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 Crataegus scabrifolia (Franch.) Rehd (Rosaceae), a medicinal and edible plant in Southwest China.

ABSTRACT: Crataegus scabrifolia (Franch.) Rehd is a medicinal and edible plant in Southwest China. The chloroplast genome of C. scabrifolia was analyzed by high-throughput sequencing technology, and its genetic relationship to related species was discussed. The chloroplast genome is 159,637 bp long, with two inverted repeat (IR) regions (26,384 bp each) that separate a large single-copy (LSC) region (87,730 bp) and a small single-copy (SSC) region (19,139 bp). A total of 127 genes were annotated, including 83 protein-coding genes, 8 rRNA genes, and 36 tRNA genes. The phylogenetic tree shows that C. hupehensis is closely related to C. scabrifolia with strong bootstrap support.

SUBMITTER: Pu T

PROVIDER: S-EPMC9833407 | biostudies-literature | 2023

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

The complete chloroplast genome of Crataegus scabrifolia (Franch.) Rehd (Rosaceae), a medicinal and edible plant in Southwest China.

Pu Tian T Zhao Zhen-Ning ZN Yu Xiao X

Mitochondrial DNA. Part B, Resources 20230108 1

Crataegus scabrifolia (Franch.) Rehd is a medicinal and edible plant in Southwest China. The chloroplast genome of C. scabrifolia was analyzed by high-throughput sequencing technology, and its genetic relationship to related species was discussed. The chloroplast genome is 159,637 bp long, with two inverted repeat (IR) regions (26,384 bp each) that separate a large single-copy (LSC) region (87,730 bp) and a small single-copy (SSC) region (19,139 bp). A total of 127 genes were annot ...[more]

PMID: 36643811

Similar Datasets

The complete chloroplast genome of Crataegus hupehensis Sarg. (Rosaceae), a medicinal and edible plant in China.

Project description:Crataegus hupehensis Sarg. is well-known for its medicinal and nutritive value. In this study, the complete chloroplast genome sequence of C. hupehensis was determined by using Illumina high-throughput sequencing approach. The complete chloroplast genome is 159,766 bp with 36.6% GC content. It contained a pair of inverted repeat regions of 26,385 bp, a large single-copy region of 87,852 bp, and a small single-copy region of 19,144 bp. It contained 112 distinct genes, including 78 protein-coding genes, 4 ribosomal RNA genes, and 30 transfer RNA genes. Phylogenetic analysis based on chloroplast genomes indicated that C. hupehensisis was closely related to C. kansuensis and C. marshallii in the subfamily Maloideae. This complete chloroplast genome will provide valuable insight into evolution, molecular breeding, and phylogenetic analysis of Crataegus species.

| S-EPMC7872584 | biostudies-literature

Characterisation of the complete chloroplast genome of Gentiana delavayi Franch. (gentianaceae), a medicinal plant in southwest of China.

Project description:Gentiana delavayi is a medicinal plant commonly used in southwest of China. In this study, we sequenced the complete chloroplast (cp) genome sequence of G. delavayi to investigate its phylogenetic relationship in the family Gentianaceae. The chloroplast genome of G. delavayi was 151,569 bp in length with 37.8% overall GC content, including a large single copy (LSC) region of 81,177 bp, a small single copy (SSC) region of 16,921 bp and a pair of inverted repeats (IRs) of 25,471 bp. The cp genome contained 114 genes, including 78 protein coding genes, 30 tRNA genes, and 4 rRNA genes. The phylogenetic analysis indicated G. delavayi was closely related to G. stipitata.

| S-EPMC7707525 | biostudies-literature

The complete chloroplast genome of Crataegus bretschneideri Schneid. (Rosaceae).

Project description:Crataegus bretschneideri Schneid., with an unclear phylogenic position, is mainly distributed in northeast and inner mongolia area of China. In this study, the complete chloroplast genome sequence of C. bretschneideri was determined by using Illumina high-throughput sequencing method. The chloroplast genome was 159,607 bp in length and consisted of a large single-copy (LSC) region (87,601 bp), a small single-copy (SSC) region (19,312 bp), separated by a pair of inverted repeat (IRs: 26,347 bp, each) regions. It comprised a total of 114 unique genes, including 80 protein-coding genes, 30 tRNA genes, and 4 rRNA genes. Phylogenetic analysis based on complete chloroplast genomes indicated that C. bretschneideri was closely related to C. marshallii Eggl in the subfamily Maloideae. This complete chloroplast genome will provide valuable insight into evolution, molecular breeding, and phylogenetic analysis of Crataegus species.

| S-EPMC8567899 | biostudies-literature

The complete chloroplast genome of Rubus rosifolius (Rosaceae), an ornamental and medicinal plant.

Project description:Rubus rosifolius belongs to the genus Rubus in the family Rosaceae and is widely distributed globally. It has white flowers and red fruits. Moreover, it has medicinal value for diseases of the stomach and other areas. However, the complete chloroplast (cp) genome of R. rosifolius remains unclear. In the present study, we sequenced the complete cp genome of R. rosifolius (GenBank accession no. OL435124), which had a typical quadripartite structure and a size of 155,650 bp. Fifteen genes (trnK-UUU, rps16, trnG-UCC, atpF, rpoC1, trnL-UAA, trnV-UAC, petB, petD, rpl16, rpl2, ndhB, trnI-GAU, trnA-UGC, and ndhA) contained an intron, and two genes (clpP and ycf3) contained two introns. The gene rps12 showed trans-splicing. Phylogenetic analysis showed that R. rosifolius was closely related to Rubus taiwanicola, Rubus rubroangustifolius, and Rubus glandulosopunctatus.

| S-EPMC9297712 | biostudies-literature

Characterization of the complete chloroplast genome sequence of medicinal plant: Potentilla bifurca (Rosaceae).

