12/14/2023 0 Comments Clc rna seqDe novo assembly using the CLC Genomic Workbench produced 86,020 transcripts and a reference transcriptome with an N50 of 683 base pair. Results: The RNA sequencing generated a total of 14,680,108 paired-end reads from the control and stressed conditions. neei in response to growth in saline water containing 3 mM ammonium. To identify the molecular mechanisms related to ammonium response, we analyzed the transcriptome of S. Ībstract = "Background: Salicornia neei is a halophyte plant that has been proposed for use in the phytoremediation of the saline wastewater generated by land-based aquaculture. RNA-seq analysis and transcriptome assembly of Salicornia neei reveals a powerful system for ammonium detoxification. How to cite: Díaz-Silva M, Maldonado J, Veloso P, et al. For an immersive experience a head-mounted display can be used. To view the video correctly, it is necessary to scroll through the screen to navigate across the laboratory where you will find 6 interactive points. This manuscript includes an interactive 360 degree video, supplementary to the materials and methods section. The present transcriptome profiling method could be useful when investigating the response of halophyte plants to saline wastewater from land-based aquaculture. neei when exposed to ammonium and saline water. Conclusions: Our results support the hypothesis that an ammonium detoxification system mediated by glutamine and glutamate synthase was activated in S. In addition, a set of 72 genes was directly involved in ammonium metabolism, including glutamine synthetase 1, glutamate synthase 1, and ferredoxin-dependent glutamate synthase chloroplastic. The upregulated genes were mainly involved in cell wall biosynthesis, transmembrane transport and antiporter activities, including biological Kyoto Encyclopedia of Genes and Genomes, pathways linked to the biosynthesis of secondary metabolites, plant hormone signal transduction, autophagy, and nitrogen metabolism. As regards differentially expressed genes, a total of 9,140 genes were differentially expressed in response to ammonium in saline water of these, 7,396 could be annotated against functional databases. A total of 45,327 genes were annotated, representing 51.2% of the contig predicted from de novo assembly. Graph and table of background distribution and the false discovery rateĬlick the Here to learn more about CLCBio ( Salicornia neei is a halophyte plant that has been proposed for use in the phytoremediation of the saline wastewater generated by land-based aquaculture.Chromatin immunoprecipitation sequencing (ChIP-seq) analysis.RNA-seq including support for paired data and transcript-level expression.Support for multiplexing with DNA barcoding.SNP detection using advanced quality filtering.Advanced visualization, scrolling, and zooming tools.De novo assembly of genomes of any size (only limited by RAM available).Read mapping of Sanger, Illumina, PacBio, and IonTorrent sequencing data.CLC Genomics Workbench, for analyzing and visualizing Next Generation Sequencing data, incorporates cutting-edge technology and algorithms, while also supporting and integrating with the rest of your typical NGS workflow.
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