Browse
Submit Data
Databases
API
Help

Dataset Information

24 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

The complete chloroplast genome sequence of Cerasus jingningensis (Rosaceae), an endemic plant to Zhejiang province, China.

ABSTRACT: Cerasus jingningensis is a deciduous shrub endemic to Zhejiang province, China. In our study, we assembled and characterised the chloroplast (CP) genome of C. jingningensis based on high-throughput Illumina sequencing data. The CP genome is 157,913?bp in length with an overall GC content of 36.7%, and it consists of two inverted repeats of 26,427?bp each, a large single copy of 85,934?bp, and a small single copy of 19,125?bp. The genome harbours 131 genes, including 85 protein-coding genes, 37 tRNA genes, eight rRNA genes, and a pseudogene ycf1. Phylogenetic analysis revealed that C. jingningensis is a sister of C. serrulata var. spontanea.

SUBMITTER: Jiang M

PROVIDER: S-EPMC7707190 | biostudies-literature | 2019 Oct

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

The complete chloroplast genome sequence of Cerasus jingningensis (Rosaceae), an endemic plant to Zhejiang province, China.

Jiang Ming M Wang Junfeng J

Mitochondrial DNA. Part B, Resources 20191011 2

Cerasus jingningensis is a deciduous shrub endemic to Zhejiang province, China. In our study, we assembled and characterised the chloroplast (CP) genome of C. jingningensis based on high-throughput Illumina sequencing data. The CP genome is 157,913 bp in length with an overall GC content of 36.7%, and it consists of two inverted repeats of 26,427 bp each, a large single copy of 85,934 bp, and a small single copy of 19,125 bp. The genome harbours 131 genes, including 85 protein-codi ...[more]

PMID: 33366063

Similar Datasets

Complete chloroplast genome of Cerasus fengyangshanica (Rosaceae), a wild flowering cherry endemic to China.

Project description:Cerasus fengyangshanica is a wild flowering cherry endemic to Mount Fengyang, China. Here, we reported the complete chloroplast (cp) genome of C. fengyangshanica (GenBank accession number: MW160272). The cp genome was 157,964 bp long, with a large single-copy region (LSC) of 85,972 bp and a small single-copy region (SSC) of 19,086 bp separated by a pair of inverted repeats (IRs) of 26,453 bp. It encodes 129 genes, including 84 protein-coding genes, 37 tRNA genes, and 8 ribosomal RNA genes. We also reconstructed the phylogeny of Prunus sensu lato using maximum likelihood (ML) method, including our data and previously reported cp genomes of related taxa. The phylogenetic analysis indicated that C. fengyangshanica is closely related with Prunus maximowiczii.

| S-EPMC7832537 | biostudies-literature

Complete chloroplast genome of Cerasus kumanoensis (Rosaceae), a wild flowering cherry endemic to Kii Peninsula, Japan.

Project description:Cerasus kumanoensis is a recently described wild cherry species from the Kii Peninsula, Japan. Here we determined the first complete chloroplast genome of C. kumanoensis using genome skimming approach. The cp genome was 157,898?bp long, with a large single-copy region (LSC) of 85,926?bp and a small single-copy region (SSC) of 19,070?bp separated by a pair of inverted repeats (IRs) of 26,451?bp. It encodes 129 genes, including 84 protein-coding genes, 37 tRNA genes, and 8 ribosomal RNA genes. Besides, we reconstructed the phylogeny of Prunus using maximum likelihood (ML) method, including our data and previously reported cp genomes of related taxa. The phylogenetic analysis indicated that C. kumanoensis is close related with a group including Prunus takesimensis and P. speciosa.

| S-EPMC7706986 | biostudies-literature

Complete chloroplast genome of Tricyrtis xianjuensis Li, Chen & Ma 2014 (Liliaceae): a species endemic to Zhejiang province, China.

Project description:Tricyrtis xianjuensis Li, Chen & Ma 2014 is a rare and endangered species endemic to Zhejiang province, with fewer than 200 individuals in the wild. In our present study, the complete chloroplast genome of T. xianjuensis was assembled by using high-throughput sequencing data, and its genomic features were described and comparative genomic analyses within Liliaceae family were performed. The complete chloroplast genome of T. xianjuensis was 155,748 bp in length, exhibiting a GC content of 37.3%. This genome structure contained two inverted repeats (IRs), as well as a small single-copy (SSC) and a large single-copy (LSC) region. The IR region measured 26,371 bp, while the SSC and LSC regions were 17,729 bp and 85,277 bp in length, respectively. A total of 137 genes were identified, including 85 protein-coding genes, 38 tRNA genes, eight rRNA genes, and six pseudogenes. Phylogenic analysis revealed T. xianjuensis shared a clade with T. formosana Baker 1879 and T. macropoda Miq. 1867, with a support rate of 100%. The assembly and analysis of T. xianjuensis chloroplast genome provided an insight into further studies on the conservation genetics of this endangered species.

| S-EPMC10776049 | biostudies-literature

Characterization of the complete chloroplast genome sequence of Hemsleya zhejiangensis (cucurbitaceae), a rare and endangered wild plant species in Zhejiang province, China.

Project description:Hemsleya zhejiangensis is a rare and endangered plant species which is listed as a key protected wild plant in Zhejiang province, China. In our present study, we assembled the complete chloroplast (CP) genome of H. zhejiangensis using high-throughput sequencing data. The whole genome sequence of H. zhejiangensis is 157,289 bp in size, with a GC content of 37.1%. Sequencing analyses reveal that the CP genome encodes 133 genes, including 84 protein-coding genes, 8 rRNA genes, 37 tRNA genes, and four pseudogenes. Phylogenetic analysis results indicate that H. zhejiangensis is clustered with H. lijiangensis, with a support value of 100%, and they are sister to the three Gynostemma species.

| S-EPMC7707793 | biostudies-literature

The complete chloroplast genome of Cerasus dictyoneura, an ornamental plant of China.

