Browse
Submit Data
Databases
API
Help

Dataset Information

23 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Complete chloroplast genome features and phylogenetic implications of Cardamine fallax (O. E. Schulz) Nakai.

ABSTRACT: Cardamine fallax (O. E. Schulz) Nakai. is a perennial plant distributed in Eastern Asia. However, no extensive genomic studies are available on C. fallax. In this paper, the authors describe the complete chloroplast (cp) genome of C. fallax and its phylogenetic analysis. The cp genome is 154,797 bp in length with 36.3% GC content and consists of a pair of inverted repeats (IRs) of 26,521 bp that separated a large single-copy (LSC) region of 83,817 bp and a small single-copy (SSC) region of 17,938 bp. It was found to contain 113 unique genes, of which 80 were protein-coding genes, 29 were transfer RNAs, and four were ribosomal RNAs. Also, six PCGs, eight tRNA and four rRNA genes were duplicated in the IR region and one gene as a pseudogene. Phylogenetic analysis showed that all Cardamine species are highly conserved, and C. fallax was associated with the sister clade C. amaraeformis and C. parviflora.

SUBMITTER: Raman G

PROVIDER: S-EPMC8405073 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

The complete chloroplast genome of an endemic plant to Korea, Cardamine amaraeformis Nakai.: genome structure and phylogenetic analysis.

Project description:The plant Cardamine amaraeformis Nakai. is considered an endemic plant to Korea. However, due to the similar morphological characteristics of C. amaraeformis with C. scutata, it is not easy to distinguish these two species. Here, the complete chloroplast genome of C. amaraeformis was sequenced and characterized. The chloroplast genome of C. amaraeformis was 155,598 bp in length, comprising a large single-copy (LSC) region of 84,574 bp and a small single-copy (SSC) region of 17,976 bp and a pair of inverted repeats (IRs) of 26,524 bp. The genome contained 131 genes, including 86 protein-coding (PCGs), 37 tRNA and 8 rRNA genes. Of those, 6 PCGs, 8 tRNA and 4 rRNA genes were duplicated in the IR region and one gene was a pseudogene. The GC content of the C. amaraeformis chloroplast genome was 36.3%. Phylogenetic analysis revealed that all Cardamine species formed a monophyletic clade and C. amaraeformis was closely associated with C. parviflora. Therefore, the present study could help to distinguish C. scutata and resolve the phylogenetic relationships among the Cardamine lineage.

| S-EPMC8405106 | biostudies-literature

The complete chloroplast genome of Atractylodes koreana (Nakai) Kitam and its phylogenetic analysis.

Project description:Atractylodes koreana (Nakai) Kitam is a perennial herb of Asteraceae, mainly distributed in China and Korea, which is the main adulterant of traditional herbal medicine 'Cangzhu'. In the present study, we reported the complete chloroplast (cp) genome of A. koreana with the total length of 153,232 bp, which is consisted of four regions, including one large single copy (LSC) region of 84,250 bp, one small single copy (SSC) region of 18,690 bp, and two inverted repeat regions (IRa and IRb) of 25,146 bp. The GC content of the complete cp genome is 37.7%. A total of 110 unique genes were annotated, comprising 79 protein-coding genes, 27 transfer RNA (tRNA) genes and four ribosome RNA (rRNA) genes. Moreover, nine protein-coding genes contained one intron and three protein-coding genes (clpP, ycf3, and rps12) contained two introns. The phylogenetic analysis indicated that A. koreana is a sister group of A. chinensis and A. lancea.

| S-EPMC8218844 | biostudies-literature

Complete chloroplast genome features and phylogenetic analysis of Eruca sativa (Brassicaceae).

