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 and phylogenetic analysis of Saussurea wettsteiniana (Compositae).

ABSTRACT: Saussurea wettsteiniana is a medicinally important herb endemic to Hengduan Mountains. Here, we report and characterize the complete chloroplast genome sequence of S. wettsteiniana to provide genomic resources useful for future study. The complete chloroplast genome is 152,631 bp in length, consisting of a large single copy and a small single copy of 83,552 bp and 18,637 bp, which were separated by a pair of inverted repeats of 25,221 bp. Totally 133 genes were annotated, including 87 protein-coding genes, 36 tRNA genes, and eight rRNA genes. We also detected two pseudo-genes (ycf1 and rps19). The overall GC content of the whole genome is 37.7%. The phylogenetic tree based on 23 complete plastomes indicated that S. wettsteiniana was closely related to S. involucrata of Compositae.

SUBMITTER: Luo DL

PROVIDER: S-EPMC8205082 | biostudies-literature | 2021 Jun

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

The complete chloroplast genome and phylogenetic analysis of Saussurea wettsteiniana (Compositae).

Luo Deng-Li DL Zhang Ying-Min YM Zhang Ti-Cao TC Li Guo-Dong GD

Mitochondrial DNA. Part B, Resources 20210614 7

Saussurea wettsteiniana is a medicinally important herb endemic to Hengduan Mountains. Here, we report and characterize the complete chloroplast genome sequence of S. wettsteiniana to provide genomic resources useful for future study. The complete chloroplast genome is 152,631 bp in length, consisting of a large single copy and a small single copy of 83,552 bp and 18,637 bp, which were separated by a pair of inverted repeats of 25,221 bp. Totally 133 genes were annotated, including ...[more]

PMID: 34179496

Similar Datasets

Characterization of the complete chloroplast genome of Saussurea integrifolia (Compositae).

Project description:The complete chloroplast genome sequence of Saussurea integrifolia, a flowering plant occurring in Hengduan Mountains with high altitudes, is determined in this study. The plastome is 152,584 bp in length, with one large single-copy region of 83,497 bp, one small single-copy region of 18,646 bp, and two inverted repeat (IR) regions of 25,221 bp. It contains 123 genes, including 86 protein-coding genes, 8 ribosomal RNA, and 36 transfer RNA. Phylogenetic tree shows that this species is a sister to Arctium lappa. The published plastome within Saussurea provides significant insight for elucidating the phylogenetic relationship of taxa within tribe Compositae.

| S-EPMC7707334 | biostudies-literature

Complete chloroplast genome of Saussurea inversa (Asteraceae) and phylogenetic analysis.

Project description:Saussurea inversa Raab-Straube is a small perennial and polycarpic herb that is distributed on the rocky slopes of the Qinghai-Tibetan plateau (QTP) at an altitude of 3700-5400 meters. It has a chloroplast genome structure similar to that of other species of Saussurea. It is 152,102 bp in size, including a large single-copy (LSC) region of 83,450 bp, a small single-copy (SSC) region of 18,286 bp and a pair of inverted repeats (IRs) of 25,183 bp. The chloroplast genome of S. inversa encodes 113 genes, containing 80 protein-coding genes (PCGs), 29 tRNA and four rRNA genes. Phylogenetic analysis shows that S. inversa is clustered with S. pseudosimpsoniana and S. laniceps.

| S-EPMC7801092 | biostudies-literature

Complete Chloroplast Genomes of Saussurea katochaete, Saussurea superba, and Saussurea stella: Genome Structures and Comparative and Phylogenetic Analyses

Project description: Not available

| S-EPMC10670953 | biostudies-literature

Characterization of the complete chloroplast genome of Saussurea involuerata (Compositae), an endangered species endemic to China.

