Browse
Submit Data
Databases
API
Help

Dataset Information

33 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

The complete chloroplast genome of Secale sylvestre (Poaceae: Triticeae).

ABSTRACT: Secale sylvestre is a wild species of rye, morphologically distinct from domestic species. To draw comparisons between species based on molecular features, it is important to have high-quality sequences, especially in the case of organellar genomes. For such reason, the complete chloroplast genome of Secale sylvestre Host introd. no. 6047 will provide useful data for ecological, agricultural, and phylogenetic purposes. Here we present the complete, annotated chloroplast genome sequence of Secale sylvestre Host introd. no. 6047. The genome is 137116 base pair (bp) long. It is the first complete chloroplast genome that can be used as a reference genome for further analysis. The genome can be accessed on GenBank with the accession number (MW557517).

SUBMITTER: Skuza L

PROVIDER: S-EPMC8755654 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Secale sylvestre

Project description:The complete chloroplast genome and annotation of Secale sylvestre Raw sequence reads

| PRJNA754260 | ENA

The complete chloroplast genome of Cenchrus ciliaris (Poaceae).

Project description:Cenchrus ciliaris is an important pasture resource for arid region and owing to apomixis, it has been very important for development and distribution of cultivars and agro-types. In present study complete chloroplast genome of C. ciliaris was sequenced. The size of chloroplast genome is 138737 bp length with overall GC content 38.6%. It exhibited regular quadripartite structure with 81053 bp of LSC region, 16108 bp of SSC region and 20788 bp of each IR region. A total of 130 genes were identified, including 87 coding genes, 32 tRNAs, 7 ribosomal RNAs and 4 pseudogenes. Phylogenetic analysis was performed using 13 other members representing major subfamilies of Poaceae.

| S-EPMC7800180 | biostudies-literature

The complete chloroplast genome of Saccharum fulvum (Poaceae).

Project description:Saccharum species are of great importance as fruit crops due to their economic and food value. S. fulvum is a wild relative of sugarcane that has a wide geographic distribution and is well-adapted to various environmental conditions. It exhibits high resistance to pests, diseases, drought, cold, and degraded soils, making it a valuable resource for sugarcane research. Here, we report the chloroplast genome of S. fulvum. This chloroplast genome was 141,151 bp in length with a GC content of 38.41%. The large single-copy, small single-copy, and inverted repeat regions were 83,030 bp, 12,533 bp, and 22,794 bp in length, respectively. The chloroplast genome contained 111 different genes, including 77 protein-coding genes, 4 rRNA genes, and 30 tRNA genes. Phylogenetic analysis indicated that S. fulvum was closely related to S. narenga. This study not only enriches the genome information of Saccharum, but also will be useful for the evolutionary study of the family Poaceae.

| S-EPMC10956914 | biostudies-literature

The complete chloroplast genome sequence of Melica scabrosa (Poaceae).

Project description:Melica scabrosa Trin. is an important forage grass of Poaceae, wildly distributed in the Northeast Asia to Qinghai-Xizang Plateau. The complete chloroplast genome sequence of M. scabrosa was obtained by de novo assembly using whole genome sequence data. The chloroplast genome is 134,889?bp in length, containing 80,560?bp in a large single copy (LSC), 12,706?bp in a small single copy (SSC) and 20,810?bp in a pair of inverted repeats (IRs). A total of 129 genes including 83 protein-coding genes and 38 structural RNA genes were identified. Phylogenetic analysis represented close relationship among Melica species. This chloroplast genome sequencing offers a useful resource for future genetics and phylogenetic studies.

| S-EPMC7706687 | biostudies-literature

The complete chloroplast genome of Phyllostachys angusta McClure (Poaceae).

Project description:Phyllostachys angusta McClure is a precious wood-use bamboo resource, with almost straight stem. The complete chloroplast genome of the P. angusta McClure was assembled for the first time from Illumina pair-end sequencing data in this work. The total genome size of P. angusta McClure was 139,678 bp in length, containing a large single-copy (LSC) region of 83,212 bp, a small single-copy (SSC) region of 12,870 bp, and a pair of inverted repeat (IR) regions of 21,798 bp. The overall GC content of the genome was 38.89%, and the corresponding values of the LSC, SSC, and IR regions were 36.97, 33.17, and 44.22%, respectively. A total of 131 genes were annotated, including 85 protein-coding genes, 36 tRNA genes, and 8 rRNA genes. Phylogenetic analysis results strongly supported that P. angusta McClure was closely related to P. reticulate.

| S-EPMC7832504 | biostudies-literature

The complete chloroplast genome sequence of Pennisetum flaccidum (Poaceae).

