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 sequence of Rosa minutifolia.

ABSTRACT: Here we report the chloroplast genome sequence of Rosa minutifolia. This rose grows in warm climates, it has been reported as an endangered species. The complete chloroplast genome size was 157,396 bp, and exhibited a quadripartite structure with dual inverted repeats (IRs) regions (26,041 bp), a small single-copy (SSC) region (18,775 bp), and a large single-copy (LSC) region (86,539 bp). The genome contained a total of 137 genes including 90 protein-coding genes, 39 tRNA genes, and 8 rRNA genes. Phylogenetic analysis revealed that R. minutifolia is closely related to R. rugosa and R. hybrid cultivar Augusta.

SUBMITTER: Zhao X

PROVIDER: S-EPMC7782609 | biostudies-literature | 2020 Sep

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

The complete chloroplast genome sequence of Rosa minutifolia.

Zhao Xia X Gao Chengwen C

Mitochondrial DNA. Part B, Resources 20200908 3

Here we report the chloroplast genome sequence of Rosa minutifolia. This rose grows in warm climates, it has been reported as an endangered species. The complete chloroplast genome size was 157,396 bp, and exhibited a quadripartite structure with dual inverted repeats (IRs) regions (26,041 bp), a small single-copy (SSC) region (18,775 bp), and a large single-copy (LSC) region (86,539 bp). The genome contained a total of 137 genes including 90 protein-coding genes, 39 tRNA genes, and 8 rRN ...[more]

PMID: 33458151

Similar Datasets

The complete chloroplast genome sequence of Rosa laevigata (Rosaceae).

Project description:The complete chloroplast genome of Rosa laevigata has been characterized by reference-based assembly using Illumina paired-end data. The complete cp genome is 156,342 bp in length, containing a large single-copy region of 85,459 bp, a small single-copy region of 18,785 bp, which are separated by a pair of inverted repeat regions of 26,049 bp, a total of 140 genes were predicted from the cp genome, including 87 protein-coding genes, 39 tRNA genes, and 8 rRNA genes . Most genes occur as a single copy, while 19 gene species are duplicated. Phylogenetic analysis reveals that R. laevigata and Rosa roxburghii f. normalis are more closely related to each other than either is to Rosa banksiae var. normalis.

| S-EPMC7707283 | biostudies-literature

The complete chloroplast genome sequence of Rosa 'Limoncello' (Rosales: Rosaceae).

Project description:Rosa 'Limoncello' finds applications in gardening and landscaping. In this study, we assembled and annotated the complete chloroplast genome of this variety for the first time. The length of its chloroplast genome was 156,493 bp, containing two short inverted repeat regions of 26,052 bp, each separated by a large single-copy region of 85,649 bp and a small single-copy region of 18,740 bp. The chloroplast DNA of R. 'Limoncello' consisted of 135 genes, including 90 protein-coding genes, eight ribosomal RNA genes, and 37 transfer RNA genes. On comparing the complete chloroplast sequence of R. 'Limoncello' with that of other Rosa species, R. 'Limoncello' was found to be closely related to Rosa cymosa. Thus, information on the chloroplast genome sequence of this rose variety can facilitate phylogenetic studies of the genus Rosa.

| S-EPMC10768736 | biostudies-literature

Complete chloroplast genome sequence of Rosa roxburghii and its phylogenetic analysis.

Project description:Rosa roxburghii Tratt. is a famous Chinese traditional medicine with long history, here we characterized the whole chloroplast (cp) genome sequence of R. roxburghii by Illumina pair-end sequencing. The complete cp genome was 156,749 bp in length, containing a large single copy (LSC) region of 85,862 bp and a small single copy (SSC) region of 18,791 bp, which were separated by a pair of 26,053 bp inverted repeat regions (IRs). The genome contained 139 genes, including 88 protein-coding genes (82 PCG species), 39 tRNA genes (32 tRNA species), and eight ribosomal RNA genes (four rRNA species). Most of the gene species occur as a single copy, while 17 gene species occur in double copies. The overall AT content of R. roxburghii cp genome is 62.8%, while the corresponding values of the LSC, SSC, and IR regions are 64.8, 68.7, and 57.4%, respectively. Further, phylogenetic analysis suggested that R. roxburghii is closely related to R. odorata var. gigantea.

| S-EPMC7800368 | biostudies-literature

Sequence and phylogenetic analysis of the chloroplast genome for Rosa xanthina.

Project description:Rosa xanthina is a wild shrub rose that is native to open slopes and scrubby areas in central China. In this study, the chloroplast genome sequence of R. xanthina been assembled and characterized by Illumina sequencing. The complete chloroplast genome was 157,214 bp in length, containing a large single-copy region (LSC) of 86,302 bp and a small single-copy region (SSC) of 18,770 bp, which were separated by a pair of 26,071 bp inverted repeat regions (IRs), each. A total contained 137 genes, including 90 protein-coding, 8 rRNA, and 39 tRNA genes. Maximum-likelihood phylogenetic analysis of 15 representative plastomes within the order Rosa suggests that R. xanthina closely related to the Rosa berberifolia.

| S-EPMC7782961 | biostudies-literature

Phylogenetic relationships and characterization of the complete chloroplast genome of Rosa sterilis.

