Browse
Submit Data
Databases
API
Help

Dataset Information

16 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Characterization of the complete chloroplast genome of the Solanum tuberosum L. cv. Shepody (Solanaceae).

ABSTRACT: Potato (Solanum tuberosum L.), a species of the family Solanaceae, is the fourth most important food crop worldwide. Solanum tuberosum L. cv. Shepody is a long, smooth, white-skinned potato cultivar with medium green leaves. It has good specific gravity and boils and bakes well. To support more molecular data for breeding of S. tuberosum, the complete chloroplast (cp) genome sequence of S. tuberosum L. cv. Shepody was determined using the next-generation sequencing. In leaves, the chloroplast genome accounts for 3.88% of the total genome. The entire cp genome was determined to be 155,296 bp in length. It contained large single-copy (LSC) and small single-copy (SSC) regions of 85,737 and 18,373 bp, respectively, which were separated by a pair of 25,593 bp inverted repeat (IR) regions. The genome contained 132 total genes, including 87 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. The overall GC content of the genome is 37.9%. A phylogenetic tree reconstructed by 60 chloroplast genomes reveals that S. tuberosum L. cv. Shepody was closely related to S. tuberosum L. cv. Desiree with bootstrap support values of 100%.

SUBMITTER: Chen S

PROVIDER: S-EPMC8284121 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Characterization of the complete chloroplast genome of the Solanum tuberosum L. cv. Favorita (Solanaceae).

Project description:Potato (Solanum tuberosum L.), a species of the family Solanaceae, is the fourth most important food crop worldwide. Solanum tuberosum L. cv. Favorita is a long oval, smooth, yellowish-skinned potato variety with green and plump leaves. It has a dry matter content of 17.7% and starch content of 12.4-14.01% in the tuber. In order to support more genetic data for the taxonomy of S. tuberosum, the complete chloroplast (cp) genome sequence of S. tuberosum L. cv. Favorita was determined using next-generation sequencing. In leaves, the chloroplast genome accounts for 5.17% of the total genome. The entire cp genome was determined to be 155,296 bp in length. It contained large single-copy (LSC) and small single-copy (SSC) regions of 85,737 and 18,373 bp, respectively, which were separated by a pair of 25,593 bp inverted repeat (IR) regions. The genome contained 132 total genes, including 87 protein-coding genes, 37 tRNA genes, and eight rRNA genes. The overall GC content of the genome is 37.9%. A phylogenetic tree reconstructed by 60 chloroplast genomes reveals that S. tuberosum L. cv. Favorita is most closely related to S. tuberosum L. cv. Desiree and S. tuberosum L. cv. Atlantic.

| S-EPMC7971314 | biostudies-literature

The complete mitochondrial genome sequences of potato (Solanum tuberosum L., Solanaceae).

Project description:Potato (Solanum tuberosum) from the Solanaceae is the fourth most important food crop worldwide. In this study, five complete mitochondrial genome sequences of S. tuberosum were characterized through de novo assembly of whole genome sequencing data. The resulting circular mitochondrial DNA molecules ranged from 49,171?bp to 297,014?bp in size and contained a total of 80 non-redundant genes, comprising 34 protein-coding genes, 24 hypothetical open reading frames, 19 tRNA genes, and 3 rRNA genes. Phylogenetic analysis using common protein-coding sequences confirmed that S. tuberosum belongs to the Solanoideae subfamily in the Solanaceae family.

| S-EPMC7800320 | biostudies-literature

The complete chloroplast genome of Solanum betacea (Solanaceae, Solaneae).

