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 Digitaria sanguinalis (Graminales: Gramineae).

ABSTRACT: Digitaria sanguinalis (Linnaeus) Scopoli 1722 is an annual herbal plant that has important medicinal and ecological value. The chloroplast genome was 138,079 bp in length. In total, 129 genes were predicted, including 82 protein-coding genes, 39 tRNA genes, and 8 rRNA genes. The overall AT content of the genome was 61.39%. The phylogenetic analysis showed that D. sanguinalis and D. glauca formed a base clade in Panicoideae close to Thyridolepis xerophila. This study will help to understand the genetic diversity of the Digitaria plants.

SUBMITTER: Liu Y

PROVIDER: S-EPMC9245991 | biostudies-literature | 2022

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

The complete chloroplast genome of Digitaria sanguinalis (Graminales: Gramineae).

Liu You Y Jin Chenzhong C Zhang Xuejiao X Zhou Yunyun Y Hu Yihong Y

Mitochondrial DNA. Part B, Resources 20220623 6

Digitaria sanguinalis (Linnaeus) Scopoli 1722 is an annual herbal plant that has important medicinal and ecological value. The chloroplast genome was 138,079 bp in length. In total, 129 genes were predicted, including 82 protein-coding genes, 39 tRNA genes, and 8 rRNA genes. The overall AT content of the genome was 61.39%. The phylogenetic analysis showed that D. sanguinalis and D. glauca formed a base clade in Panicoideae close to Thyridolepis xerophila. This ...[more]

PMID: 35783036

Similar Datasets

The complete chloroplast genome of Tripsacum laxum (Gramineae).

Project description:Tripsacum laxum (Guatemalan grass) is a perennial fodder grasses, which is commonly growing in large parts of Africa for a source of livestock feed. It has a high economic value as a forage. In this study, we obtained a complete chloroplast genome of T. laxum by Illumina sequencing. The results showed a circular genome of 140,556 bp, including the large single copy region (LSC, 82,939 bp), the small single-copy region (SSC, 12,573 bp), and a pair of 22,522 bp inverted repeat regions (IRs). The circular genome contained 120 genes, including 74 protein-coding genes, eight ribosomal RNA genes and 38 tRNA genes. Evolutionary relationship analysis indicates that T. laxum is more closely related to previously reported T. dactyloides.

| S-EPMC8525997 | biostudies-literature

Digitaria sanguinalis

Project description:Digitaria sanguinalis Transcriptome or Gene expression

| PRJNA1082474 | ENA

Digitaria sanguinalis

Project description:Digitaria sanguinalis overview

| PRJNA1134869 | ENA

Characterization of the complete chloroplast genome of Festuca sinensis (Gramineae).

Project description:The complete chloroplast genome from Festuca sinensis, an important perennial bunchgrass of the Gramineae, is determined in this study. The whole chloroplast genome sequence of F. sinensis has been characterized by Illumina pair-end sequencing. The circular genome is 134,177 bp long, containing a large single-copy region (LSC) of 79,367 bp and a small single-copy region (SSC) of 12,510 bp, which are separated by a pair of 21,150 bp inverted repeat regions (IRs). It encodes a total of 150 genes, including 93 protein-coding genes (75 PCG species), 49 tRNA genes (30 tRNA species) and eight ribosomal RNA genes (4 rRNA species). The most of gene species occur as a single copy, while 30 gene species occur in double copies. The overall A + T content of is 61.6%, while the corresponding values of the LSC, SSC, and IR regions are 63.7, 67.4, and 56.0%, respectively. Phylogenetic analysis suggested that Festuca sinensis was relatively close to Festuca ovina compared with other species of Festuca genera in Gramineae among the species analyzed. This complete chloroplast genome will provide valuable insight into conservation and exploitation efforts for this species as well as useful resources for studying the Gramineae phylogeny.

| S-EPMC7748645 | biostudies-literature

Complete chloroplast genome sequence of bamboo Dendrocalamopsis vario-striata (Gramineae Bambusoideae).

Project description:Dendrocalamopsis vario-striata is one of the most economical and ornamental significant bamboo. It has the characteristics of annual flowering but no death. Here, we report on the first complete chloroplast (cp) genome of D. vario-striata. Its full-length of 139,458 bp, include large single-copy (LSC) region of 83,279 bp, small single-copy (SSC) region of 12,143bp, a pair of invert repeats (IR) regions of 22,018bp. Plastid genome contains 264 genes, 170 protein-coding genes, 78 tRNA genes, and 16 rRNA genes. The maximum likelihood phylogenetic analysis shows that D. vario-striata was sister to all other species of Bambusoideae.

| S-EPMC7707846 | biostudies-literature

Digitaria sanguinalis soil rhizosphere microorganisms

Project description:Digitaria sanguinalis soil rhizosphere microorganisms Raw sequence reads

| PRJNA1118069 | ENA

Differential gene expression for Curvularia eragrostidis pathogenic incidence in crabgrass (Digitaria sanguinalis) revealed by cDNA-AFLP analysis.