Project description:Rosa sterilis is an economically and important fruit that is extensively grown in Southwestern China. In this study, we determined the complete chloroplast genome of R. sterilis using high-throughput Illumina sequencing. The chloroplast genome of R. sterilis is 156,561 bp in size, containing a large single-copy region (LSC)(85,701 bp), a small single-copy region (SSC) (18,746 bp), and a pair of inverted repeat (IR) regions (each one of 26,057 bp). The overall GC content of the chloroplast genome is 37.23%, while the corresponding values of GC contents of the LSC, SSC, and IR regions are 35.20%, 31.37%, and 42.70%, respectively. The chloroplast genome of R. sterilis contains 130 genes, including 84 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. The phylogenetic maximum-likelihood tree revealed that Rosa chinensis or Rosa chinensis var. spontanea is the closest related to R. sterilis in the phylogenetic relationship. This complete chloroplast genome can be further used for genomic studies, evolutionary analyses, and genetic engineering studies of the family Rosaceae.

| S-EPMC8079020 | biostudies-literature

The chloroplast genome of Rosa rugosa × Rosa sertata (Rosaceae): genome structure and comparative analysis.

Project description:Rosa rugosa × Rosa sertata, which belongs to the family Rosaceae, is one of the native oil-bearing roses in China. Most research has focused on its essential oil components and medicinal values. However, there have been few studies about its chloroplast genome. In this study, the whole chloroplast genome of R. rugosa × R. sertata was sequenced, analyzed, and compared to other genus Rosa species. The chloroplast genome of R. rugosa × R. sertata is a circular structure and 157,120 bp in length. The large single copy and small single copy is 86,173 bp and 18,743 bp in size, respectively, and the inverted repeats are 26,102 bp in size. The GC content of the whole genome is 37.96%, while those of regions of LSC, SSC, and IR are 35.20%, 31.18%, and 42.73%, respectively. There are 130 different genes annotated in this chloroplast genome, including 84 protein coding genes, 37 tRNA genes, 8 rRNA genes, and 1 pseudogene. Phylogenetic analysis of 19 species revealed that R. rugosa × R. sertata belong to the Sect. Cinnamomeae. Overall, this study, providing genomic resources of R. rugosa × R. sertata, will be beneficial for species identification and biological research.

| S-EPMC9540792 | biostudies-literature

The complete chloroplast genome sequence of Lemna turionifera (Araceae).

Project description:Lemna turionifera is native to North America and northern Asia, with significant potential for industrial wastewater remediation. The complete nucleotide sequence of the L. turionifera chloroplast genome (cpDNA) was determined. The cpDNA is a circular molecule of 166,606 bp and containing a pair of inverted repeats (IRs) measuting 31,663 bp each. These IRs are flanked by a small single-copy region of 13,542 bp and a large single-copy region of 89,738 bp. The chloroplast genome of L. turionifera consisted of 112 unique genes, including 78 protein-encoding genes, 30 tRNA genes, and four rRNA genes. The phylogenetic analysis utilizing cpDNA provided a well-supported resolution of the relationships among subfamilies within the Araceae family. Our findings indicated a close relationship between L. turionifera and a clade consisting of L. minor, L. japonica, and L. gibba. The availability of the complete chloroplast genome sequence of L. turionifera presents valuable data for future phylogenetic investigations within the Lemnaceae family.

| S-EPMC11293259 | biostudies-literature

Complete chloroplast genome sequence of Hedychium coronarium.

Project description:The first complete chloroplast genome of Hedychium coronarium (Zingiberaceae) was reported in this study. The H. coronarium chloroplast genome was 163,949 bp in length and comprised a pair of inverted repeat (IR) regions of 29,780 bp each, a large single-copy (LSC) region of 88,581 bp and a small single-copy (SSC) region of 15,808 bp. It encoded 141 genes, including 87 protein-coding genes (79 PCG species), 46 tRNA genes (28 tRNA species), and eight rRNA genes (four rRNA species). The nucleotide composition was asymmetric (31.68% A, 18.35% C, 17.74% G, 32.23% T) with an overall AT content of 63.92%. Phylogenetic analysis showed that H. coronarium was classified into a monophyletic group within the genus Hedychium in family Zingiberaceae.

| S-EPMC7706620 | biostudies-literature

Complete chloroplast genome sequence of Prunus mahaleb.

Project description:Prunus mahaleb (L.) Mill. is a kind of ornamental species which originated from Europe and Western Asia. Here, we use Illumina paired-end sequencing to obtain the complete chloroplast genome of P. mahaleb. The complete cp genome of P. mahaleb with a size of 157,824 bp in length is a circular molecular genome, including a pair of inverted repeat (IR) region of 26,410 bp each, separated by a large single copy (LSC) region of 85,926 bp and a small single-copy (SSC) region of 19,078 bp. The genome consisted of 129 genes, including 84 protein-codon genes (PCGs), 37 tRNA genes, and eight rRNA genes. The GC content of the whole chloroplast genome is 36.7%. Phylogenetic analysis revealed that P. mahaleb was the closest related to P. cerasoides and P. maximowiczii.

| S-EPMC7687457 | biostudies-literature

Complete chloroplast genome sequence of Kosteletzkya pentacarpos.

Project description:Kosteletzkya pentacarpos is a promising plant being developed as a salt-tolerant biofuel crop that also the ability to fix heavy metals. Here, high-throughput sequencing technology was used to sequence and assemble the chloroplast genome of K. pentacarpos. The full length of the chloroplast genome is 161,777 bp, comprising a large single-copy region of 90,019 bp, a small single-copy region of 18,978 bp, and a pair of inverted repeats of 26,390 bp. A total of 113 genes were annotated, including 79 protein-coding, 30 transfer RNA, and 4 ribosomal RNA genes. Phylogenetic analysis based on whole chloroplast genome sequences showed that K. pentacarpos has a close relationship with Abelmoschus in Malvaceae. This study increases the available genomic information on K. pentacarpos, and provides a basis for the rational exploitation and utilization of germplasm resources.

| S-EPMC9262370 | biostudies-literature