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

The genome of elephant grass (Cenchrus purpureus)

Project description:The genome of elephant grass (Cenchrus purpureus)

| PRJEB50934 | ENA

Investigation of ctitrinin and pigment biosynthesis mechanisms in Monascus purpureus by transcriptomic analysis

Project description:M. purpureus YY-1 is widely used in food colorant production in China. In our previous study, the whole-genome information of YY-1 was clearly illustrated, which provided useful hints for evolution esearch and industrial applications. However, the presence of citrinin, which has nephrotoxic, hepatotoxic, and carcinogenic activities, attracts people′s attention to the safety of Monascus products. In order to reduce the harm of citrinin in Monascus related products, in this study, a random mutant of M. purpureus YY-1, with scarce citrinin production (designated as winter) was obtained. To analyze the biosynthesis and regulation mechanism of pigment and citrinin, transcriptomic analysis of M. purpureus YY-1 and winter was performed. Comparative transcriptomic analysis reveals pksCT, the essential gene for citrinin synthesis, showed low expression level in M. purpureus YY-1 and winter, which suggested there might be isoenzymes in M. purpureus YY-1 that were responsible for the citrinin synthesis during evolution. In addition, the expression change of transcription factors may also influence the regulatory network of citrinin synthesis pathway of in M. purpureus. Moreover, the yields of pigments produced by the winter mutant were significantly increased. Repressing central carbon metabolism and improving the acetyl-CoA pool can contribute to the high yield of pigments, and enhanced NADPH regeneration also lead the metabolic flux to pigments in M. purpureus. Investigations on biosynthesis and regulation of citrinin and pigment production in M purpureus will enhance our knowledge of the mechanisms in fungal secondary metabolite biosynthesis.

2018-05-02 | GSE107628 | GEO

Cenchrus americanus

Project description:Cenchrus americanus Genome sequencing and assembly

| PRJNA749490 | ENA