Project description:The complete cp genome of Cerasus dictyoneura was 158,084 bp in length, consisting of a LSC of 86,275 bp and a SSC of 19,039 bp, which were separated by a pair of 26,385 bp IRs. The genome contained 131 genes, including 86 proteincoding genes, 37 tRNA genes, and 8 rRNA genes. The overall GC content is 36.7%, while the corresponding values of the LSC, SSC, and IR regions are 34.6, 29.5, and 42.6%, respectively. Furthermore, phylogenetic analysis based on 16 complete cp genome sequences indicated that C. dictyoneura is within Eurosids I.

| S-EPMC7707308 | biostudies-literature

Characterization of the complete plastome sequence of Torreya grandis var. jiulongshanensis (Taxaceae), a rare and endangered plant species endemic to Zhejiang province, China.

Project description:Torreya grandis var. jiulongshanensis (Taxaceae) is an evergreen tree endemic to Zhejiang province, China, and it is listed as a rare plant species with extremely small populations. In our present study, we assembled the chloroplast (CP) genome of T. grandis var. jiulongshanensis using high-throughput sequencing data generated by an Illumina Hiseq X Ten platform. The results indicate that the complete CP genome is 136,705 bp in size with an overall guanine and cytosine content of 35.5%. The plastome has lost its quadripartite structure. In the CP genome, there are a total of 119 genes, including 82 protein-coding genes, 4 ribosomal RNA genes, and 33 transfer RNA genes. Phylogenetic analysis revealed that T. grandis var. jiulongshanensis is a sister species to T. grandis.

| S-EPMC7748455 | biostudies-literature

The complete chloroplast genome sequence of Chimonobambusa luzhiensis, an endangered species endemic to Guizhou Province, China.

Project description:Chimonobambusa luzhiensis (Poaceae: Bambusoideae) is an endangered plant endemic to Guizhou Province, China. Here, we report the complete chloroplast genome of C. luzhiensis. The plastid genome revealed a typical quadripartite structure with a length of 139,896 bp, including a large single-copy (LSC, 83,191 bp) region, a small single-copy (SSC, 12,811 bp) region, and a pair of inverted repeat (IR) regions (IRa and IRb, 21,797 bp). A total of 131 genes, including 86 protein-coding genes (PCGs), eight ribosomal RNA (rRNA) genes, and 37 transfer RNA (tRNA) genes were annotated, and the overall GC content was 38.8%. Phylogenetic analysis showed that the relationship between C. luzhiensis is sister to C. tumidisinoda.

| S-EPMC9331209 | biostudies-literature

The complete chloroplast genome of a Chinese endemic ornamental plant Sorbus unguiculata Koehne (Rosaceae).

Project description:Sorbus unguiculata is a pinnate-leaved deciduous shrub growing in mixed forests in Sichuan province, China. It is one of the least known species in the genus with high ornamental value. In this study, we firstly assembled and annotated the complete chloroplast genome of the species using the next-generation sequencing method. The results showed that the chloroplast genome size is 159,900?bp, comprising of a large single-copy (LSC) region of 87,888?bp, a small single-copy (SSC) region of 19,256?bp, and a pair of IR regions of 26,378?bp. The whole cp genome predicted 109 genes in total, including 76 protein-coding genes, 29 tRNAs, and 4 tRNAs. The overall GC content of the chloroplast genome is 36.6%. The phylogenetic relationship exhibited that S. unguiculata is closely clustered with S. helenae in Sorbus.

| S-EPMC7687415 | biostudies-literature

The complete chloroplast genome of Prunus clarofolia (Rosaceae), a wild cherry endemic to China.

Project description:Prunus clarofolia (Schneid.) Yu et Li is a very attractive wild flowering cherry endemic to China. In this study, the complete chloroplast genome of P. clarofolia was assembled. The total length of the chloroplast genome was 157,899 bp, containing a pair of inverted repeat regions of 26,393 bp each, separated by a small single-copy region of 19,142 bp, and a large single-copy region of 85,971 bp. The overall GC content of the chloroplast genome was 36.71%. The genome contained 131 genes, including 85 protein-coding genes, 37 tRNA genes, eight rRNA genes, and one pseudogene. Phylogenetic analysis revealed that P. clarofolia and P. pseudocerasus showed the closest relationship.

| S-EPMC8741222 | biostudies-literature

The complete chloroplast genome sequence of Annamocarya sinensis (Juglandaceae), an Endangered species endemic to Yunnan Province, China.

Project description:Annamocarya sinensis, a plant species with extremely small populations endemic to Xichou county of Yunnan province, has been classified as a national second-class protected wild plant. In this study, we assembled its complete chloroplast genome. The total genome size of A. sinensis was 158,484 bp in length, containing a large single-copy region of 89,871 bp, a small single-copy region of 20,558 bp, and a pair of inverted repeat regions of 24,029 bp. The all GC content of A. sinensis chloroplast genome was 36.2%. It encodes a total of 114 unique genes, including 79 protein-coding genes, 31 tRNA genes, and four rRNA genes. Eleven genes contain a single intron, and three genes have two introns. Phylogenetic analysis results strongly supported that Annamocarya sinensis was closely related to Carya kweichowensis.

| S-EPMC7782989 | biostudies-literature