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 of Craigia yunnanensis, an endangered plant species with extremely small populations (PSESP) from South China.

ABSTRACT: Craigia yunnanensis is an Endangered tree species, enlisted in the national plant species with extremely small population (PSESP) of China for urgent protection. The chloroplast genome is characterized using Illumina pair-end sequencing data. The whole chloroplast genome is 163,166?bp in length and consists of a pair of inverted repeat (IR) regions of 25,573?bp each, which are separated by the large single copy (LSC: 91,580?bp) region and small single copy (SSC: 20,440?bp) regions. The chloroplast genome encodes 113 unique genes, including 79 protein-coding genes (PCGs), 30 tRNA, and 4 rRNA genes. The overall GC content of the whole chloroplast genome is 36.4%. The phylogenetic tree revealed a close relationship between C. yunnanensis and Tilia species of Malvaceae family.

SUBMITTER: Wariss HM

PROVIDER: S-EPMC7706985 | biostudies-literature | 2019 Jul

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

The complete chloroplast genome of Craigia yunnanensis, an endangered plant species with extremely small populations (PSESP) from South China.

Wariss Hafiz Muhammad HM Chen Yaling Y Yang Jing J

Mitochondrial DNA. Part B, Resources 20190723 2

Craigia yunnanensis is an Endangered tree species, enlisted in the national plant species with extremely small population (PSESP) of China for urgent protection. The chloroplast genome is characterized using Illumina pair-end sequencing data. The whole chloroplast genome is 163,166 bp in length and consists of a pair of inverted repeat (IR) regions of 25,573 bp each, which are separated by the large single copy (LSC: 91,580 bp) region and small single copy (SSC: 20,440 bp) regions. The ch ...[more]

PMID: 33365708

Similar Datasets

The complete chloroplast genome of Horsfieldia hainanensis, an Endangered species with extremely small populations.

Project description:Horsfieldia hainanensis is an Endangered species with extremely small populations, inhabiting the dense forest in ravines. It has high development and utilization value in the seed oil, fatty acids, volatile oils, and liposoluble constituent. In this study, the complete chloroplast genome of Horsfieldia hainanensis was sequenced. It is 155,774 bp in size with a typical quadripartite structure: a large single-copy (LSC) region of 87,124 bp, a small single-copy (SSC) region of 20,612 bp, and 2 inverted repeat (IR) regions of 24,020 bp. The genome contains 117 genes, including 75 protein-coding genes, 34 tRNA genes, and 8 rRNA genes, 13 genes have one intron and 3 three genes have two introns. The overall GC contents of the chloroplast genome was 39.1%. The phylogenetic tree based 11 complete chloroplast genome sequences of Magnoliales shows that H. hainanensis is closely related to Horsfieldia pandurifolia.

| S-EPMC7706491 | 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

The complete chloroplast genome sequence of Pellacalyx yunnanensis: an endangered species in China.

Project description:Pellacalyx yunnanensis is an endangered plant species occurring in Yunnan province of China. The first complete chloroplast genome (cpDNA) sequence of P. yunnanensis was determined from Illumina HiSeq pair-end sequencing data in this study. The cpDNA is 163,743?bp in length, contains a large single-copy region (LSC) of 91,075?bp and a small single-copy region (SSC) of 18,668?bp, which were separated by a pair of inverted repeats (IR) regions of 27,000?bp. The genome contains 128 genes, including 83 protein-coding genes, 8 ribosomal RNA genes, and 37 transfer RNA genes. The overall GC content of the whole genome is 35.7%, and the corresponding values of the LSC, SSC, and IR regions are 33.0%, 29.6%, and 42.3%, respectively. Further phylogenomic analysis showed that P. yunnanensis clustered in a unique clade in family Rhizophoraceae.

| S-EPMC7707691 | biostudies-literature

The complete chloroplast genome of Cephalotaxus lanceolata (Taxaceae), a plant species with extremely small populations.

