Browse
Submit Data
Databases
API
Help

Dataset Information

51 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

The complete chloroplast genome sequence of Tapiscia sinensis (Staphyleaceae).

ABSTRACT: Tapiscia sinensis, belong to Tapisciaceae, is endangered tree endemic to China. Here, we provide the complete plastid genomic data of T. sinensis with the aim of providing data for future conservation efforts research and revealing its phylogenetic position. The complete chloroplast sequence is 161,093 bp, including a large single-copy (LSC) region of 87,782 bp, a small single-copy (SSC) region of 18,517 bp, a pair of invert repeats (IR) regions of 27,387 bp. Plastid genome contains 131 genes, 85 protein-coding genes, 38 tRNA genes, and eight rRNA genes. Phylogenetic analysis base on 19 plastid genomes indicates that T. sinensis located Malvids branch, and is more closely related to the species of the order Sapindales than those of the order Malvales.

SUBMITTER: Zhang JY

PROVIDER: S-EPMC7781918 | biostudies-literature | 2020 Jul

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

The complete chloroplast genome sequence of Tapiscia sinensis (Staphyleaceae).

Zhang Jing-Yao JY Chen De-Qiang DQ Xiang Shuang S Wu Xi X Wang Yi-Fan YF Le Yi-Xun YX Sun Wei-Hong WH Zou Shuang-Quan SQ Zhou Yun-Wei YW Zou Xiao-Xing XX

Mitochondrial DNA. Part B, Resources 20200706 3

Tapiscia sinensis, belong to Tapisciaceae, is endangered tree endemic to China. Here, we provide the complete plastid genomic data of T. sinensis with the aim of providing data for future conservation efforts research and revealing its phylogenetic position. The complete chloroplast sequence is 161,093 bp, including a large single-copy (LSC) region of 87,782 bp, a small single-copy (SSC) region of 18,517 bp, a pair of invert repeats (IR) regions of 27,387 bp. Plastid genome contain ...[more]

PMID: 33457896

Similar Datasets

The complete chloroplast genome sequence of Turpinia montana (Staphyleaceae).

Project description:The Rosids are characterized by remarkable morphological and ecological diversity. Here, we provide the completed plasmid genome of Turpinia montana. The complete chloroplast size of T. montana is 160,111 bp, including a large single-copy (LSC) region of 89,631 bp, a small single-copy (SSC) region of 18,247 bp, a pair of invert repeats (IR) regions of 26,120 bp. Plastid genome contains 131 genes, 86 protein-coding genes, 37 tRNA genes, and eight rRNA genes. Phylogenetic analysis base on 23 plastid genomes indicates that T. montanas is clustered with the plants of the Euscaphis japonica and Staphylea bumalda.

| S-EPMC7783033 | biostudies-literature

The complete chloroplast genome sequence of Euscaphis japonica (Staphyleaceae).

Project description:Euscaphis japonica is not only an ideal ornamental plant, but also a traditional medicinal plant, which is an extremely valuable species to study. We determined the complete chloroplast genome sequence for E. japonica using Illumina sequencing technology. The complete chloroplast sequence is 160,467 bp in length, including a large single-copy (LSC) region of 88,716 bp, a small single-copy (SSC) region of 18,614 bp, and a pair of invert repeats (IR) regions of 26,568 bp. Plastid genome contains 142 genes, 46 protein-coding genes, 39 tRNA genes, and eight rRNA genes. Phylogenetic analysis base on 14 chloroplast genomes indicates that E. japonica forms an isolated clade and sisters to Glycosmis-Gossypium clade with strong support.

| S-EPMC7707347 | biostudies-literature

Development and characterization of 11 polymorphic microsatellite markers in Tapiscia sinensis (Staphyleaceae).

Project description:We developed and characterized five polymorphic microsatellite loci from an AC-enriched genomic library of a rare tree, Tapiscia sinensis, and six compound microsatellite primers using a dual-suppression-PCR-based approach, to investigate geographical genetic structure. • The polymorphism of these loci was assessed in 102 samples collected from three populations. The number of alleles per locus ranged from one to nine. Expected heterozygosity per locus ranged from 0.000 to 0.709 and observed heterozygosity ranged from 0.000 to 0.750. Five loci deviated from Hardy-Weinberg equilibrium after Bonferroni correction. • This set of microsatellites may be useful for investigating broad-scale genetic variation in the extant populations of the endangered tree species T. sinensis.

| S-EPMC4103118 | biostudies-literature

The complete chloroplast genome of Turpinia arguta (Staphyleaceae).

Project description:The complete chloroplast genome of Turpinia arguta was sequenced and assembled for the first time. The chloroplast genome was 160,139 bp in length, containing a large single-copy region (LSC) of 89,625 bp and a small single-copy region (SSC) of 18,262 bp, separated by a pair of inverted repeats (IRs) of 26,126 bp. The genome contained 113 unique genes, including 79 protein-coding genes, 30 tRNA genes, and four rRNA genes. Among them, 15 genes had one intron each and 3 genes containing two introns. The overall GC content was 37.4%, while the corresponding values of LSC, SSC, and IR regions were 35.4%, 31.8%, and 42.8%, respectively. Phylogenetic analysis showed that T. arguta is more closely related to Staphylea trifolia and provided new insight into the evolution of Staphyleaceae.

| S-EPMC7782190 | biostudies-literature

The complete chloroplast genome sequence of Sloanea sinensis.