Project description:Pennisetum flaccidum Grisebach is a typical high-quality forage and adrought-tolerant grass. In this study, we firstly reported the complete chloroplast (cp) genome of P. flaccidum, which was 138,336 bp in length, including a pair of inverted repeats (IR: 22,293 bp), a large single copy (LSC: 81,329 bp), and a small single copy (SSC: 12,421 bp) region. A total of 131 genes were annotated, containing seven rRNA genes, 38 tRNA genes, and 86 protein-coding genes. The GC content of the cp genome was 38.63%. The maximum-likelihood (ML) phylogenetic tree indicated that P. flaccidum was closely related to P. cetaceum in Poaceae.

| S-EPMC8344247 | biostudies-literature

The complete chloroplast genome sequence of Oryza eichingeri (Poaceae).

Project description:The complete chloroplast genome sequence of Oryza eichingeri (GenBank accession number: KX085496) was generated by de novo assembly with low-coverage whole-genome sequence data. The chloroplast genome is 134,821 bp in length and showed conserved typical chloroplast structure. The cpDNA contained four rRNA, 39 tRNA, and 79 unique protein-coding genes. Seventeen genes contain one intron, only ycf3 contains two introns; rps12 is trans-spliced, one of its exons is in the LSC region (5'_end) and the two reside in the IR regions (3'_end) separated. A pair of gene ndhH, due to the 5' part of ndhH which overlaps the IR/SSC junctions, was two unique genes. The AT content of O. eichingeri cp genome is 61%. Phylogenomic analysis showed that O. eichingeri is closely related to O. officinalis. The complete cpDNA of O. eichingeri provides essential and important DNA molecular data for further phylogenetic and evolutionary analysis for the genus Oryza.

| S-EPMC7800631 | biostudies-literature

The complete chloroplast genome sequence of Oryza rhizomatis (Poaceae).

Project description:The complete chloroplast genome sequence of Oryza rhizomatis (GenBank accession number: KX085497) was generated by de novo assembly with low-coverage whole-genome sequence data. The genome was 134,796 bp in length, containing a pair of inverted repeat (IRa and IRb) regions of 20,818 bp, which were separated by a large single-copy (LSC) region of 80,829 bp and a small single-copy (SSC) region of 12,330 bp, respectively. The genic regions account for 43.77% of whole cpDNA, and the AT content of the cpDNA was 60.99%. The O. rhizomatis cpDNA encodes 112 unigenes (79 protein-coding genes, four rRNA genes, and 29 tRNA genes). Eighteen genes contain introns, ycf3 contains two introns, and the rest of the gene contains one intron; rps12 is trans-spliced, one of its exons is in the LSC region (5'_end) and the two reside in the IR regions (3'_end) separated. A pair of gene ndhH, due to the 5' part of ndhH which overlaps the IR/SSC junctions, was two unique genes. The four rRNA genes are all located in the IR. Phylogenomic analysis showed that O. rhizomatis is closely related to O. officinalis. The new data will help to determine the phylogenetic placement of the genus Oryza and fill gaps in our understanding of Oryzae biology.

| S-EPMC7799503 | biostudies-literature

Characterization of the complete plastome of Elymus tangutorum (Poaceae: Triticeae).

Project description:Elymus tangutorum (Nevski) Handel-Mazzetti (Poaceae: Triticeae), a hexaploid perennial herb, is a kind of forage plant with large biomass. In this study, the complete plastome sequence of E. tangutorum was reported. The size of the plastome is 134,949 bp in length, including a large single copy region (LSC) of 80,556 bp, a small single copy region (SSC) of 12,767 bp, and a pair of inverted repeat (IR) regions with 20,813 bp. Moreover, a total of 131 functional genes were annotated, including 85 protein-coding genes, 38 tRNA genes, and 8 rRNA genes. The maximum likelihood (ML) phylogenetic tree suggested that E. tangutorum was closely related to Elymus libanoticus and Dasypyrum villosum.

| S-EPMC7707338 | biostudies-literature

Complete Chloroplast Genome Sequence of Cane Needle Grass, Nassella hyalina (Poaceae: Stipeae).

Project description:Nassella hyalina (cane needle grass) is on the Alert List for Environmental Weeds in Australia. We present here the first complete chloroplast sequence of N. hyalina reconstructed from Illumina whole-genome sequencing. The complete chloroplast sequence is 137,606 bp in size and has a gene content and structure similar to those of other published chloroplast genomes of Stipeae.

| S-EPMC5701466 | 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