Project description:Cephalotaxus lanceolata K. M. Feng ex C. Y. Cheng W. C. Cheng and L. K. Fu (Taxaceae) is a threatened plant species and a typical plant species with extremely small populations (PSESP) with only four individuals found in Gaoligong Mountain. With the aim of providing data for future conservation efforts, we sequenced the whole chloroplast (cp) genome of C. lanceolata. The results showed that the plastid genome is 136,404 bp in size. In total, 116 unique genes were annotated, including 83 protein-coding genes, 29 tRNA genes, and 4 rRNA genes. The total GC content was 35.1%. We performed phylogenetic analyses based on 12 cp genomes of Taxaceae, and we determined that the genus Cephalotaxus forms a sister group to Taxus and Pseudotaxus.

| S-EPMC7995812 | biostudies-literature

De novo genome assembly of the endangered Acer yangbiense, a plant species with extremely small populations endemic to Yunnan Province, China.

Project description:BACKGROUND:Acer yangbiense is a newly described critically endangered endemic maple tree confined to Yangbi County in Yunnan Province in Southwest China. It was included in a programme for rescuing the most threatened species in China, focusing on "plant species with extremely small populations (PSESP)". FINDINGS:We generated 64, 94, and 110 Gb of raw DNA sequences and obtained a chromosome-level genome assembly of A. yangbiense through a combination of Pacific Biosciences Single-molecule Real-time, Illumina HiSeq X, and Hi-C mapping, respectively. The final genome assembly is ?666 Mb, with 13 chromosomes covering ?97% of the genome and scaffold N50 sizes of 45 Mb. Further, BUSCO analysis recovered 95.5% complete BUSCO genes. The total number of repetitive elements account for 68.0% of the A. yangbiense genome. Genome annotation generated 28,320 protein-coding genes, assisted by a combination of prediction and transcriptome sequencing. In addition, a nearly 1:1 orthology ratio of dot plots of longer syntenic blocks revealed a similar evolutionary history between A. yangbiense and grape, indicating that the genome has not undergone a whole-genome duplication event after the core eudicot common hexaploidization. CONCLUSION:Here, we report a high-quality de novo genome assembly of A. yangbiense, the first genome for the genus Acer and the family Aceraceae. This will provide fundamental conservation genomics resources, as well as representing a new high-quality reference genome for the economically important Acer lineage and the wider order of Sapindales.

| S-EPMC6629541 | biostudies-literature

The complete chloroplast genome of Cycas Szechuanensis, an extremely endangered species.

Project description:In this study, we determined the complete chloroplast genome of Cycas szechuanensis (Cycadaceae, Cycas) using the Illumina sequencing data. The genome is 162,083?bp in length, including a pair of inverted repeats (IRs) of 25,003?bp each, which are separated by a large single-copy region (LSC) and a small single-copy region (SSC) with the size of 88,970 and 23,108?bp, respectively. The genome comprises 131 encoded genes in total, including 86 protein-coding genes (82 PCG species), 8 ribosomal RNA genes (4 rRNA species), and 37 transfer RNA genes (30 tRNA species). The overall GC content of the C. szechuanensis chloroplast genome is 39.42%, while the LSC, SSC, and IRs occupy 38.70, 42.03 and 36.52%, respectively. Based on complete chloroplast genome sequences from 13 species, we reconstructed the phylogenetic relationship of the 13 species and found that C. szechuanensis is closely related to C. debaoensis.

| S-EPMC7800925 | biostudies-literature

Complete chloroplast genome sequence of an endangered plant Oreocharis cotinifolia (Gesneriaceae) from Guangxi, China.