Project description:Potentilla bifurca is a medicinal plant, the root extracts have been applied for the treatment of certain viral infections as folk medicinal herbs. The complete chloroplast genome sequence of is 155,841 bp in length, contains 128 complete genes, including 84 protein-coding genes (84 PCGs), 8 ribosomal RNA genes (4 rRNAs), and 37 tRNA genes (37 tRNAs). The overall GC content of cp DNA is 37.1%, the corresponding values of the LSC, SSC, and IR regions are 35.0%, 31.0%, and 42.8%. Phylogenetic tree shows that P. bifurca was identified as the basal clade of Potentilla.

| S-EPMC7832467 | biostudies-literature

The complete chloroplast genome of the Crataegus kansuensis (Rosaceae): characterization and phylogeny.

Project description:Crataegus kansuensis Wils. is an important wild eco economical species of the family Rosaceae. The complete chloroplast genome reported here is 159,865 bp in length, including two inverted repeats (IRs) of 26,384 bp, which are separated by a large single-copy (LSC) and a small single-copy (SSC) of 87,815 bp and 19,282 bp, respectively. The whole chloroplast genome of C. kansuensis contains 113 genes, including 79 protein-coding genes, 30 transfer RNA, and 4 ribosome RNA. Phylogenetic analysis indicated that C. kansuensis is closely related to that of C. chungtienensis and C. marshallii, and the genus Crataegus L. was sister to the genus Amelanchier Medik.

| S-EPMC7782147 | biostudies-literature

The complete chloroplast genome of Prunus japonica thunb.(Rosaceae), an ornamental and medicinal plant.

Project description:Prunus japonica is an ornamental and medicinal plant that is widely cultivated. The complete chloroplast genome of P. japonica was sequenced using Illumina Hiseq X Ten platform. The chloroplast genome was 158,080 bp in length, containing two short inverted repeat (IRa and IRb) regions of 26,385 bp, which was separated by a large single copy (LSC) region of 86,270 bp and a small single copy (SSC) region of 19,040 bp. The GC content of the whole chloroplast genome was 36.8%. The chloroplast DNA of P. japonica comprised 112 distinct genes, including 78 protein-coding genes, 4 ribosomal RNA genes and 30 transfer RNA genes. Phylogenetic analysis indicated that all species of Prunus formed a monophyletic group, P. japonica was closely related to P. hulimis.

| S-EPMC7819125 | biostudies-literature

The complete chloroplast genome of Rosa cymosa (Rosaceae), a traditional medicinal plant in South China.

Project description:Rosa cymosa is a traditional medicinal and ornamental plant in China. Here, we report the complete chloroplast genome of R. cymosa. The chloroplast genome is 156,607 bp in length with 37.48% GC content, containing a small single-copy (SSC) region (18,763 bp), a large single-copy (LSC) region (85,722 bp), and a pair of inverted repeats (IRs: 26,061 bp each). A total of 139 genes were predicted, including 92 protein-coding genes, eight ribosomal RNA genes, and 39 tRNA genes. Phylogenetic analysis based on chloroplast genomes of 16 plant species shows that R. cymosa is closest to R. chiensis 'Old Bush' and R. lucidissima. These complete chloroplast genomes can be subsequently used for researches of Rosaceae.

| S-EPMC7782239 | biostudies-literature

The complete chloroplast genome of Prinsepia uniflora (Rosaceae), a medicinal plant found in northwest China.

Project description:Prinsepia uniflora Batalin 1892 is a medicinal plant widely distributed in northwest China. In this study, we report and characterize the complete chloroplast (cp) genome sequence of P. uniflora. The entire sequence is 159,179 bp in length, consisting of the large single-copy region (LSC) and small single copy region (SSC) (87,239 and 19,180 bp, respectively); these two regions are separated by a pair of 26,380-bp inverted repeat (IR) regions. The genome contains 131 genes, including 86 protein-coding genes, 37 tRNA genes, and eight rRNA genes. The overall GC content of the genome is 36.7%. A phylogenetic tree constructed from 18 chloroplast genomes revealed that P. uniflora was clustered with Prinsepia sinensis and Prinsepia utilis, all of which belong to the genus Prinsepia, which is supported as a sister group by a moderate bootstrap support value of 55% with the Malus and Pyrus genera.

| S-EPMC8475127 | biostudies-literature

The complete chloroplast genome of Rubus pinfaensis, an edible and medicinal dual-purpose plant.

Project description:Rubus pinfaensis H. Lév. & Vaniot is of great importance in the phylogeny and evolution amongst Rosaceae, genus Rubus L. plants. The chloroplast genome of R. pinfaensis was reported in this study, which is 155,523 bp in size, with an average GC content of 37.13%. The complete chloroplast genome has a typical quadripartite structure, including a large single copy (LSC) region (85,211 bp) and a small single copy (SSC) region (18,718 bp), which were separated a pair of inverted repeats (IRs, 25,797 bp). This plastome contained 129 different genes (112 unique), including 85 protein-coding genes (79 unique), 36 tRNA genes (29 unique), and 8 rRNA genes (4 unique). The chloroplast genome of R. pinfaensis has completed that will be based on the phylogeny and genomic studies in the family Rosaceae, genus Rubus L.

| S-EPMC10402827 | biostudies-literature