Urochloa decumbens cultivar:Basilisk
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ABSTRACT:
PROVIDER: PRJNA393715 | ENA |
REPOSITORIES: ENA
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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:Transcriptomic analysis of fungus Penicillium decumbens and brlA deletion strains in liquid medium and solid medium respectivelly Examination of differential gene expressions by Penicillium decumbens strains 114-2 and brlA deletion stains in liquid medium and solid medium
2013-04-09 | E-GEOD-45855 | biostudies-arrayexpress
Project description:Forage grasses of the African genus Urochloa (syn. Brachiaria) are the basis of Brazilian beef production, and there is a strong demand for high quality, productive and adapted forage plants. Among the approximately 100 species of the genus Urochloa, Urochloa decumbens is one of the most important tropical forage grasses used for pastures due to several of its agronomic attributes. However, the level of understanding of these attributes and the tools with which to control them at the genetic level are limited, mainly due to the apomixis and ploidy level of this species. In this context, the present study aimed to identify and characterize molecular microsatellite markers of U. decumbens and to evaluate their cross-amplification in other Urochloa species.Microsatellite loci were isolated from a previously constructed enriched library from one U. decumbens genotype. Specific primers were designed for one hundred thirteen loci, and ninety-three primer pairs successfully amplified microsatellite regions, yielding an average of 4.93 alleles per locus. The polymorphism information content (PIC) values of these loci ranged from 0.26 to 0.85 (average 0.68), and the associated discriminating power (DP) values ranged from 0.22 to 0.97 (average 0.77). Cross-amplification studies demonstrated the potential transferability of these microsatellites to four other Urochloa species. Structure analysis revealed the existence of three distinct groups, providing evidence in the allelic pool that U. decumbens is closely related to Urochloa ruziziensis and Urochloa brizantha. The genetic distance values determined using Jaccard's coefficient ranged from 0.06 to 0.76.The microsatellite markers identified in this study are the first set of molecular markers for U. decumbens species. Their availability will facilitate understanding the genetics of this and other Urochloa species and breeding them, and will be useful for germplasm characterization, linkage mapping and marker-assisted selection.
| S-EPMC4785737 | biostudies-literature
Project description:Transcriptomic analysis of fungus Penicillium decumbens and brlA deletion strains in liquid medium and solid medium respectivelly
2013-04-09 | GSE45855 | GEO
Project description:To examine the mechanisms that control flower development, we sequenced the flower bud transcriptomes of ‘High Noon’, a reblooming cultivar of P. suffruticosa × P. lutea. Both full-length isoforms and RNA-seq were sequenced in 3 floral developmental stages. A total of 15.94 Gb raw data and 457.0 million reads were generated in full-length transcript sequencing and RNA-seq.
2019-06-29 | GSE133476 | GEO
Project description:Morus alba L. Raw protein sequence reads and sequence
2024-02-08 | PXD049451 |
Project description:BACKGROUND AND AIMS:Signal grass (Urochloa decumbens) is a widely used pasture grass in tropical and sub-tropical areas due to its high aluminiun (Al) resistance. However, the underlying mechanisms conferring this resistance are not clearly understood. METHODS:The Al concentrations of bulk root tissues and the intracellular compartment were examined, including the impact of a metabolic inhibitor, carbonyl cyanide m-chlorophenyl hydrazone (CCCP). Next, we examined changes in the properties of signal grass root tissues following exposure to toxic levels of Al, including the cell wall cation exchange capacity (CEC), degree of methylation and concentrations of cell wall fractions. KEY RESULTS:Although signal grass was highly resistant to Al, there was a delay of 24-48 h before the expression of this resistance. We found that this delay in the expression of Al resistance was not related to the total Al concentration in the bulk apical root tissues, nor was it related to changes in the Al bound to the cell wall. We also examined changes in other properties of the cell wall, including the CEC, degree of methylation and changes in the concentration of pectin, hemicellulose and cellulose. We noted that concentrations of intracellular Al decreased by approx. 50 % at the same time that the root elongation rate improved after 24-48 h. Using CCCP as a metabolic inhibitor, we found that the intracellular Al concentration increased approx. 14-fold and that the CCCP prevented the subsequent decrease in intracellular Al. CONCLUSIONS:Our results indicate that the delayed expression of Al resistance was not associated with the Al concentration in the bulk apical root tissues or bound to the cell wall, nor was it associated with changes in other properties of the cell wall. Rather, signal grass has an energy-dependent Al exclusion mechanism, and this mechanism requires 24-48 h to exclude Al from the intracellular compartment.
| S-EPMC7182589 | biostudies-literature