Project description:Solanum betacea is a sub-tropical tree, and the fruit has high nutritional value, unique flavor and color. It is used as a functional ingredient in health care, food, cosmetic and pharmaceutical applications. The complete chloroplast(Cp) genome of S. betacea has been assembled and annotated in this paper. Its length was 155,937 bp, containing a large single-copy region of 86,731 bp, a small single-copy region of 18,450 bp, and a pair of IR regions of 25,378 bp in each. The complete chloroplast genome of S. betacea contained 134 genes, including 90 protein-coding genes, 36 transfer RNA genes (tRNAs), and 8 ribosome RNA genes (rRNAs). The overall GC content was 37.7% and the GC contents of the LSC, SSC, and IR regions were 35.7%, 31.8%, and 43.1%, respectively. Phylogenetic analysis with the reported chloroplast genomes revealed that S. betacea has been most closely related to Solanum torvum. These findings will provide useful information for further investigation of chloroplast genome evolution in Solanum betacea.

| S-EPMC8143614 | biostudies-literature

Characterization of the complete chloroplast genome of traditional Chinese herb, Solanum japonense Nakai. (Solanaceae).

Project description:Solanum japonense Nakai. (Solanaceae) is a traditional Chinese medicine and animal fodder in Asian continent. Here, the complete chloroplast genome sequence of S. japonense was determined by the Illumina Hiseq technology. The complete chloroplast genome of S. japonense was 155,415 bp and the GC content was 37.81%. The typical circular quadripartite structure was composed with two inverted repeat (IR) regions with 25,588 bp, a large single-copy (LSC) region (85,931 bp) and a small single-copy (SSC) region (18,344 bp). The chloroplast genome of S. japonense contained 132 unigenes, which contained 86 protein-coding genes, 37 tRNA and 8 rRNA genes and one pseudo-gene. Moreover, 183 SSRs were identified and 65% (119)of them located at LSC region. A Maximum-Likelihood (ML) phylogenetic analysis based on chloroplast genomes indicated that S. japonense was closely related to S.dulcamara, S.nigrum. Our results would provide a valuable resource for resource utilization and the phylogenetic studies of species of Dulcamara sect. in Solanaceae.

| S-EPMC7832539 | biostudies-literature

The complete chloroplast genome sequence of an invasive plant Solanum rostratum (Solanaceae).

Project description:Solanum rostratum is native to Neotropics and southwestern United States and considered as an invasive plant in Americas, Europe, Asia, Africa, and Australia. However, information on the chloroplast (cp) genome of this species is limited. In this study, we present the complete chloroplast genome sequence of S. rostratum obtained by high-throughput nextgeneration sequencing technology. The whole cp genome was 155,559 bp long and comprised 130 genes, including 85 protein-coding genes, 37 tRNA genes, and eight rRNA genes. The S. rostratum cp genome had a GC content of 37.76%. Based on the concatenated coding sequences of cp PCGs, phylogenetic analysis showed that Phylogenetic tree revealed that S. rostratum and S. elaeagnifolium are closely related to each other within the genus Solanum.

| S-EPMC7748722 | biostudies-literature

Characterization of the complete chloroplast genome of Allium tuberosum.

Project description:Allium tuberosum is a popular vegetable, condiment, and even a traditional Chinese medicine. Here, the complete chloroplast genome sequence of Allium tuberosum was reported. The size of the chloroplast genome is 154,056 bp in length, including a large single copy region (LSC) of 83,068 bp, a small single copy region (SSC) of 17,958 bp, and a pair of inverted repeat (IR) regions with 26,515 bp. The Allium tuberosum chloroplast genome encodes 132 genes, including 87 protein-coding genes, 38 tRNA genes, and 8 rRNA genes. Phylogenetic tree analysis suggested that Allium tuberosum was closely related to Allium sativum.

| S-EPMC7706802 | biostudies-literature

Characterization of the complete chloroplast genome of Lycium ruthenicum (Solanaceae).