Project description:Gene expression profiles of Digitaria sanguinalis infected by Curvularia eragrostidis strain QZ-2000 at two concentrations of conidia and two dew durations were analyzed by cDNA amplified fragment length polymorphisms (cDNA-AFLP). Inoculum strength was more determinant of gene expression than dew duration. A total of 256 primer combinations were used for selective amplification and 1214 transcript-derived fragments (TDFs) were selected for their differential expression. Of these, 518 up-regulated differentially expressed TDFs were identified. Forty-six differential cDNA fragments were chosen to be cloned and 35 of them were successfully cloned and sequenced, of which 25 were homologous to genes of known function according to the GenBank database. Only 6 genes were up-regulated in Curvularia eragrostidis-inoculated D. sanguinalis, with functions involved in signal transduction, energy metabolism, cell growth and development, stress responses, abscisic acid biosynthesis and response. It appears that a few pathways may be important parts of the pathogenic strategy of C. eragrostidis strain QZ-2000 on D. sanguinalis. Our study provides the fundamentals to further study the pathogenic mechanism, screen for optimal C. eragrostidis strains as potential mycoherbicide and apply this product to control D. sanguinalis.

| S-EPMC3792964 | biostudies-literature

ALS gene overexpression and enhanced metabolism conferring Digitaria sanguinalis resistance to nicosulfuron in China.

Project description:Crabgrass (Digitaria sanguinalis) is a common malignant weed in corn fields in China. Recently, the acetolactate synthase (ALS) inhibitor, nicosulfuron, has shown decreasing efficacy against crabgrass. In order to elucidate the molecular basis of resistance to nicosulfuron in crabgrass, we conducted bioassays, combined with gene sequence analysis, relative expression and relative copy number analysis, to characterize resistance in crabgrass populations collected from Beijing, Heilongjiang, Jilin and Anhui provinces. Whole-plant dose-response results indicated that only population collected in Heilongjiang province (HLJ) had developed low level of resistance to nicosulfuron compared with the sensitive population (SD22). No known resistant mutation of ALS gene was found in HLJ population. The real-time fluorescence quantitative PCR results showed that the ALS gene copy number did not differ significantly between the HLJ and SD22 populations. However, the ALS gene expression in the HLJ was 2.07-fold higher than that of the SD22 population at 24 h after treatment with nicosulfuron. Pretreatment with the cytochrome P450 (CYP450) inhibitor malathion, piperonyl butoxide (PBO), and the glutathione S-transferase (GST) inhibitor 4-Chloro-7-nitro-1,2,3-benzoxadiazole (NBD-Cl) all partially reversed HLJ resistance. Among them, the synergistic effect of PBO and nicosulfuron is the most significant. This is the first report of resistance to nicosulfuron in crabgrass through ALS gene overexpression and possible metabolic resistance.

| S-EPMC10690955 | biostudies-literature

Cytochrome P450s-Involved Enhanced Metabolism Contributes to the High Level of Nicosulfuron Resistance in Digitaria sanguinalis from China.

Project description:Large crabgrass (Digitaria sanguinalis (L.) Scop.) is one of the major malignant grass weeds in Chinese maize (Zea mays L.) fields, and it has recently developed resistance to the acetolactate synthase (ALS)-inhibiting herbicide nicosulfuron. This study focused on a suspected nicosulfuron-resistant (R) population (LJ-01) of D. sanguinalis, collected from Lujiang County in Anhui Province, China, to explore the resistance level and potential resistance mechanism. Whole-plant dose-response testing confirmed that the LJ-01 population evolved a high level of resistance to nicosulfuron (11.5-fold) compared to the susceptible (S) population, DY-02. The ALS gene sequencing and relative expression assay of the R plants indicated that target gene mutation and overexpression were not responsible for the resistance phenotype. However, pretreatment with malathion, a known cytochrome P450 monooxygenase (P450) inhibitor, alleviated the resistance of the R population to nicosulfuron by approximately 36%. High-performance liquid chromatography (HPLC) analysis revealed that the R plants metabolized nicosulfuron faster than the S plants. Moreover, cross-resistance testing suggested that the R population exhibited low levels of resistance to thifensulfuron-methyl and pyrazosulfuron-ethyl, but it remained susceptible to rimsulfuron. Multiple resistance patterns showed that the R population evolved low resistance to the photosystem inhibitors bromoxynil octanoate and atrazine and sensitivity to the acetyl-CoA carboxylase (ACCase) inhibitor cyhalofop-butyl and the 4-hydroxyphenylpyruvate dioxygenase (HPPD) inhibitors tembotrione, mesotrione, and topramezone. This study reports, for the first time, the simultaneous resistance to ALS and different photosystem inhibitors in D. sanguinalis. The nicosulfuron resistance observed in the R population could primarily be attributed to an enhanced metabolism involving P450 enzymes.

| S-EPMC10525941 | biostudies-literature

Keteleeria cyclolepis complete chloroplast genome

Project description:Keteleeria cyclolepis complete chloroplast genome Raw sequence reads

| PRJNA723268 | ENA