Browse
Submit Data
Databases
API
Help

Dataset Information

39 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 | 2021

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

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

Raman Gurusamy G Park SeonJoo S

Mitochondrial DNA. Part B, Resources 20210825 9

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 smal ...[more]

PMID: 34471691

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

The complete chloroplast genome of Sparganium fallax (Typhaceae).

Project description:Sparganium fallax is an aquatic perennial herb distributed in eastern Asia. The complete chloroplast genome of S. fallax was sequenced and assembled. The genome size was 161,838 bp in length with 36.8% GC content. Its quadripartite structure consisted of the large single copy (LSC, 89,042 bp) and small single copy (SSC, 18,774bp) regions, separated by a pair of inverted repeats (IRS) of 27,011bp. The genome contained 114 genes, including 80 protein-coding genes, 30 tRNA genes, and four rRNA genes. The phylogenetic analysis within order Poales including three Sparganium species showed that Sparganium is monophyletic and most closely related to Typha.

| S-EPMC8218840 | 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 of Nyctocalos pinnatum: chloroplast features and phylogenetic relationships within Bignoniaceae.

Project description:Nyctocalos is a genus of flowering lianas belonging to the family Bignoniaceae, and occurring from South-Central China to Malesia. In this study, we assembled the first complete chloroplast genome of N. pinnatum. The total length of the chloroplast genome is 159591 bp, with a GC content of 38.04%, which includes a pair of inverted repeats of 30,480 bp, a small single-copy region of 12,774 bp and a large single-copy region of 85,857 bp. The chloroplast genome contains 135 genes, consisting of 89 protein-coding genes, 38 transfer RNAs, and 8 ribosomal RNAs. We constructed a phylogenomic tree with representative chloroplast genomes from Bignoniaceae. N. pinnatum is revealed to be sister to Oroxylum in the tribe Oroxyleae, with a high bootstrap support. This is the first chloroplast genome assembled in Nyctocalos, and it provides essential information for further ecology and evolutionary studies in this genus and Bignoniaceae.

| S-EPMC9225756 | 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 of Gynura japonica and its phylogenetic implications.

Project description:Gynura japonica (Asteraceae) is a folk herbal medicine with multi-pharmacological functions involving analgesic, hemostatic and antiangiogenic activities. The study was conducted to assemble the complete chloroplast (cp) genome of G. japonica through a genome-skimming approach. The assembled cp genome was 151,023 bp in size, with 62.8% AT content, consisting of a large single copy (LSC) of 83,185 bp, two copies of inverted repeat (IRa and IRb) of 24,847 bp, and a small single copy (SSC) of 18,144 bp. The cp genome of G. japonica contained 133 genes, including eight ribosomal RNA genes (rRNAs), 37 transfer RNA genes (tRNAs), 86 protein-coding genes (PCGs), and two pseudogenes (ψycf1 and ψrps19). Our phylogenomic analysis based on whole plastid genomes strongly supports G. japonica is a sister to the clade including Crassocephalum crepidioides and Jacobaea vulgaris.

| S-EPMC9341369 | 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