Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Screening Genes related to Bur Lignification Development in field sandbur (Cenchrus pauciflorus Benth.) Based on Full-Length Transcriptome Sequencing

ABSTRACT: Full-length transcriptome of field sandbur (Cenchrus pauciflorus Benth.) was constructed, and high-throughput sequencing was conducted on mixed samples from four stages (BS1-BS4) of bur development and the root, stem, and leaf organs using the PacBio platform. After quality control and redundancy removal, 266,986 isoforms were obtained, of which 245,910 were annotated to seven major functional databases, accounting for 92.11%. This result showed the highest similarity with other grass species in the Trib. Paniceae R. Br., such as Setaria viridis. A total of 155,474 coding sequences (CDS) with coding capability were predicted, including 3,957 isoforms that have the ability to code for transcription factors. KEGG functional distribution analysis indicated that the number of genes involved in cellular anatomical entities reached 125,020; KOG annotation identified 4,889 genes involved in the synthesis, transport, and metabolism of secondary metabolites. Within the phenylpropanoid biosynthesis pathway, 1,900 isoforms were identified as participating in the lignin biosynthesis pathway of bur, and these genes may be candidate genes for lignification development in the bur. This study lays the foundation for elucidating the molecular mechanisms underlying the lignification development of the invasive plant field sandbur in the Horqin grassland.

ORGANISM(S): Cenchrus spinifex

PROVIDER: GSE279112 | GEO | 2026/04/09

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Screening Genes related to Bur Lignification Development in field sandbur (Cenchrus pauciflorus Benth.) Based on Full-Length Transcriptome Sequencing

Project description:Screening Genes related to Bur Lignification Development in field sandbur (Cenchrus pauciflorus Benth.) Based on Full-Length Transcriptome Sequencing

| PRJNA1170890 | ENA

Lignin biosynthesis and lignification cDNAs in Digitaria exilis

Project description:Identification and sequencing of lignin biosynthesis, lignification and lignin pathway control in the orphan grain crop, Digitaria exilis

| PRJEB29768 | ENA

transcription of ectopic lignification-Identification of genes differentiallty expressed in mur1 basal stems

Project description:ra15-04_elim1 - transcription of ectopic lignification - What are genes involved in lignin modifications in mur1 stems? - RNA extractions have been performed on mur1 and WT stems of 13 cm. Three biological repeats were used for the transcriptomic analysis.

2015-12-01 | GSE74857 | GEO

The lignin biosynthetic and lignification pathways in Miscanthus sinensis cv Andante

Project description:Deciphering and assembling the key lignification and lignin biosynthesis pathways in the bioenergy crop Miscanthus sinensis cv Andante

| PRJEB30269 | ENA

The microbial functional diversity in response to altered precipitation on Tibet Plateau as characterized by GeoChip

Project description:Global warming substantially changes precipitation patterns in the Tibetan plateau, with projection of increased precipitation in southern and northern Tibet but decreased precipitation in the center. Understanding mechanisms of such changes in greenhouse gas emissions is of vital importance in predicting ecosystem feedbacks to climate changes. Nonetheless, it has been hampered by limited knowledge in soil microbial communities, one of the major drivers of greenhouse gas emission. Here, we report a field experiment simulating drying and wetting conditions in the Tibetan grassland. Our field site is located at the Haibei Alpine Grassland Ecosystem Research Station in the northeast of Tibet Plateau, China, and we employed GeoChip 5.0 180K to analyze microbial responses.

2016-05-28 | GSE82006 | GEO

The microbial functional diversity in response to altered precipitation on Tibet Plateau as characterized by GeoChip

2016-05-28 | E-GEOD-82006 | biostudies-arrayexpress

Novel resources to investigate leaf plasmodesmata formation in C3 and C4 monocots

