Browse
Submit Data
Databases
API
Help

Dataset Information

19 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Characterization of the complete plastid genome of Abies forrestii (Pinaceae) from southwest China.

ABSTRACT: Abies forrestii is endemic to southwest China and ecologically important as a major component of the cold temperate forests. This study was the first report complete chloroplast (cp) genome of A. forrestii. The complete chloroplast genome was 120,022 bp in size. In total, 114 genes were identified, including 68 peptide-encoding genes, 35 tRNA genes, four rRNA genes, six open reading frames and one pseudogene. Thirteen genes contain introns. In phylogenetic analysis, A. forrestii was found to be closely related with A. nukiangensis, A. fanjingshanensis and A. delavayi subsp. fansipanensis. Our study will provide potential genetic resources for further evolutionary studies of this ecologically important species.

SUBMITTER: Dong NL

PROVIDER: S-EPMC8405101 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Characterization of the complete chloroplast genome of Abies chensiensis (Pinaceae), an endemic to China.

Project description:Abies chensiensis, an endemic evergreen trees distributed in Qinling Mountains, is listed in China Species Red List as an endangered species. In this study, the complete chloroplast genome (cpDNA) sequence of Abies chensiensis was determined from Illumina pair-end sequencing data. The cpDNA is 121,329?bp in length, contains a large single copy region (LSC) of 72,843?bp and a small single copy region (SSC) of 46,126?bp, which were separated by a pair of inverted repeat (IR) regions of 1180?bp. The genome contains 120 genes, including 81 protein-coding genes, 4 ribosomal RNA genes, and 35 transfer RNA genes. The overall GC content of the whole genome is 38.3%, and the corresponding values of the LSC, SSC, and IR regions are 38.8, 37.1, and 37.5%, respectively. Phylogenetic analysis based on 20 chloroplast genomes indicates that A. chensiensis is closely related to A. sibirica.

| S-EPMC7510650 | biostudies-literature

Characterization of the complete chloroplast genome of Ajuga forrestii (Lamiaceae), a medicinal plant in southwest of China.

Project description:Ajuga forrestii is a medicinal plant commonly used in southwest of China. In this study, we sequenced the complete chloroplast (cp) genome sequence of A. forrestii to investigate its phylogenetic relationship in the family Lamiaceae. The chloroplast genome of A. forrestii was 150,492 bp in length with 38.3% overall GC content, including a large single copy (LSC) region of 82,148 bp, a small single copy (SSC) region of 17,160 bp and a pair of inverted repeats (IRs) of 25,592 bp. The cp genome contained 112 genes, including 79 protein coding genes, 29 tRNA genes, and 4 rRNA genes. The phylogenetic analysis indicated Ajuga was closely related to Scutellaria.

| S-EPMC7707673 | biostudies-literature

The complete chloroplast genome sequence of Abies chensiensis (Pinaceae).

Project description:Abies chensiensis is listed as a threatened species in the Red List and categorized as key protected wild plants in China. Here, we determined the complete chloroplast genome of A. chensiensis using the Illumina MiSeq platform. The genome was 121,795 bp in length, comprising a large single copy (LSC) region of 67,160 bp, a small single copy (SSC) region of 54,107 bp, and two inverted repeat regions (IRa and IRb) of 264 bp each. It was composed of 114 genes, including 68 peptide-encoding genes, 35 transfer RNAs (tRNAs), four ribosomal RNAs (rRNAs), six open reading frames and one pseudogene. Phylogenetic analysis revealed that A. chensiensis was most closely related to A. beshanzuensis, with high bootstrap values. The present research will provide potential genetic resources for further conservation and management strategies.

| S-EPMC7687642 | biostudies-literature

The complete chloroplast genome of the Abies yuanbaoshanensis, an endangered Pinaceae species in Southern China.

Project description:Abies yuanbaoshanensis is critically endangered and endemic to Guangxi province of China, with no more than 900 surviving individuals. In this study, we reported the complete chloroplast (cp) genome of A. yuanbaoshanensis. The complete chloroplast genome is 121897 bp in size. In total, 112 genes were identified, including 74 protein-coding genes, 34tRNA genes, and four rRNA genes. In phylogenetic analysis, the tree supported the monophyly of the genus Abies. The complete plastome of A. yuanbaoshanensis will provide potential genetic resources for further conservation and evolutionary studies of this highly endangered species.

| S-EPMC7707238 | biostudies-literature

The complete chloroplast genome sequence of Abies chensiensis (Pinaceae: Abietoideae), an endangered species endemic to China.