Project description:Saussurea involuerata (S. involuerata), a kind of composite and perennial herbage plant, is a rare and precious alpine medicinal plants with high medicinal value, it can regulate human's body and has health care function, therefore attracts attention of many scholars. 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 S. involucrata by Illumina paired-end reads data. The whole genome was 152,490 bp, consisting of a pair of inverted repeats of 69,041 bp, large and small single-copy regions of 69,045bp and 18,638 bp in length, respectively. The cp genome contained 134 genes, including 90 protein-coding genes, 36 tRNA genes, and 8 rRNA genes. The overall GC content of the whole genome was 37.7%. A neighbor-joining phylogenetic analysis demonstrated a close relationship between S. involuerata and Arctium lappa.

| S-EPMC7748709 | biostudies-literature

Characterization and phylogenetic analysis of the complete chloroplast genome of Saussurea sagittifolia (Asteraceae, Cardueae).

Project description:The species of Saussurea sagittifolia Y. S. Chen & S. R. Yi belongs to the family Asteraceae (Cardueae). The complete chloroplast genome of S. sagittifolia was assembled and annotated for the first time in this study. The complete chloroplast genome of S. sagittifolia was 152,535 bp, including a large single-copy (LSC) region of 83,511 bp, a small single-copy (SSC) region of 18,632 bp, and a pair of inverted repeats (IRs) of 25,196 bp. The overall GC content of the chloroplast genome was 37.7%. The chloroplast genome encoded 131 genes, including 87 protein-coding genes, 36 tRNA genes, and eight rRNA genes. Phylogenetic analysis based on complete chloroplast sequences revealed that it related closely to Saussurea medusa.

| S-EPMC10769533 | biostudies-literature

Comparative and phylogenetic analysis based on chloroplast genome of Heteroplexis (Compositae), a protected rare genus.

Project description:BackgroundHeteroplexis Chang is an endangered genus endemic to China with important ecological and medicinal value. However, due to the lack of genetic data, our conservation strategies have repeatedly been delayed by controversial phylogenetic (molecular) relationships within the genera. In this study, we reported three new Heteroplexis chloroplast (cp.) genomes (H. vernonioides, H. impressinervia and H. microcephala) to clarify phylogenetic relationships between species allocated in this genus and other related Compositae.ResultsAll three new cp. genomes were highly conserved, showing the classic four regions. Size ranged from 152,984 - 153,221 bp and contained 130 genes (85 protein-coding genes, 37 tRNA, eight rRNA) and two pseudogenes. By comparative genomic and phylogenetic analyses, we found a large-scale inversion of the entire large single-copy (LSC) region in H. vernonioides, H. impressinervia and H. microcephala, being experimentally verified by PCR. The inverted repeat (IR) regions showed high similarity within the five Heteroplexis plastomes, showing small-size contractions. Phylogenetic analyses did not support the monophyly of Heteroplexis genus, whereas clustered the five species within two differentiated clades within Aster genus. These phylogenetic analyses suggested that the five Heteroplexis species might be subsumed into the Aster genus.ConclusionOur results enrich the data on the cp. genomes of the genus Heteroplexis, providing valuable genetic resources for future studies on the taxonomy, phylogeny, and evolution of Aster genus.

| S-EPMC9773445 | biostudies-literature

Characterization of the complete chloroplast genome of Sinosenecio oldhamianus (Compositae).

Project description:The complete chloroplast (cp) genome sequence of Sinosenecio oldhamianus, a common medicinal plant is widely distributed in South China. The plastome is 150,926 bp in length, with one large single-copy region of 94,588 bp, one small single-copy region of 18,130 bp, and two inverted repeat (IR) regions of 24,852 bp. It contains 134 genes, including 87 protein-coding genes, 8 ribosomal RNA, and 37 transfer RNA. The phylogenetic tree shows that this species is a sister to the genus Ligularia. The published plastome within Sinosenecio provides significant insight for elucidating the phylogenetic relationship of taxa within tribe Compositae.

| S-EPMC7707185 | biostudies-literature

The complete chloroplast genome sequence of medicinal plant Centipeda minima (Compositae).