Project description:Plasmodesmata (PD) are nanochannels that facilitate cell-to-cell transport in plants. More productive and photosynthetically efficient C4 plants form more PD at the mesophyll (M)-bundle sheath (BS) interface in their leaves than their less efficient C3 relatives. In C4 leaves, PD play an essential role in facilitating the rapid metabolite exchange between the M and BS cells to operate a biochemical CO2 concentrating mechanism, which increases the CO2 partial pressure at the site of Rubisco in the BS cells and hence photosynthetic efficiency. The genetic mechanism controlling PD formation in C3 and C4 leaves is largely unknown, especially in monocot crops, due to the technical challenge of quantifying these nanostructures with electron microscopy. To address this issue, we have generated stably transformed lines of Oryza sativa (rice, C3) and Setaria viridis (setaria, C4) with fluorescent protein-tagged PD to build the first spatiotemporal atlas of leaf pit field (cluster of PD) density in monocots without the need for electron microscopy. Across leaf development, setaria had consistently more PD connections at the M-BS wall interface than rice while the difference in M-M pit field density varied. While light was a critical trigger of PD formation, cell type and function determined leaf pit field density. Complementary temporal mRNA sequencing and gene co-expression network analysis revealed that the pattern of pit field density correlated with differentially expressed PD-associated genes and photosynthesis-related genes. PD-associated genes identified from our co-expression network analysis are related to cell wall expansion, translation and chloroplast signalling.

2024-11-21 | GSE260855 | GEO

Transcriptome Exploration in Anisodus acutangulus for Further Understanding of the Tropane Alkaloids Biosynthesis

Project description:We analyzed the transcriptome of A. acutangulus roots by deep RNA sequencing to dig TAs biosynthetic genes. KOG (Eukaryotic Orthologous Groups) and KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway enrichment analyses identified 48 unigenes referring to the tropane, piperidine and pyridine alkaloid biosynthesis, 145 unigenes presumably involved in distribution of arginine to TAs biosynthesis, and 86 unigenes referring to the terpenoid backbone biosynthesis. Furthermore, 82 unigenes annotated as cytochrome P450 family members seemed to be involved in secondary metabolism pathways. Previously unknown TAs biosynthetic genes in A. acutangulus, which encode littorine mutase/monooxygenase (CYP80F1) and diamine oxidase (DAO), were identified by this study.

2016-07-08 | GSE62162 | GEO

Silicon effect on suberization and lignification in roots of rice (Oryza sativa)

Project description:This study was performed to study the effect of silicon (Si) nutrition on suberization and lignification in roots of rice. Besides physiological and histochemical examinations of the roots, transcription of candidate genes related to synthesis of suberin and lignin was investigated using microarray analysis. 14 days old rice seedlings (Oryza sativa, cv. Selenio) were cultivated for 28 days in non-aerated nutrient solution (mM: 1.43 NH4NO3, 0.32 NaH2PO4 x H2O, 0.51 K2SO4, 1 CaCl2 x 2 H2O, 1.6 MgSO4 x 7 H2O; µM: 1.82 MnSO4, 0.03 (NH4)6Mo7O24, 9 H3BO3, 0.3 ZnSO4 x 7 H2O and 0.15 CuSO4). The pH-value was adjusted to 6.0 by addition of 10 % (v/v) H2SO4 and 0.75 M KOH.Plants were supplied with Si in form of K2SiO3 at concentrations 0 ppm Si (control) and 50 ppm Si (1.78 mM) and potassium in the control treatment was balanced with K2SO4 supply. The plants were grown in a growth chamber (photoperiod: 14 h light, 10 h dark; temperature 25°C day / 20°C night; relative humidity 75 %; light intensity 220 µmol m2 s-1). Adventitious roots were harvested at 0-2 cm and 4-6 cm distance from the root tip and frozen immediately in liquid nitrogen. For RNA isolation, roots were ground under liquid nitrogen and total RNA was isolated using TRIsure® Reagent (Bioline, Luckenwalde, Germany) following the instructions of the manufacturer. To examine transcription of genes related to suberin and lignin synthesis, a self developed microarray containing amongst others ABC transporter, aclytransferases, ß-ketoacyl-CoA synthases and peroxidases was used .

2010-10-10 | GSE23723 | GEO

Brassinosteroids modulate meristem fate and differentiation of unique inflorescence morphology in Setaria viridis

Project description:RNA-seq was performed to profile the transcriptomes of inflorescence primordia hand-dissected from the bristleless1-1 (bsl1-1)mutant in Setaria viridis compared to wild-type controls sampled under the same conditions. Bsl1 encodes a rate limiting enzyme in BR biosynthesis, which is the ortholog of D11 from rice. Mutants are characterized by a homeotic conversion of sterile bristles to spikelets in the inflorescence.

2017-12-23 | GSE100423 | GEO