Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

The complete chloroplast genome of Atraphaxis jrtyschensis (polygonaceae), an endemic and endangered desert shrub to Xinjiang, China.

ABSTRACT: Atraphaxis jrtyschensis (Polygonacae) is an endangered desert shrub endemic to China in Xinjiang province with great ecological importance for sand fixation. However, its genomic resources are still very limited. Here, we generated the first chloroplast (cp) genome of A. jrtyschensis using genome skimming sequencing. The whole cp genome is 164,192?bp and comprises 130 genes, including 83 protein-coding genes, 37 tRNA genes, 8 rRNA genes, and 2 pseudogenes (rpl23). The overall GC content of A. jrtyschensis cp genome is 37.5%. The phylogenic analysis placed A. jrtyschensis at the base of Trib Rumiceae, which contained the genera Rheum and Oxyria. This study will be useful for future researches to investigate the conservation genetics and potential applications in sand fixation of the endangered desert shrub.

SUBMITTER: Wang Q

PROVIDER: S-EPMC7799618 | biostudies-literature | 2018 Sep

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

The complete chloroplast genome of Atraphaxis jrtyschensis (polygonaceae), an endemic and endangered desert shrub to Xinjiang, China.

Wang Qiuyan Q Yuan Zhenyan Z Zhang Yue Y Mamtimin Sulayman S Tian Xinmin X

Mitochondrial DNA. Part B, Resources 20180922 2

Atraphaxis jrtyschensis (Polygonacae) is an endangered desert shrub endemic to China in Xinjiang province with great ecological importance for sand fixation. However, its genomic resources are still very limited. Here, we generated the first chloroplast (cp) genome of A. jrtyschensis using genome skimming sequencing. The whole cp genome is 164,192 bp and comprises 130 genes, including 83 protein-coding genes, 37 tRNA genes, 8 rRNA genes, and 2 pseudogenes (rpl23). The overal ...[more]

PMID: 33474434

Similar Datasets

The complete chloroplast genome sequence of Ammodendron bifolium (Fabaceae), an endangered desert shrub from China

Project description: Not available

| S-EPMC10913713 | biostudies-literature

Complete chloroplast genome of Prunus canescens: an endemic shrub in China.

Project description:Prunus canescens is an endemic cherry species in China, which is distributed in Shaanxi, Gansu, Hubei, and Sichuan provinces of China. The chloroplast (cp) genome of P. canescens is 157,890 bp in size containing 125 unique genes, including 8 rRNA genes, 37 tRNA genes, and 80 protein-coding genes (PCGs). Phylogenetic analysis exhibited that P. canescens is most related to P. pseudocerasus.

| S-EPMC7687575 | biostudies-literature

The complete chloroplast genome of Salix psamaphila, a desert shrub in northwest China.

Project description:Salix psammophila C. Wang & Chang Y. Yang is a desert plant species distributed in Northwest China. Here, we report the complete choroplast genome sequences in order to enrich its genetic resource. The total genome is 155,278?bp in length and contains a typical quadripartite structure, including a large single copy (LSC) region of 84,457?bp, a small single copy (SSC) region of 15,891?bp, and a pair of inverted repeats (IRs) of 27,465?bp. There were 130 genes in the genome, including 85 protein-coding genes, 37 tRNA genes and eight rRNA genes. The overall CG content in the plastome of S. psammophila is 36.72%. The phylogenetic tree based on 18 complete plastomes of Salicaceae support close relationships among S. psammophila, Salix taoensis, and Salix rehderiana.

| S-EPMC7707305 | biostudies-literature

The complete chloroplast genome of Salsola abrotanoides (Chenopodiaceae), a desert halophyte shrub in China.

Project description:Salsola abrotanoides, one of the dominant plant species of desert vegetation, adapts well to the arid, saline, and alkaline environment in the Qinghai-Tibetan Plateau. Here, we reported the complete chloroplast sequence and characters of S. abrotanoides based on the Illumina NovaSeq Platform. The chloroplast genome is 151,622 bp in length, containing a pair of inverted repeated (IR) regions of 23,701 bp, a large single copy (LSC) region of 84,658 bp, and a small single copy (SSC) region of 19,562 bp. And the chloroplast genome sequence encodes 130 genes totally, including 85 mRNA genes, 37 tRNA genes, and 8 rRNA genes. S. abrotanoides is the first species of Genus Salsola and the chloroplast sequence will provide a valuable resource for the phylogenetic studies of Chenopodiaceae.

| S-EPMC7995892 | biostudies-literature

The complete chloroplast genome of Forsythia mira, an endemic medicinal shrub in China.