Project description:The complete chloroplast genome sequence of Centipeda minima (L.) A. Braun et Aschers (Compositae) has been characterized by Illumina pair-end sequencing. The chloroplast genome is 152,351 bp in length, including a pair of inverted repeats (IRs) of 25,004 bp (12.1%) and a large single copy (LSC) and a small single copy (SSC) region of 83,972 bp (55.1%) and 18,371 bp (32.8%), respectively. The chloroplast genome includes 127 genes, which contain 83 protein-coding genes, 36 transfer RNA genes, and 8 ribosomal RNA genes. The nucleotide composition is asymmetric (31.1% A, 18.5% C, 19.0% G, 31.4% T). The overall GC content of C. minima chloroplast genome is 37.5%. Phylogenetic analysis illustrates that C. minima is closely related to other Asteraceae species, including Helianthus annuus subsp. texanus, Tithonia diversifolia and Xanthium sibiricum with a strong bootstrap value of 100.

| S-EPMC8820791 | biostudies-literature

Complete Chloroplast Genome Sequence and Phylogenetic Analysis of Paeonia ostii.

Project description:Paeonia ostii, a common oil-tree peony, is important ornamentally and medicinally. However, there are few studies on the chloroplast genome of Paeonia ostii. We sequenced and analyzed the complete chloroplast genome of P. ostii. The size of the P. ostii chloroplast genome is 152,153 bp, including a large single-copy region (85,373 bp), a small single-copy region (17,054 bp), and a pair of inverted repeats regions (24,863 bp). The P. ostii chloroplast genome encodes 111 genes, including 77 protein-coding genes, four ribosomal RNA genes, and 30 transfer RNA genes. The genome contains forward repeats (22), palindromic repeats (28), and tandem repeats (24). The presence of rich simple-sequence repeat loci in the genome provides opportunities for future population genetics work for breeding new varieties. A phylogenetic analysis showed that P. ostii is more closely related to Paeonia delavayi and Paeonialudlowii than to Paeoniaobovata and Paeoniaveitchii. The results of this study provide an assembly of the whole chloroplast genome of P. ostii, which may be useful for future breeding and further biological discoveries. It will provide a theoretical basis for the improvement of peony yield and the determination of phylogenetic status.

| S-EPMC6017096 | biostudies-literature

Complete chloroplast genome sequence and phylogenetic analysis of Spathiphyllum 'Parrish'.

Project description:Spathiphyllum is a very important tropical plant used as a small, potted, ornamental plant in South China, with an annual output value of hundreds of millions of yuan. In this study, we sequenced and analyzed the complete nucleotide sequence of the Spathiphyllum 'Parrish' chloroplast genome. The whole chloroplast genome is 168,493 bp in length, and includes a pair of inverted repeat (IR) regions (IRa and IRb, each 31,600 bp), separated by a small single-copy (SSC, 15,799 bp) region and a large single-copy (LSC, 89,494 bp) region. Our annotation revealed that the S. 'Parrish' chloroplast genome contained 132 genes, including 87 protein coding genes, 37 transfer RNA genes, and 8 ribosomal RNA genes. In the repeat structure analysis, we detected 281 simple sequence repeats (SSRs) which included mononucleotides (223), dinucleotides (28), trinucleotides (12), tetranucleotides (11), pentanucleotides (6), and hexanucleotides (1), in the S. 'Parrish' chloroplast genome. In addition, we identified 50 long repeats, comprising 18 forward repeats, 13 reverse repeats, 17 palindromic repeats, and 2 complementary repeats. Single nucleotide polymorphism (SNP) and insertion/deletion (indel) analyses of the chloroplast genome of the S. 'Parrish' relative S. cannifolium revealed 962 SNPs in S. 'Parrish'. There were 158 indels (90 insertions and 68 deletions) in the S. 'Parrish' chloroplast genome relative to the S. cannifolium chloroplast genome. Phylogenetic analysis of five species found S. 'Parrish' to be more closely related to S. kochii than to S. cannifolium. This study identified the characteristics of the S. 'Parrish' chloroplast genome, which will facilitate species identification and phylogenetic analysis within the genus Spathiphyllum.

| S-EPMC6808432 | biostudies-literature