Project description:Eruca sativa Mill. (Brassicaceae) is an important edible vegetable and a potential medicinal plant due to the antibacterial activity of its seed oil. Here, the complete chloroplast (cp) genome of E. sativa was de novo assembled with a combination of long PacBio reads and short Illumina reads. The E. sativa cp genome had a quadripartite structure that was 153,522 bp in size, consisting of one large single-copy region of 83,320 bp and one small single-copy region of 17,786 bp which were separated by two inverted repeat (IRa and IRb) regions of 26,208 bp. This complete cp genome harbored 113 unique genes: 79 protein-coding genes, 30 tRNA genes, and four rRNA genes. Forty-nine long repetitive sequences and 69 simple sequence repeats were identified in the E. sativa cp genome. A codon usage analysis of the E. sativa cp genome showed a bias toward codons ending in A/T. The E. sativa cp genome was similar in size, gene composition, and linearity of the structural region when compared with other Brassicaceae cp genomes. Moreover, the analysis of the synonymous (Ks) and non-synonymous (Ka) substitution rates demonstrated that protein-coding genes generally underwent purifying selection pressure, expect ycf1, ycf2, and rps12. A phylogenetic analysis determined that E. sativa is evolutionarily close to important Brassica species, indicating that it may be possible to transfer favorable E. sativa alleles into other Brassica species. Our results will be helpful to advance genetic improvement and breeding of E. sativa, and will provide valuable information for utilizing E. sativa as an important resource to improve other Brassica species.

| S-EPMC7954331 | biostudies-literature

The complete chloroplast genome of Dryopteris crassirhizoma Nakai.

Project description:Dryopteris crassirhizoma Nakai is a fern plant with important evolutionary and medicinal values. Herein, we assembled the complete chloroplast genome of D. crassirhizoma by next-generation sequencing technology. The complete chloroplast genome of D. crassirhizoma was 153,355 bp in length, and the GC content was 42.86%; the genome consisted of a pair of inverted repeats (IRs, 23,470 bp), a small single copy region (SSC, 21,570 bp) and a large single copy region (LSC, 84,854 bp). The genome contained 111 genes, namely, 73 protein-coding genes, 34 tRNA genes and four rRNA genes. The phylogenetic analysis suggested that both D. crassirhizoma and D. decipiens from Dryopteridaceae were most closely related to Lepisorus clathratus from Polypodiaceae.

| S-EPMC8168769 | biostudies-literature

Comparative Analysis of the Chloroplast Genome of Cardamine hupingshanensis and Phylogenetic Study of Cardamine.

Project description:Cardamine hupingshanensis (K. M. Liu, L. B. Chen, H. F. Bai and L. H. Liu) is a perennial herbal species endemic to China with narrow distribution. It is known as an important plant for investigating the metabolism of selenium in plants because of its ability to accumulate selenium. However, the phylogenetic position of this particular species in Cardamine remains unclear. In this study, we reported the chloroplast genome (cp genome) for the species C. hupingshanensis and analyzed its position within Cardamine. The cp genome of C. hupingshanensis is 155,226 bp in length and exhibits a typical quadripartite structure: one large single copy region (LSC, 84,287 bp), one small single copy region (17,943 bp) and a pair of inverted repeat regions (IRs, 26,498 bp). Guanine-Cytosine (GC) content makes up 36.3% of the total content. The cp genome contains 111 unique genes, including 78 protein-coding genes, 29 tRNA genes and 4 rRNA genes. A total of 115 simple sequences repeats (SSRs) and 49 long repeats were identified in the genome. Comparative analyses among 17 Cardamine species identified the five most variable regions (trnH-GUG-psbA, ndhK-ndhC, trnW-CCA-trnP-UGG, rps11-rpl36 and rpl32-trnL-UAG), which could be used as molecular markers for the classification and phylogenetic analyses of various Cardamine species. Phylogenetic analyses based on 79 protein coding genes revealed that the species C. hupingshanensis is more closely related to the species C. circaeoides. This relationship is supported by their shared morphological characteristics.

| S-EPMC9690686 | biostudies-literature

Complete chloroplast genome sequence of Fagopyrum dibotrys: genome features, comparative analysis and phylogenetic relationships.

Project description:Fagopyrum dibotrys, belongs to Polygonaceae family, is one of national key conserved wild plants of China with important medicinal and economic values. Here, the complete chloroplast (cp) genome sequence of F. dibotrys is reported. The cp genome size is 159,919?bp with a typical quadripartite structure and consisting of a pair of inverted repeat regions (30,738?bp) separated by large single copy region (85,134?bp) and small single copy region (13,309?bp). Sequencing analyses indicated that the cp genome encodes 131 genes, including 80 protein-coding genes, 28 tRNA genes and 4 rRNA genes. The genome structure, gene order and codon usage are typical of angiosperm cp genomes. We also identified 48 simple sequence repeats (SSR) loci, fewer of them are distributed in the protein-coding sequences compared to the noncoding regions. Comparison of F. dibotrys cp genome to other Polygonaceae cp genomes indicated the inverted repeats (IRs) and coding regions were more conserved than single copy and noncoding regions, and several variation hotspots were detected. Coding gene sequence divergence analyses indicated that five genes (ndhK, petL rpoC2, ycf1, ycf2) were subject to positive selection. Phylogenetic analysis among 42 species based on cp genomes and 50 protein-coding genes indicated a close relationship between F. dibotrys and F. tataricum. In summary, the complete cp genome sequence of F. dibotrys reported in this study will provide useful plastid genomic resources for population genetics and pave the way for resolving phylogenetic relationships of order Caryophyllales.

