Browse
Submit Data
Databases
API
Help

Dataset Information

24 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

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

ABSTRACT: 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.

SUBMITTER: Zhao Y

PROVIDER: S-EPMC7510650 | biostudies-literature | 2019

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

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

Zhao Yuemei Y Zhou Tao T Chen Xiaodan X Zhang Xiao X Bai Guoqing G Zhao Guifang G

Mitochondrial DNA. Part B, Resources 20181121 1

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 ...[more]

PMID: 33365404

Similar Datasets

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

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

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

Project description: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.

| S-EPMC8405101 | 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

The complete chloroplast genome of Keteleeria davidiana var. calcarea (Pinaceae), an endangered species endemic to China.

Project description:Keteleeria davidiana var. calcarea is an endangered tree with considerable economic potential that used as timber wood for furniture and house construction. However, the natural population of K. davidiana var. calcarea is very fragmented, which is the cause for its low genetic diversity. In this study, we report the complete chloroplast genome of K. davidiana var. calcarea using Illumina sequencing. The chloroplast genome size is 117,670 bp in length, harboring a pair of very short inverted repeats (IRs) of 262 bp separated by a large single copy (LSC) sequence of 64,634 bp and a small single copy (SSC) sequence of 53,078 bp. The chloroplast genome K. davidiana var. calcarea contains 113 genes (74 protein genes, 35 tRNA genes, and 4 rRNA genes) and the overall GC content is 38.6%. The maximum likelihood phylogenetic analysis shows that K. davidiana var. calcarea is clustered with K. davidiana in genus Keteleeria. This complete chloroplast genome will help us to understand the evolution of K. davidiana var. calcarea and lays the foundations for future studies in this species conservation.

| S-EPMC7928163 | biostudies-literature

The complete chloroplast genome of Abies georgei Orr var. smithii, a species endemic to the Qinghai-Tibet Plateau, China.

Project description:Abies georgei Orr var. smithii is an evergreen coniferous species of Pinaceae, and is endemic to the Qinghai-Tibet Plateau of China. Considering its vital ecological functions in this unique area, the complete chloroplast (cp) genome was constructed in this study to provide genetic information for its further study of conservation and evolution. The complete cp genome is 121,213 bp in length with GC content of 38.3%, and contains a tetrad structure, including a large single copy region of 76,278 bp, a small single copy of 42,575 bp, and two very short repeats of 1,180 bp for each. Besides, it contains 113 genes in total, including 74 CDSs, 35 tRNAs, and four rRNAs. This genome has been deposited in Genbank under accession number of MT527722.

| S-EPMC7783149 | biostudies-literature

The complete chloroplast genome of Pinus squamata (Pinaceae), a critically endangered species in China.

Project description:The complete chloroplast (cp) genome of Pinus squamata, a critically endangered species in China, was reported in this study. The cp genome is 118,300?bp in length and has four regions: 65,298?bp of large single copy (LSC) region and 52,098?bp of small single copy (SSC) region separated by 452?bp of highly reduced inverted repeat (IR) regions. This cp genome with GC content of 38.8% contains 107 unique genes (73 protein-coding genes, 30 tRNA genes, and four rRNA genes). Phylogenetic analysis based on the complete cp genomes indicates that P. squamata is closer to P. gerardiana than P. bungeana.

| S-EPMC7706991 | biostudies-literature

Characterization of the complete chloroplast genome of Alsophila spinulosa, an endangered species endemic to China.

Project description:Tree fern Alsophila spinulosa is an endangered relic plant in the world. It is currently on the International Union for Conservation of Nature (IUCN) red list of threatened species. In this study, we first assembled the complete chloroplast (cp) genome of A. spinulosa by Illumina paired-end reads data. The whole genome was 156,661 bp, consisting of a pair of inverted repeats of 24,364 bp, large single copy region and a small single copy region (70,352 and 21,624 bp in length, respectively). The cp genome contained 133 genes, including 92 protein-coding genes, 33 trRNA genes, and eight rRNA genes. The overall GC content of the whole genome was 40.4%. A neighbour-joining phylogenetic analysis demonstrated a close relationship between A. spinulosa and Cystoathyrium chinense Ching.

| S-EPMC7510675 | biostudies-literature

Characterization of the complete chloroplast genome of styrax macrocarpus (Styracaceae), an endemic species from China.

Project description:The whole chloroplast genome of Styrax macrocarpus, an endemic species distributed in China, is determined in this study. The whole chloroplast genome size is 157,805 bp in length, containing a large single-copy region (LSC, 87,628 bp) and a small single-copy region (SSC, 18,267 bp), which were separated by a pair of inverted repeats (IRs, 25,955 bp). One hundred thirty one genes were detected from this genome, including 85 protein-coding genes, 38 transfer RNA genes, and 8 ribosomal RNA genes. The phylogenetic analysis suggested that the S. macrocarpus is closely clustered with S. japonicus with strong support values.

| S-EPMC7782959 | biostudies-literature

Characterization of the complete chloroplast genome of Pedicularis shansiensis (Orobanchaceae), an endemic species of China.

Project description:The complete chloroplast genome sequence of Pedicularis shansiensis Tsoong was determined and described. The circular chloroplast genome is 151,902 bp in length and contains a large single-copy region of 83,180 bp, a small single-copy region of 17,284 bp and two inverted repeat regions of 25,719 bp. The chloroplast genome contains 132 genes, including 86 protein-coding, 8 rRNA, and 38 tRNA genes. Phylogenetic analysis shows Pedicularis species cluster together and P. shansiensis forms a clade with P. dissect.

| S-EPMC8788376 | biostudies-literature