Project description:Sloanea sinensis (Hance) Hu is a tree species and member of the Elaeocarpaceae family. It's an excellent commercial tree species which has a relatively high net growth as forests. Here, we report the complete chloroplast genome sequence of a Sloanea genus for the first time. The complete chloroplast sequence of S. sinensis is 158,001 bp in length, including a large single copy region (LSC: 88,481 bp) and a small single copy region (SSC: 17,481 bp), the latter of which is separated by a pair of inverted repeat regions (IRs: 26,051 bp). Phylogenetic analysis indicates that the Elaeocarpaceae is a family within the Oxalidales may be more appropriate than belongs to Malvales as traditional plant taxonomy.

| S-EPMC7889274 | biostudies-literature

The complete chloroplast genome sequence of Camellia sinensis var. sinensis cultivar Tieguanyin (Theaceae).

Project description:Camellia sinensis var. sinensis cultivar Tieguanyin (TGY) is an important Oolong tea variety in China. In this study, we reported a complete chloroplast (cp) genome based on the Illumina sequencing technology and combined de novo and reference-guided assembly strategies. The complete cp genome of 'TGY' displayed the regular quadripartite structure: a total of 157,126 bp in length, comprising a large single-copy (LSC, 86,904 bp) region, a small single-copy (SSC, 18,532 bp) region, and a pair of inverted repeats (IRs, 26,095 bp) regions. A lot of 132 predicted genes, including 87 protein-coding genes, 37 tRNA genes, and eight rRNA genes. The overall GC content is 37.3%. Maximum likelihood (ML) phylogenetic tree involving 18 cp genomes of the Camellia genus revealed a relatively independent event of local domestication among three types of cultivars. The complete cp genome of 'TGY' provides an insight into tea plants for further understanding evolutionary research on tea plants.

| S-EPMC7872547 | biostudies-literature

The complete chloroplast genome sequence of Camellia sinensis var. sinensis cultivar "Yuexiangzao".

Project description:Camellia sinensis var. sinensis cultivar "Yuexiangzao" (YXZ) was a new tea cultivar in China. In this study, we reported a complete chloroplast (CP) genome based on the DNGSEQ sequencing technology. The CP genome sequence of YXZ was 157,041 bp in length and contained a large single copy (LSC, 86,594 bp), a small single copy (SSC, 18,291 bp), and two inverted repeats (IRs, 26,078 bp). The GC contents of LSC, SSC, and two IRs were 35.31%, 30.53%, and 42.94%, respectively. The phylogenetic analysis showed that YXZ was closely related to C. sinensis cv. "Tieluohan" and C. sinensis cv. "Xinyang 10."

| S-EPMC11823394 | biostudies-literature

The complete chloroplast genome sequence of Camellia sinensis var. sinensis cultivar 'FuDingDaBaiCha'.

Project description:The complete chloroplast (cp) genome sequence of Camellia sinensis var. sinensis cultivar 'FuDingDaBaiCha' (FD), one of the key contributors to the history of tea breeding in China, was determined in this study. The cp genome of FD is 157,025 bp in length, including a large single-copy (LSC, 86,586 bp), a small single-copy (SSC, 18,277 bp), and a pair of inverted repeats (IRa and IRb, 26,081 bp). The overall GC content is 37.3%. A total of 137 genes were predicted, including 92 protein-coding genes, 37 tRNA genes, and eight rRNA genes. Phylogenetic analysis showed that FD was closely related to C. sinensis cv. 'AnHua', C. sinensis cv. 'QianCha 1', and C. sinensis cv. 'BanTianYao'. The determination of the complete cp genome sequence of FD provides a way for the subsequent study of the genetic background and phylogenetic relationships of different tea plant cultivars.

| S-EPMC9833401 | biostudies-literature

The complete chloroplast genome sequence of Hippophae rhamnoides subsp. sinensis.

Project description:The complete chloroplast genome sequence of Hippophae rahmnoides subsp. sinensis was characterized from Illumina pair-end sequencing. The chloroplast genome of H. rahmnoides subsp. sinensis was 156,355 bp in length, containing a large single-copy region (LSC) of 84,002 bp, a small single-copy region (SSC) of 19,055 bp, and two inverted repeat (IR) regions of 26,649 bp. The overall GC content is 36.6%, while the corresponding values of the LSC, SSC, and IR regions are 64.5%, 69.2%, and 60.1%, respectively. The genome contains 131 complete genes, including 88 protein-coding genes, 38 tRNA genes (29 tRNA species), and 8 rRNA genes (4 rRNA species). The neighbour-joining phylogenetic analysis showed that H. rahmnoides subsp. sinensis and H. rahmnoides clustered together as sisters to other H. rahmnoides species.

| S-EPMC7748493 | biostudies-literature

Complete chloroplast genome sequence of Annamocarya sinensis (Juglandaceae), an endangered perennial plant.

Project description:Annamocarya sinensis (Juglandaceae) is a tertiary relict tree restricted to southeastern China and northern Vietnam. Here, we first report and characterize its complete chloroplast genome based on Illumina paired-end sequencing data. The complete plastid genome was 160,065 bp, which contained inverted repeats (IR) of 25,786 bp separated by a large single-copy (LSC) and a small single copy (SSC) of 89,759 bp and 18,734 bp, respectively. The cpDNA contains 130 genes, comprising 85 protein-coding genes, 36 tRNA genes, 8 rRNA genes, and one processed pseudogene. The overall GC content of the plastome is 36.3%. The phylogenetic analysis of 18 selected chloroplast genomes demonstrated that A. sinensis was close to the species Carya kweichowensis.

| S-EPMC7707428 | biostudies-literature