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 Hippeastrum rutilum (Ker-Gawl.) Herb.

ABSTRACT: Hippeastrum rutilum (Ker-Gawl.) Herb. is a high-end ornamental flower in the family Amaryllidaceae. In this study, the complete chloroplast genome sequence of H. rutilum (Ker-Gawl.) Herb. was determined from Illumina pair-end sequencing data. The sequencing results indicated the complete chloroplast genome sequence of H. rutilum (Ker-Gawl.) Herb. 162,696 base pairs (bp) in length, including one large single-copy region (LSC, 86,933 bp), one small single-copy region (SSC, 5418 bp), and a pair of inverted repeat regions (IRs) of 34,932 bp. Besides, the complete chloroplast genome contained 128 genes, including 82 protein-coding genes, 38 tRNA, and 8 rRNA. The phylogenetic analysis suggested that H. rutilum (Ker-Gawl.) Herb. is closely related to H. rutilum. The complete chloroplast genome sequencing results will provide a reference for the further investigation and research of H. rutilum (Ker-Gawl.) Herb.

SUBMITTER: He L

PROVIDER: S-EPMC7995863 | biostudies-literature | 2021 Mar

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

The complete chloroplast genome of Hippeastrum rutilum (Ker-Gawl.) Herb.

He Li L Zou Bowen B Gao Haidong H Liu Lei L Wu Yang Y

Mitochondrial DNA. Part B, Resources 20210324 3

Hippeastrum rutilum (Ker-Gawl.) Herb. is a high-end ornamental flower in the family Amaryllidaceae. In this study, the complete chloroplast genome sequence of H. rutilum (Ker-Gawl.) Herb. was determined from Illumina pair-end sequencing data. The sequencing results indicated the complete chloroplast genome sequence of H. rutilum (Ker-Gawl.) Herb. 162,696 base pairs (bp) in length, including one large single-copy region (LSC, 86,933 bp), one small single-copy region (SSC, 541 ...[more]

PMID: 33796769

Similar Datasets

The complete chloroplast genome sequence of the Canna edulis Ker Gawl. (Cannaceae).

Project description:Canna edulis Ker Gawl. is an essential traditional tuber crop used for fresh consumption and to isolate starch in some tropical and semitropical regions. The complete chloroplast genome sequence of C. edulis has been determined in this study. The total genome size is 164,650 bp in length and contains a pair of inverted repeats (IRs) of 27,278 bp, which were separated by large single-copy (LSC) and small single-copy (SSC) of 91,421 bp and 18,673 bp, respectively. A total of 131 genes were predicted including 86 protein-coding genes, 8 rRNA genes and 37 tRNA genes. Further, maximum-likelihood phylogenetic analysis revealed that C. edulis belongs to Cannaceae in Zingiberales. The chloroplast genome of C. edulis is first complete genome sequence in Cannaceae and would play a significant role in the development of molecular markers in plant phylogenetic and population genetic studies.

| S-EPMC7782134 | biostudies-literature

The complete chloroplast genome of a rare species in Korea, Lilium Dauricum Ker Gawl.

Project description:Lilium dauricum Ker Gawler is a wild lily species that belongs to section Sinomartagon and is one of the ancestors of the Asiatic hybrid lilies. Unique traits such as disease resistance and early flowering make L. dauricum a desirable resource for interspecific hybridization. However, in Korea, the natural resources of L. dauricum are being exhausted by excessive exploitation and require urgent conservation. In this study, the complete chloroplast genome of L. dauricum was generated using Illumina paired-end sequencing technology, and its structure was compared with that of other Lilium species. The chloroplast genome was 152,063 bp long, with a typical quadripartite structure including a pair of inverted repeat regions (26,492 bp) separated by a large (81,485 bp) and small (17,584 bp) single-copy (SC) region. The genome encodes 131 different genes, including 85 protein-coding genes, 38 tRNA genes, and 8 rRNA genes. A phylogenetic analysis strongly supported the relationship of L. dauricum with other members of Sinomartagon and Martagon lilies.

| S-EPMC7707306 | biostudies-literature

The complete plastid genome sequence of Dracaena fragrans (L.) Ker Gawl. (Asparagaceae).