Project description:Forsythia mira M. C. Chang (Oleaceae) is an endemic medicinal shrub in China. In this study, we first characterized its whole plastid genome sequence using the Illumina sequencing platform. The plastid genome was 156,485 bp in length, comprising of a large single copy (LSC) region of 87,223 bp, a small single copy (SSC) region of 17,830 bp, and two inverted repeat regions (IRs) of 51,432 each. The genome of F. mira contained 133 genes, including 86 protein-coding genes, 37 transfer RNAs (tRNA), and 8 ribosomal RNAs (rRNA). The phylogenetic analysis showed that F. mira was placed as a sister to the congeneric F. suspensa.

| S-EPMC7720978 | biostudies-literature

The complete chloroplast genome of Vaccinium fragile (Vacciniaceae), a shrub endemic to China.

Project description:Vaccinium fragile, an endemic species in China, is a plant of the family Vacciniaceae. It is an evergreen shrubby tree distributed in Sichuan, Guizhou, Yunnan, and Tibet province of China. The chloroplast (cp) genome of V. fragile is 169,480 bp in size containing 123 unique genes, including 8 rRNA genes, 38 tRNA genes, and 77 protein-coding genes (PCGs). Phylogenetic analysis exhibited that both V. macrocarpon and V. fragile were phylogenetically closer to Arbutus unedo than other taxa in this study.

| S-EPMC7687607 | biostudies-literature

The complete chloroplast genome of Sauvagesia rhodoleuca, an endangered species endemic to China.

Project description:Sauvagesia rhodoleuca is an endangered and national key protected species of China, with limited natural distribution in Guangdong and Guangxi, Southern China. Here we reported the first complete chloroplast genome of S. rhodoleuca using genome skimming approach. The chloroplast genome is 157,300 bp in length, with a large single-copy region (LSC) of 86,021 bp and a small single-copy region (SSC) of 18,137 bp separated by a pair of inverted repeats (IRs) of 26,571 bp. It encodes 112 unique genes, including 80 protein-coding genes, 28 transfer RNA genes, and four ribosomal RNA genes. Phylogenetic analysis results strongly supported that S. rhodoleuca was closely related to Medusagyne oppositifolia.

| S-EPMC8284140 | biostudies-literature

The complete chloroplast genome of Zelkova schneideriana (Rosales: Ulmaceae), an Endangered species endemic to China.

Project description:Zelkova schneideriana Hand.-Mazz. (Ulmaceae) is an endangered species endemic to China. In this study, we reported its complete chloroplast (cp) genome based on Illumina pair-end sequencing. The whole genome was 158,999 bp long, consisting of a pair of inverted repeat (IR) regions of 26,427 bp, a large single copy (LSC) region of 87,397 bp and a small single copy (SSC) region of 18,748 bp. The cp genome contained 133 genes, including 88 protein-coding genes (80 PCG species), 37 tRNA genes (30 tRNA species), and eight rRNA genes (4 rRNA species). The overall G+C content of the whole genome was 35.6%, and the corresponding values of the LSC, SSC, and IR regions were 33.0, 28.3, and 42.4%, respectively. The maximum likelihood phylogenetic analysis of 25 selected chloroplast genomes demonstrated that Z. schneideriana was closely related to Ulmus macrocarpa and Ulmus pumila.

| S-EPMC7800157 | biostudies-literature

The complete chloroplast genome sequence of Barthea barthei (Melastomataceae), a shrub endemic to southern China.

Project description:The plant genus Barthea is monotypic, comprising of only a single species (Barthea barthei), and is endemic to southern China. In this study, we report the complete chloroplast genome of B. barthei, assembled from whole-genome high-throughput sequencing data, as a resource for future studies on the taxonomy and evolution of Barthea. The chloroplast genome was 155,951 bp in length, with a large single-copy (LSC) region of 85,882 bp, a small single-copy (SSC) region of 16,445 bp, separated by two inverted repeat (IR) regions of 26,812 bp each. It was predicted to contain a total of 130 genes, with an overall GC content of 36.99%. Phylogenetic analysis placed B. barthei closest to Opisthocentra sp. in Melastomataceae.

| S-EPMC7799996 | biostudies-literature

Complete chloroplast genome of Vincetoxicum hainanense (Apocynaceae: Asclepiadoideae), an endangered liana endemic to China.

Project description:Vincetoxicum hainanense is an endangered liana species endemic to China. Habitat destruction coupled with difficulties in natural pollination has reduced its population size over time. As present studies have focussed more on breeding programmes instead of molecular aspects, here we reported on the complete chloroplast (cp) genome sequence of V. hainanense. The cp genome is 161,280 bp in size and includes two inverted repeat (IR) regions of 24,884 bp each, which is separated by a large-single copy (LSC) region of 92,084 bp and a small-single copy (SSC) region of 19,428 bp. A total of 131 genes were predicted, including 37 tRNA, 8 rRNA, and 86 protein-coding genes. Phylogenetic analysis showed that V. hainanense is clustered with other Apocynaceae species and sister to Biondia chinensis.

| S-EPMC7707277 | biostudies-literature