) are found in G. yunnanensis plastome, and the frequency of mononucleotide repeats is significantly higher than other repeat types. Phylogenetic analysis indicates that Goodyera is resolved into four clades. G. yunnanensis belongs to the monophyletic clade A, and its phylogenetic position can be reasonably supported by morphological and molecular data.

| S-EPMC10776080 | biostudies-literature

The complete chloroplast genome of Ranunculus yunnanensis (Ranunculaceae).

Project description:Ranunculus yunnanensis Franch is endemic in Yunnan and Sichuan Provinces, southwestern China. Here, we report the complete chloroplast (cp) genome of R. yunnanensis. The chloroplast genome is 156,050 bp in length, with 111 encoded genes, including 78 protein-coding genes, 29 tRNA genes, and four rRNA genes. Maximum-likelihood phylogenetic reconstruction using the existing data of Ranunculus shows that R. yunnanensis is revealed at the basal position of the marsh buttercup clade. This result has improved a better understanding of the internal relationship of the Ranunculus.

| S-EPMC8682826 | biostudies-literature

The complete chloroplast genome of Meeboldia yunnanensis (Apiaceae).

Project description:Meeboldia yunnanensis Wolff (Apiaceae) is a perennial species naturally distributed in Yunnan and Xizang. The complete chloroplast genome sequence of M. yunnanensis was generated by de novo assembly using whole-genome next-generation sequencing data. The complete chloroplast genome of M. yunnanensis was 154,865 bp in total sequence length and divided into four distinct regions: small single-copy region (17,370 bp), large single-copy region (84,641 bp), and a pair of inverted repeat regions (26,427 bp). The genome annotation displayed a total of 130 genes, including 85 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. Phylogenetic analysis with the reported chloroplast genomes revealed that M. yunnanensis has close relationship to Pterygopleurum neurophyllum.

| S-EPMC7706806 | biostudies-literature

The complete chloroplast genome sequence of the medicinal plant Salvia yunnanensis C. H. Wright. (Lamiaceae).

Project description:Salvia yunnanensis is a medicinal plant commonly used in the southwest of China. In this study, we sequenced the complete chloroplast (cp) genome sequence of S. yunnanensis to investigate its phylogenetic relationship in the family Lamiaceae. The total length of the cp genome was 151,338 bp, with 38.0% overall GC content and exhibited typical quadripartite structure, a pair of IRs (inverted repeats) of 25,578 bp each were separated by a small single-copy (SSC) region of 17,564 bp and a large single-copy (LSC) region of 82,618 bp. The cp genome contained 114 genes, including 80 protein coding genes, 30 tRNA genes, and 4 rRNA genes. The phylogenetic analysis indicated S. yunnanensis was closely related to S. miltiorrhiza, which afforded a scientific evidence that S. yunnanensis could be used as original species of Radix et Rhizoma Saliviae Miltiorrhizae (Danshen).

| S-EPMC7707504 | biostudies-literature

Transcriptome and comparative chloroplast genome analysis of Taxus yunnanensis individuals with high and low paclitaxel yield.

Project description:Paclitaxel is a potent anti-cancer drug that is mainly produced through semi-synthesis, which still requires plant materials as precursors. The content of paclitaxel and 10-deacetyl baccatin III (10-DAB) in Taxus yunnanensis has been found to differ from that of other Taxus species, but there is little research on the mechanism underlying the variation in paclitaxel content in T. yunnanensis of different provenances. In this experiment, the contents of taxoids and precursors in twigs between a high paclitaxel-yielding individual (TG) and a low paclitaxel-yielding individual (TD) of T. yunnanensis were compared, and comparative analyses of transcriptomes as well as chloroplast genomes were performed. High-performance liquid chromatography (HPLC) detection showed that 10-DAB and baccatin III contents in TG were 18 and 47 times those in TD, respectively. Transcriptomic analysis results indicated that genes encoding key enzymes in the paclitaxel biosynthesis pathway, such as taxane 10-β-hydroxylase (T10βH), 10-deacetylbaccatin III 10-O-acetyltransferase (DBAT), and debenzoyl paclitaxel N-benzoyl transferase (DBTNBT), exhibited higher expression levels in TG. Additionally, qRT-PCR showed that the relative expression level of T10βH and DBAT in TG were 29 and 13 times those in TD, respectively. In addition, six putative transcription factors were identified that may be involved in paclitaxel biosynthesis from transcriptome data. Comparative analysis of plastid genomes showed that the TD chloroplast contained a duplicate of rps12, leading to a longer plastid genome length in TD relative to TG. Fifteen mutation hotspot regions were identified between the two plastid genomes that can serve as candidate DNA barcodes for identifying high-paclitaxel-yield individuals. This experiment provides insight into the difference in paclitaxel accumulation among different provenances of T. yunnanensis individuals.

| S-EPMC10918223 | biostudies-literature

The complete chloroplast genome of Pholidota yunnanensis Rolfe (Orchidaceae: Coelogyninae).

Project description:In this study, the complete chloroplast genome of Pholidota yunnanensis is presented, which represents first complete plastid genome of the genus Pholidota in the subtribe Coelogyninae. The chloroplast genome size is 159,729 bp, including a GC content of 37.3% and 135 genes (89 protein-coding genes, 38 tRNA genes, 8 rRNA genes). The genome structure is typical quadripartite, consisting of a pair of inverted repeat regions (26,638 bp) separated by a large single-copy region (LSC, 87,610 bp) and a small single-copy region (SSC, 18,843 bp). Phylogenetic analysis among 15 species based on cp genomes recovered a well-supported phylogenetic tree and indicated a close relationship between Pholidota yunnanensis and Pleione bulbocodioides.

| S-EPMC7783148 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data