| S-EPMC6098159 | biostudies-literature

The complete chloroplast genome sequence of Zelkova sinica and phylogenetic implications in Rosales

Project description:Abstract Zelkova sinica is a popular landscape plant in China because of its wide adaptation, strong disease resistance, large crown and beautiful fall color. Here, we assembled the complete chloroplast (cp) genome of Z. sinica based on genome skimming data. The cp genome is 158,924 bp in length including two copies of inverted region (IR, 26,427 bp) separated by the large single copy (LSC, 87,318 bp) and small single copy (SSC, 18,752 bp) regions. It encodes 111 unique genes, containing 77 protein-coding genes, 30 tRNA genes, and 4 rRNA genes, with 18 duplicated genes in the IR regions. Phylogenetic analysis shows that Z. sinica is sister to Z. schneideriana in Ulmaceae family.

| S-EPMC8567943 | biostudies-literature

The complete chloroplast genome sequence of Hosta capitata (Koidz.) Nakai (Asparagaceae).

Project description:Hosta capitata (Koidz.) Nakai is an herbaceous perennial plant belonging to the Asparagaceae family and has become a popular ornamental plant. In this study, the chloroplast genome sequence of H. capitata was completed by de novo assembly with whole genome sequence data. The chloroplast genome of H. capitata is 156,416 bp in length, which is composed of a large single-copy (LSC) of 84,788 bp, a small single-copy (SSC) of 18,206 bp, and a pair of inverted repeat regions (IRa and IRb) of 26,711 bp, as four distinct parts. In total, 114 genes were identified including 80 protein-coding genes, 30 tRNA genes, and four rRNA genes. The phylogenetic analysis revealed that H. capitata has a close relationship with other Hosta species, H. minor and H. ventricosa, but is farther than the distance between them.

| S-EPMC7799732 | biostudies-literature

The complete chloroplast genome sequence of Dendrobium densiflorum and its phylogenetic implications.

Project description:Dendrobium is one of the largest genera in Orchidaceae with approximately 1500 species. Many of them have been used as Traditional Chinese Medicine (TCM) for hundreds of years. Here, the first complete chloroplast genome sequence of D. densiflorum was reported and characterized. The complete cpDNA of D. densiflorum is a circular molecule of 153,122 bp, which contains 76 protein-coding genes, 30 tRNA genes, and four rRNA genes. Our phylogenetic analysis indicated that the newly sequenced cpDNA of D. densiflorum could be used for the phylogenetic study of Dendrobium species.

| S-EPMC7782869 | biostudies-literature

Characterization of the complete chloroplast genome sequence of Dalbergia species and its phylogenetic implications.

Project description:The pantropical plant genus Dalbergia comprises approximately 250 species, most of which have a high economic and ecological value. However, these species are among the most threatened due to illegal logging and the timber trade. To enforce protective legislation and ensure effective conservation of Dalbergia species, the identity of wood being traded must be accurately validated. For the rapid and accurate identification of Dalbergia species and assessment of phylogenetic relationships, it would be highly desirable to develop more effective DNA barcodes for these species. In this study, we sequenced and compared the chloroplast genomes of nine species of Dalbergia. We found that these chloroplast genomes were conserved with respect to genome size, structure, and gene content and showed low sequence divergence. We identified eight mutation hotspots, namely, six intergenic spacer regions (trnL-trnT, atpA-trnG, rps16-accD, petG-psaJ, ndhF-trnL, and ndhG-ndhI) and two coding regions (ycf1a and ycf1b), as candidate DNA barcodes for Dalbergia. Phylogenetic analyses based on whole chloroplast genome data provided the best resolution of Dalbergia, and phylogenetic analysis of the Fabaceae showed that Dalbergia was sister to Arachis. Based on comparison of chloroplast genomes, we identified a set of highly variable markers that can be developed as specific DNA barcodes.

| S-EPMC6938520 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data