Project description:Dracaena fragrans is a shrub native to tropical Africa classified in the family Asparagaceae. It is a common horticultural plant grown as a hedge as well as an ornamental house plant for its green leaves, attractive shape and fragrant flowers. The species has been used for many medicinal purposes including inducing labor, treating malnutrition and fighting illness. Here, we investigated the complete plastid genome of D. fragrans using Illumina 150 bp next-generation sequencing technologies. De novo assembly and annotation showed that the chloroplast genome is a typical quadripartite structure with 37.5% GC content. A pair of inverted repeats (IRs, 26,507 bp each) were separated by one large single-copy region (LSC, 83,703 bp) and one small single-copy region (SSC, 18,466 bp). The chloroplast genome is 155,183 bp in length and contained 131 genes of which 12 are intron-containing genes, comprising 85 protein-coding, 38 tRNA, and 8 rRNA genes. Phylogenetic analysis of D. fragrans and 11 plastomes obtained from GenBank shows that it is closely related to D. elliptica.

| S-EPMC7928031 | biostudies-literature

Alkaloid Composition and Biological Activities of the Amaryllidaceae Species Ismene amancaes (Ker Gawl.) Herb.

Project description:Natural products have always played a significant role in the search for new drugs. One of the most relevant alkaloid-containing plant groups is the Amaryllidaceae family, a source of exclusive structures with a wide variety of pharmacological activities. The aim of this work was to determine the alkaloid composition and biological potential of an extract from the bulbs of an endemic Peruvian Amaryllidaceae species Ismene amancaes (Ker Gawl.) Herb. The alkaloid profiling was carried out by GC-MS, which revealed the presence of 13 compounds, 2 of them unidentified. The plant extract was found to contain high amounts of lycoramine, a galanthamine-type alkaloid. The extract also presented low inhibitory potential against the enzymes AChE and BuChE, with IC50 values of 14.6 ± 0.6 and 37.6 ± 1.4 μg·mL-1, respectively, and good to moderate inhibitory activity against the protozoan Plasmodium falciparum strain FCR-3 (chloroquine-resistant), with IC50 values of 3.78 ± 0.3 μg·mL-1. This is the first report of the alkaloid profile of a plant of the Ismene genus, which could be an interesting source of bioactive compounds.

| S-EPMC9331871 | biostudies-literature

The complete chloroplast genome of Hippeastrum vittatum (Amaryllidaceae).

Project description:Hippeastrum vittatum (L'Hér.) Herb. is a perennial herb in the Amaryllidaceae, which has been used as a medicinal and ornamental plant. Here, we assembled and characterized the complete chloroplast (cp) genome of H. vittatum by high throughput sequencing. As a result, the length of the complete cp genome is 158,082 bp with a canonical quadripartite structure, consists of a large single-copy region (LSC) of 86,165 bp, a small single-copy region (SSC) of 18,283 bp, and two inverted repeat (IR) regions of 26,817 bp, each. A total of 137 genes were identified, including 87 protein-coding genes, 42 tRNA genes, and 8 rRNA genes. The phylogenomic analysis was performed based on the complete cp genomes of 30 species, which revealed the closest relationship between H. vittatum and H. rutilum in the genus Hippeastrum.

| S-EPMC7781927 | biostudies-literature

Complete chloroplast genomes and comparative analyses of Hippeastrum 'milady', Hippeastrum albertii and Hippeastrum reticulatum (Amaryllidaceae).

Project description:Hippeastrum is a genus of ornamental plants with large, brightly colored flowers. Due to the very high seed-setting rate of the hybridization of Hippeastrum, the large population of hybrid progeny and the existence of superparent inheritance, it is difficult to trace the origin of the varieties collected from the market during breeding. In this study, we analyzed the chloroplast genomes of Hippeastrum 'Milady', H. alberti, and H. reticulatum using the Illumina NovaSeq sequencing platform and generated full-length sequences of 158,067, 158,067, and 158,522 bp, respectively. All three genomes had the typical tetrad structure. The large single copy, small single copy, and inverted repeat regions of H. reticulatum were observed to be respectively 277, 138, and 20 bp longer than the corresponding regions of H. 'Milady' and H. alberti. The results of comparative analysis of simple sequence repeats (SSRs), Ka/Ks ratios, codon preferences, and complete sequences of chloroplasts of these three taxa and 14 other plant species were as follows. First, the chloroplast genomes of H. 'Milady', H. alberti, and H. reticulatum contain 209, 209, and 211 SSR sites, respectively, most of which (123, 123, and 122, respectively) are single nucleotide repeats. Second, leucine, arginine, and serine are the most frequently used amino acids in the three chloroplast genomes. Third, H. 'Milady', H. alberti, and H. reticulatum are more closely related to Lycoris and Narcissus than to Allium and Agapanthus. Our results will provide information on the study of origins or relatedness of native species, and the identification of cultivars.

| S-EPMC9355175 | biostudies-literature

The complete chloroplast genome sequence of Hippeastrum rutilum (Amaryllidoideae).