Project description:Lycium ruthenicum is a precious desert plant with high medicinal and ecological values. It contains rich anthocyanins, which are safe natural pigments and could be used for natural food colorants. In this study, the complete chloroplast (cp) genome of L. ruthenicum was assembled on the basis of next generation sequencing. The whole genome is 154,996?bp in length, including two single copy regions (LSC: 85,993?bp and SSC: 18,213?bp) and two inverted repeat regions (IR: 25,395?bp). The overall G?+?C content of the genome is 37.9%. The cp genome consists of 111 unique genes, including 30 tRNA genes, 4 rRNA genes and 77 protein-coding genes. Phylogenetic analysis indicates that L. ruthenicum is closely clustered with Atropa belladonna, Przewalskia tangutica, and Scopolia parviflora.

| S-EPMC7800349 | biostudies-literature

The complete chloroplast genome of Capsicum frutescens (Solanaceae).

Project description:PREMISE OF THE STUDY:We report the complete sequence of the chloroplast genome of Capsicum frutescens (Solanaceae), a species of chili pepper. METHODS AND RESULTS:Using an Illumina platform, we sequenced the chloroplast genome of C. frutescens. The total length of the genome is 156,817 bp, and the overall GC content is 37.7%. A pair of 25,792-bp inverted repeats is separated by small (17,853 bp) and large (87,380 bp) single-copy regions. The C. frutescens chloroplast genome encodes 132 unique genes, including 87 protein-coding genes, 37 transfer RNA (tRNA) genes, and eight ribosomal RNA (rRNA) genes. Of these, seven genes are duplicated in the inverted repeats and 12 genes contain one or two introns. Comparative analysis with the reference chloroplast genome revealed 125 simple sequence repeat motifs and 34 variants, mostly located in the noncoding regions. CONCLUSIONS:The complete chloroplast genome sequence of C. frutescens reported here is a valuable genetic resource for Capsicum species.

| S-EPMC4873274 | biostudies-literature

Characterization of the complete chloroplast genome sequence of Anisodus acutangulus (Solanaceae).

Project description:Anisodus acutangulus is a Solanaceae perennial plant, which is endemic to China and classified as an endangered species. In this study, we have sequenced the complete chloroplast genome of A. acutangulus, which is 156,079 bp in length, containing a large single-copy (LSC) region of 86,526 bp, a small single-copy (SSC) region of 17,741 bp and comprises a pair of inverted repeat regions (IRs) of 25,906 bp. Totally 134 genes were annotated, including 87 protein-coding genes, 39 tRNA genes, and 8 rRNA genes. Its overall GC content is 37.6%. Phylogenetic analysis using total chloroplast genome DNA sequence of 21 species revealed that A. acutangulus was closely related to Hyoscyamus niger with 100% bootstrap value.

| S-EPMC7748740 | biostudies-literature

The chloroplast genome sequence of bittersweet (Solanum dulcamara): Plastid genome structure evolution in Solanaceae.

Project description:Bittersweet (Solanum dulcamara) is a native Old World member of the nightshade family. This European diploid species can be found from marshlands to high mountainous regions and it is a common weed that serves as an alternative host and source of resistance genes against plant pathogens such as late blight (Phytophthora infestans). We sequenced the complete chloroplast genome of bittersweet, which is 155,580 bp in length and it is characterized by a typical quadripartite structure composed of a large (85,901 bp) and small (18,449 bp) single-copy region interspersed by two identical inverted repeats (25,615 bp). It consists of 112 unique genes from which 81 are protein-coding, 27 tRNA and four rRNA genes. All bittersweet plastid genes including non-functional ones and even intergenic spacer regions are transcribed in primary plastid transcripts covering 95.22% of the genome. These are later substantially edited in a post-transcriptional phase to activate gene functions. By comparing the bittersweet plastid genome with all available Solanaceae sequences we found that gene content and synteny are highly conserved across the family. During genome comparison we have identified several annotation errors, which we have corrected in a manual curation process then we have identified the major plastid genome structural changes in Solanaceae. Interpreted in a phylogenetic context they seem to provide additional support for larger clades. The plastid genome sequence of bittersweet could help to benchmark Solanaceae plastid genome annotations and could be used as a reference for further studies. Such reliable annotations are important for gene diversity calculations, synteny map constructions and assigning partitions for phylogenetic analysis with de novo sequenced plastomes of Solanaceae.

| S-EPMC5919006 | 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