Impact of high or low levels of phosphorus and high sodium in soils on productivity and stress tolerance of Arundo donax plants

Cocozza, Claudia; Brilli, Federico; Miozzi, Laura; Pignattelli, Sara; Rotunno, Silvia; Brunetti, Cecilia; Giordano, Cristiana; Pollastri, Susanna; Centritto, Mauro; Accotto, G. P.; Tognetti, Roberto; Loreto, Francesco

doi:10.1016/j.plantsci.2019.110260

Cited by 13 publications

(10 citation statements)

References 83 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…In general, the first few bases were prone to recognition errors during sequencing, and these few bases were just the size of the random primers during the sequencing process. Thus, the recognition errors in the first few bases were speculated to be caused by incomplete pairing of random primers with RNA templates [39][40][41]. Therefore, quality control of the data generated by sequencing must be performed to obtain high-quality sequencing data for subsequent bioinformatics analysis.…”

Section: Discussionmentioning

confidence: 99%

Transcriptome analysis of differential gene expression in the longissimus dorsi muscle from Debao and landrace pigs based on RNA-sequencing

Song

Zeng

et al. 2019

Bioscience Reports

View full text Add to dashboard Cite

RNA-seq analysis was used to identify differentially expressed genes (DEGs) at the genetic level in the longissimus dorsi muscle from two pigs to investigate the genetic mechanisms underlying the difference in meat quality between Debao pigs and Landrace pigs. Then, these DEGs underwent functional annotation, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment, and protein–protein interaction (PPI) analyses. Finally, the expression levels of specific DEGs were assessed using qRT-PCR. The reference genome showed gene dosage detection of all samples which showed that the total reference genome comprised 22342 coding genes, including 14743 known and 190 unknown genes. For detection of the Debao pig genome, we obtained 14168 genes, including 13994 known and 174 unknown genes. For detection of the Landrace pig genome, we obtained 14404 genes, including 14223 known and 181 unknown genes. GO analysis and KEGG signaling pathway analysis show that DEGs are significantly related to metabolic regulation, amino acid metabolism, muscular tissue, muscle structure development etc. We identified key genes in these processes, such as FOS, EGR2, and IL6, by PPI network analysis. qRT-PCR confirmed the differential expression of six selected DEGs in both pig breeds. In conclusion, the present study revealed key genes and related signaling pathways that influence the difference in pork quality between these breeds and could provide a theoretical basis for improving pork quality in future genetic thremmatology.

show abstract

Section: Discussionmentioning

confidence: 99%

Transcriptome analysis of differential gene expression in the longissimus dorsi muscle from Debao and landrace pigs based on RNA-sequencing

Song

Zeng

et al. 2019

Bioscience Reports

View full text Add to dashboard Cite

show abstract

“…Therefore, for sRNAs sequencing, for each treatment, three samples were pooled together, while, for degradome sequencing, a pool from samples of all the treatments was prepared. More experimental details on plant growth conditions, stress treatments and sample collection are reported in the cognate paper [ 9 ].…”

Section: Methodsmentioning

confidence: 99%

“…Identical mapped reads were collapsed with the tool fastx_collapser belonging to the FASTX toolkit (v. 0.0.13; (accessed on 1 March 2022)) and, if present in at least three libraries (i.e., three different treatments) with a minimum of 5 reads, were renamed according to the corresponding miRNAs. Primary miRNA sequences (pri-miRNA) were searched in the A. donax transcriptome [ 9 ] using the Perl script SumirFind.pl (v. 1.1; (accessed on 1 March 2022)) [ 27 , 28 ] allowing two mismatches. MIReNA tool (v. 2.0; (accessed on 1 March 2022)) [ 29 ] was then used for precursors (pre-miRNAs) sequences identification and validation and for calculation of Minimum Folding Energy (MFE) and Minimal Folding Energy Index (MFEI).…”

Section: Methodsmentioning

confidence: 99%

“…One of the advantages of A. donax cultivation resides in its potential to grow in very low nutrient availability conditions [ 3 ] and to be employed for restoration of marginal lands [ 4 ] and phytoremediation [ 5 , 6 ]. Indeed, the ability of this plant to cope with different biotic and abiotic stresses and survive in degraded and marginal areas has been widely demonstrated [ 7 , 8 , 9 , 10 , 11 ].…”

Section: Introductionmentioning

confidence: 99%

“…Despite the economic importance of A. donax , its genome has not been sequenced so far, probably due to its complexity [ 17 ], and only transcriptomic studies have been performed to investigate its gene content and its molecular responses to the environment [ 9 , 10 , 18 , 19 , 20 , 21 , 22 ]. Based on the available transcriptomic data from different tissues (root, bud, culm, and leaf), an in silico prediction of A. donax miRNAs was conducted, resulting in the prediction of 141 conserved miRNAs distributed into 14 miRNA families and 462 in silico predicted target transcripts [ 23 ].…”

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Identification of Known and Novel Arundo donax L. MicroRNAs and Their Targets Using High-Throughput Sequencing and Degradome Analysis

Rotunno

Cocozza

Pantaleo

et al. 2022

Life

Self Cite

View full text Add to dashboard Cite

MicroRNAs (miRNAs) are a class of non-coding molecules involved in the regulation of a variety of biological processes. They have been identified and characterized in several plant species, but only limited data are available for Arundo donax L., one of the most promising bioenergy crops. Here we identified, for the first time, A. donax conserved and novel miRNAs together with their targets, through a combined analysis of high-throughput sequencing of small RNAs, transcriptome and degradome data. A total of 134 conserved miRNAs, belonging to 45 families, and 27 novel miRNA candidates were identified, along with the corresponding primary and precursor miRNA sequences. A total of 96 targets, 69 for known miRNAs and 27 for novel miRNA candidates, were also identified by degradome analysis and selected slice sites were validated by 5′-RACE. The identified set of conserved and novel candidate miRNAs, together with their targets, extends our knowledge about miRNAs in monocots and pave the way to further investigations on miRNAs-mediated regulatory processes in A. donax, Poaceae and other bioenergy crops.

show abstract

Biological pilot treatment reduces physicochemical and microbiological parameters of dairy cattle wastewater

Jorge

Silva

et al. 2022

Environ Sci Pollut Res

View full text Add to dashboard Cite

Impact of high or low levels of phosphorus and high sodium in soils on productivity and stress tolerance of Arundo donax plants

Cited by 13 publications

References 83 publications

Transcriptome analysis of differential gene expression in the longissimus dorsi muscle from Debao and landrace pigs based on RNA-sequencing

Transcriptome analysis of differential gene expression in the longissimus dorsi muscle from Debao and landrace pigs based on RNA-sequencing

Identification of Known and Novel Arundo donax L. MicroRNAs and Their Targets Using High-Throughput Sequencing and Degradome Analysis

Biological pilot treatment reduces physicochemical and microbiological parameters of dairy cattle wastewater

Contact Info

Product

Resources

About