Project description:Chloroplast (cp) genome sequences became a widely used tool for evolutionary and phylogenetic studies in plants. Abies chensiensis (Pinaceae: Abietoideae) is an endangered species endemic to China. To understand its evolutionary characteristics, the complete chloroplast genome of the A. chensiensis has been reconstructed from the whole-genome Illumina sequencing data. The circular genome is 121,784?bp in length and without a typical quadripartite structure due to the loss of IR region. The total GC content of whole genome sequence is 38.3%. The chloroplast genome encodes 109 genes, including 75 protein-coding genes, 30 transfer RNA genes and four ribosomal RNA genes. Among them, 35 genes involved in photosynthesis, while 58 genes involved in self-replication. The Maximum-Likelihood phylogenetic analysis showed a strong sister relationship with A. nephrolepis and A. koreana in Abietoideae. Our findings provide fundamental information for further evolutionary and phylogenetic researches of Abietoideae.

| S-EPMC7800204 | biostudies-literature

Abies forrestii

Project description:Abies forrestii Raw sequence reads

| PRJNA747743 | ENA

Characterization of the complete plastid genome of fireweed, Epilobium angustifolium, Shaanxi, China.

Project description:In this article, we studied the complete chloroplast genome of Fireweed, Epilobium angustifolium, an essential herbaceous perennial species of the genus Epilobium (Onagraceae), we used Illumina sequencing platform to characterize its whole plastid genome sequence. The results showed that its whole plastid genome is a typical qudaripartite circular molecule with 161,199 bp in total length, which contains a large single-copy region of 89,076 bp, a small single-copy region of 17,321 bp, and two inverted repeat regions of 27,401 bp. We identified 130 genes, 85 protein-coding genes, 37 tRNA, and 8 rRNA genes within this genome. The GC content in the chloroplast genome, LSC region, SSC region, and IR region were 38.1, 36.3, 33.1, and 42.7%, respectively. Phylogenetic analysis indicated that this plant was placed as a sister to the congeneric Epilobium ulleungensis, the two species were clustered into a clade with high bootstrap support.

| S-EPMC7707668 | biostudies-literature

Complete plastid genome of Rhododendron griersonianum, a critically endangered plant with extremely small populations (PSESP) from southwest China.

Project description:The complete plastid genome of Rhododendron griersonianum, a critically endangered plant species with extremely small populations, was obtained using Illumina HiSeq X Ten and ONT PromethION sequencing. The full length of the plastid genome is 206,467 bp with an overall GC content of 35.8%, which encodes 118 unique genes, including 78 protein-coding genes, 36 tRNA and 4 rRNA genes. Phylogenetic analysis revealed that all Rhododendron species formed a monophyletic clade. This study provides a valuable reference and will facilitate future studies related to the general characteristics and evolution of plastid genomes in the genus Rhododendron.

| S-EPMC7782577 | biostudies-literature

Lectotypification of Abies fanjingshanensis (Pinaceae).

Project description:The type collection of Abies fanjingshanensis W.L.Huang et al. contains four specimens in the Herbarium (GNUG). Abies fanjingshanensis is lectotypified here with L.Yang 83-427 (GNUG0002022) under Art. 9.12 of the Shenzhen Code.

| S-EPMC7360631 | biostudies-literature

Characterization of the complete chloroplast genome of Pinus wangii (Pinaceae), an endangered and endemic species in China.

Project description:The complete cp genome of Piuns wangii was 117,014 bp in size, containing a large single copy (LSC, 64,061 bp) region and a small single copy (SSC, 52,007 bp) region separated by two reduced inverted repeats (IRs, 473 bp). A total of 107 genes were predicted, including 73 protein-coding genes, 30 tRNA genes, and 4 rRNA genes. Most of the 51 simple sequence repeats (SSRs) were mononucleotides motifs of A/T types and were found to be located in non-coding regions. Phylogenetic analysis of Asian Pinus showed P. wangii clustered a strongly-supported clade with Pinus morrisonicola, Pinus sibirica, Pinus wallichiana, and Pinus pumila.

| S-EPMC7800402 | 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