Lignin production associated genes in Cenchrus purpueus
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ABSTRACT:
PROVIDER: PRJNA731177 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR14595146_1.fastq.gz | Fastqsanger.gz | |||
| SRR14595146_2.fastq.gz | Fastqsanger.gz | |||
| SRR14595147_1.fastq.gz | Fastqsanger.gz | |||
| SRR14595147_2.fastq.gz | Fastqsanger.gz | |||
| SRR14595148_1.fastq.gz | Fastqsanger.gz |
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Project description:This study aims to reveal genes related to lignin production in Cenchrus purpureus through RNA-Seq. This species is widely used as forrage for cattle, and for the last years, due to its high biomass yield, has been considered as source to lignocellulosic ethanol. Given those two importances, lignin is a molecule related to low digestibility in cattle and recalcitrance in biofuel production. Eight samples were chosen from previous lignin production and forage quality data; four samples had low lignin production, and four had high lignin production. The highest nodes were collected for RNA extraction using TRIzol reagent, following Jordon-Thaden et a;. (2015) protocol. The cDNA library preparation was generated according to Illumina TruSeq Stranded mRNA Sample Prep kit protocol, and RNA sequencing was performed using HiSeq 2500 sequencer. Quality control was measured by FastQC software v 0.11.8. The sequenced reads were aligned to Cenchrus purpureus genome through STAR software v. 2.5.2b (Dobin et al., 2012). After that, the transcriptome was assembled using Stringtie v 2.0.4 software (Pertea et al., 2015). Salmon v 0.7.2 software (Patro et al., 2017) was used to quantify the sequenced reads. The DEG was identified using DESeq2 package, and genes functions were annotated through Trinotate software (Bryant et al., 2017). In total, approximately 130 million reads were sequenced. The final assembled transcriptome was formed by 101,169 transcripts. The differential expressed genes analysis revealed 52 significatively genes. Here, we highlighted genes related to sterol, L-serine and terpene biosynthetic process.
2021-10-01 | GSE174718 | GEO
Project description:Lignin production associated genes in Urochloa humidicola
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Project description:This study aims to reveal genes related to lignin production in Urochloa humidicola through RNA-Seq. This species is widely used as forrage for cattle, being some species of Urochloa responsible for 85% of pastures in Brazil. Given this importance, lignin is a molecule directly related to low digestibility in cattle. Eight samples were chosen from previous lignin production and forage quality data; four samples had low lignin production, and four had high lignin production. The second extended leaves were collected for RNA extraction using RNeasy® Plant Mini Kit. The cDNA library preparation was generated according to Illumina TruSeq Stranded mRNA Sample Prep kit protocol, and RNA sequencing was performed using HiSeq 2500 sequencer. Quality control was measured by FastQC software v 0.11.8. As Urochloa humidicola does not have a sequenced genome, a transcriptome assembly was built by two approaches: through Trinity v 2.8.4 (Grabherr et al., 2011), and Stringtie v 2.0.4 software (Pertea et al., 2015), using Urochloa ruziziensis as reference genome. Then, the final transcriptome was assembled using those two de novo assembles by PASA v 2.2 (Haas et al., 2003). Salmon v 0.7.2 software (Patro et al., 2017) was used to quantify the sequenced reads. The DEG was identified using DESeq2 package, and genes functions were annotated through Trinotate software (Bryant et al., 2017). In total, approximately 123 million reads were sequenced. The final assembled transcriptome was formed by 48,695 transcripts. The differential expressed genes analysis revealed 258 significatively genes. Here, we highlighted genes related to flavonoid biosynthetic process, regulation of phenylpropanoid metabolic process, and Myb-like DNA-binding domain.
2021-09-30 | GSE175577 | GEO
Project description:Lignin, a recalcitrant aromatic biopolymer, represents a promising feedstock for sustainable biorefining. In this study, we characterized the transcriptional response of the fungus Curvularia clavata J1 to alkali lignin (AL) and developed a Cu2+-inducible MCM5–AID base editing system for genome-wide C-to-T and G-to-A mutagenesis. Transcriptomic analysis revealed that AL exposure triggered upregulation of genes involved in electron transport, lipid catabolism, and iron homeostasis. Using droplet microfluidics, we conducted ultrahigh-throughput screening and identified a mutant strain, M6, exhibiting superior phenotypic traits. When cultivated in lignosulfonate medium, M6 showed a 33–36% increase in lipid production and a 75–87% enhancement in laccase activity. Transcriptional profiling further indicated reinforced metabolic pathways related to fatty acid, steroid, and glycerolipid biosynthesis, redirecting carbon flux toward the formation of oil-enriched single-cell protein. This study establishes an integrated platform for lignin valorization and underscores the synergy between synthetic biology and microfluidics for precision engineering of fungal hosts.
2025-08-28 | GSE306066 | GEO
Project description:lignin degradation genes studies in aquatic environment Metagenome
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Project description:Integrated Base Editing and Microfluidics Boost Microbial Lipid Production from Lignin
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Project description:lignin degradation active genes studies in aquatic environment Raw sequence reads
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Project description:The production of lignocellulosic-derived biofuels is a highly promising source of alternative energy, but it has been constrained by the lack of a microbial platform capable to efficiently degrade this recalcitrant material and cope with by-products that can be toxic to cells. Species that naturally grow in environments where carbon is mainly available as lignin are promising for finding new ways of removing the lignin that protects cellulose for improved conversion of lignin to fuel precursors.
2018-02-13 | GSE96828 | GEO
Project description:Our previous studies, comparing russeted vs. waxy apple skin, highlighted a MYeloBlastosys (Myb) transcription factor (MdMYB52-like), which displayed a correlation with genes associated to the suberization process. The present article aims to assess its role and function in the suberization process. Phylogenetic analyses and research against Arabidopsis thaliana MYBs database were first performed and the tissue specific expression of MdMYB52-like was investigated using RT-qPCR. The function of MdMYB52-like was further investigated using Agrobacterium-mediated transient overexpression in Nicotiana benthamiana leaves. An RNA-Seq analysis was performed to highlight differentially regulated genes in response MdMYB52-like. Transcriptomic data were supported by analytical chemistry and microscopy. A massive decreased expression of photosynthetic and primary metabolism pathways was observed with a concomitant increased expression of genes associated with phenylpropanoid and lignin biosynthesis, cell wall modification and senescence. Interestingly key genes involved in the synthesis of suberin phenolic components were observed. The analytical chemistry displayed a strong increase in the lignin content in the cell walls during MdMYB52 expression. More specifically, an enrichment in G-Unit lignin residues was observed, supporting transcriptomic data as well as previous work describing the suberin phenolic domain as a G-unit enriched lignin-like polymer. The time-course qPCR analysis revealed that the observed stress response, might be explain by this lignin biosynthesis and by a possible programmed senescence triggered by MdMYB52-like. The present work supports a crucial regulatory role for MdMYB52 in the biosynthesis of the suberin phenolic domain and possibly in the fate of suberized cells in russeted apple skins.
2022-09-26 | GSE212828 | GEO