Project description:Oreocharis cotinifolia is a plant herb with a small population and narrow distribution range in southeast China. It is listed as one of the class 1 key protected wild plants in China and designated as a critically endangered species. In this study, we assembled the complete chloroplast genome of O. cotinifolia using data from high-throughput Illumina sequencing. The cp genome is 153,577 bp in length and includes two inverted repeats (IRs) of 25,292 bp, separated by a large single-copy region (LSC) and a small single-copy region (SSC) that are 84,898 bp and 18,095 bp, respectively. The GC content is 37.42%. The genome encodes 128 functional genes, including 87 protein-coding, 37 tRNA, and 4 rRNA genes. Maximum likelihood analysis showed that O. cotinifolia is closely related to the congeneric O. mileensis. The complete chloroplast genome will contribute to further studies on phylogeny and conservation of O. cotinifolia and related taxa in Oreocharis of Gesneriaceae.

| S-EPMC8451614 | biostudies-literature

The first complete chloroplast genome of Coptis quinquesecta, a critically endangered medicinal plant in China.

Project description:Coptis quinquesecta, serving as a valuable medicinal plant, is a critically endangered and national key protected species of China. In the past, researches regarding this species mainly focused on its medicinal ingredients, whereas little effort has been made on its genetic information. Here we determined the first complete chloroplast genome of C. quinquesecta using genome skimming approach. The cp genome was 154,549?bp long, with a large single-copy region (LSC) of 84,409?bp and a small single-copy region (SSC) of 17,256?bp separated by a pair of inverted repeats (IRs) of 26,442?bp. It encodes 113 unique genes, including 79 protein-coding genes, 30 transfer RNA genes, and four ribosomal RNA genes. Besides, we reconstructed the phylogeny of Ranunculaceae based on the previously reported cp genomes of related taxa. A maximum likelihood (ML) phylogenetic analysis strongly supported the monophyly of Hydrastidoideae, Coptidoideae, and Thalictroideae, while Ranunculoideae was found to be paraphyletic.

| S-EPMC7799926 | biostudies-literature

The complete chloroplast genome of Phellodendron chinense (Rutaceae), an Endangered medicinal plant in southern China.

Project description:Phellodendron chinense is an Endangered medicinal plant in southern China. In this study, the complete chloroplast genome sequence of P.chinense was characterized by de novo assembly. The length of the whole chloroplast genome was 158,537 bp, containing a large single copy region (LSC) of 86,250 bp and a small single copy region (SSC) of 18,287 bp, which were separated by a pair of 27,000 bp inverted repeat regions (IRs). The sequence contains 114 unique genes, including 30 tRNA, 4 rRNA, and 80 protein-coding genes. The overall GC content of the chloroplast genome is 38.4% and those in the LSC, SSC, and IR regions are 36.6, 33.2, and 42.9%, respectively. The phylogenetic analysis based on reported chloroplast sequences of Rutaceae showed that P. chinense is sister to P. amurense, consisting a monophyletic group, and that Phellodendron is closely related to Zanthoxylum.

| S-EPMC7703704 | biostudies-literature

The complete chloroplast genome sequence of Abies beshanzuensis, a highly endangered fir species from south China.

Project description:Abies beshanzuensis is critically endangered and endemic to Zhengjiang province of China, with only three surviving individuals. In present study, we reported the complete chloroplast (cp) genome of Abies beshanzuensis. The complete chloroplast genome size is 121,399 bp. In total, 114genes were identified, including 68 peptide-encoding genes, 35 tRNA genes, four rRNA genes, six open reading frames and one pseudogene. Loss of ndh genes was also identified in the genome of A. beshanzuensis like other genomes in the family Pinaceae. Thirteen genes contain one (11 genes) or two (rps12 and ycf3 genes) introns. Inverted repeat sequences located in 42-kb inversion points (1186 bp) include trnS-psaM-ycf12-trnG genes. In phylogenetic analysis, the tree confirms that the four Abies species are strongly supported as monophyletic. The complete plastome of A. beshanzuensis will provide potential genetic resources for further conservation and evolutionary studies of this highly endangered species.

| S-EPMC7799716 | biostudies-literature