Project description:Hippeastrum rutilum is one of the world's important ornamental plants. Here, we report the complete chloroplast genome of H. rutilum by whole-genome data. The whole cp genome is 158,357 bp in length, consisting of two inverted repeat regions (IR, 26,817 bp), one large single-copy region (LSC, 86,451 bp), and one small single-copy region (SSC, 18,272 bp). A total of 133 genes annotated for the chloroplast genome, including 87 protein-coding genes, 38 tRNAs, and eight rRNAs. Phylogenetic analysis pointed to that H. rutilum was closely related to Narcissus poeticus and Lycoris radiata.

| S-EPMC7782897 | biostudies-literature

The complete chloroplast genome of Lycoris aurea (L'Her.) Herb.

Project description:Lycoris aurea (L'Hér.) Herb is a herb widely growing in Chinese southen region, such as Guangxi, Guangdong, Fujian , Yunnan and Sichuan provinces. It not only has medicinal value, but also can be used as ornamental garden plant. The circular chloroplast genome of L. aurea was 158,690 bp in size, consisting of a pair of inverted repeat (IR) regions (26,782 bp) separated by a large single-copy (LSC) region (85,467 bp) and a small single-copy (SSC) region (18,541 bp) regions. And, it contained 127 genes, including 38 tRNA genes, 8 rRNA genes and 81 mRNA genes. The overall GC content of L. aurea is 37.73%. Phylogenetic analysis strongly supported that L. aurea and its congeneric species, L. radiata and L. squamigera, as sister group with 100% bootstrap value.

| S-EPMC7748574 | biostudies-literature

The complete chloroplast genome of Isodon rubescens, a traditional Chinese herb.

Project description:Isodon rubescens (Hemsley) H. Hara is a kind of traditional medical herb which can be used for cancer treatment. In this study, the complete chloroplast genome sequence of I. rubescens was assembled. Its complete circular chloroplast DNA length was 152,761 bp. The genome was made up of a large single-copy region of 83,655 bp, a small single-copy region of 17,660 bp, and a pair of inverted repeat regions of 25,723 bp. The genome totally encoded 129 genes, containing 85 protein-coding genes, 36 tRNA genes, and eight rRNA genes. Phylogenetic analysis indicated that I. rubescens had a close relationship with basil (Ocimum basilicum).

| S-EPMC7872541 | biostudies-literature

The complete chloroplast genome sequence of Vincetoxicum mongolicum (Apocynaceae), a perennial medicinal herb.

Project description:Vincetoxicum mongolicum Maxim. (1876), is a perennial medicinal herb, widely distributed in the Loess Plateau of China. Here, we sequenced, assembled, and annotated the complete chloroplast (cp) genome of V. mongolicum, and compared the highly variable gene regions and phylogenetic positions between V. mongolicum and other related species. Results showed that the complete cp genome of V. mongolicum was 160,157 bp in length, containing a large single copy (LSC) region of 91,263 bp, a pair of inverted repeats (IR) region of 23,892 bp, and a small single copy (SSC) region of 21,110 bp. The GC content accounts for 37.8%, and we annotated 131 single genes, which include 86 protein-coding genes, 8 rRNA genes, and 37 tRNA genes. By comparing and analyzing the variable region of the cp gene of V. mongolicum and other Vincetoxicum, we found that the variable sequences of rpoC1-rpoB, ycf4-cemA, ndhF, ndhF-rpl32, and rpl32-ccsA fragments were highly significant, which could be targeted as the DNA barcodes for evidence of V. mongolicum and its relatives in Apocynaceae. Maximum-likelihood (ML) phylogenetic tree analysis elucidated that V. mongolicum was sister to V. pycnostelma with strong support. Our results provide useful information for future phylogenetic studies and plastid super-barcodes of the family Apocynaceae.

| S-EPMC10241319 | biostudies-literature