Integrated morphological, physiological and omics analyses reveal the arylalkylamine N-acetyltransferase (AANAT) gene contributing to growth, flowering and defence in switchgrass (Panicum virgatum L.)

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“…SCRM, SPCH, MUTE and FAMA). This result was supported by previous studies (Khan et al, 2019;Huang et al, 2022). In addition, the transcript abundances of most key genes involved in carbon fixation pathways were also changed in OE-oHIOMT switchgrass.…”

“…The cDNA library was sequenced using an Illumina Hiseq platform, and clean reads were aligned to the switchgrass reference genome sequence (https://phytozome-next.jgi.doe.gov/ info/Pvirgatum_v4_1). Data were analyzed following our previously reported methods (Huang et al, 2022). For proteomic analysis, 150 mg of powder from each sample was used as the input material for protein preparation.…”

“…However, our previous study did not explore the underlying mechanism. Recent advancements in multi-omics analyses, which integrates various genomic, transcriptomic, proteomic and metabolomic analyses, have been widely accepted as powerful tools for discovering the mechanism of action of melatonin (Huang et al, 2022). In the present study, we conducted RNA sequencing and proteomic analysis (based on isobaric tags for relative and absolute quantitation) to identify differentially expressed genes and proteins in OE-oHIOMT transgenic lines with varying melatonin levels.…”

Enhanced resistance to heat and fungal infection in transgenic Trichoderma via over-expressing the HSP70 gene

“…VCEC00000000; BioProject: PRJNA543939; BioSample: SAMN11791795) using TopHat (Kim et al 2013 ). Data analysis followed the methods described in our previous study (Huang et al 2022 ). We conducted differential gene expression (DGE) analysis using DESeq R (1.18.0), Gene Ontology (GO) functional enrichment using Goseq R package software and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses using KOBAS tool.…”

“…However, few studies have focused on the effects of HSP70 on Trichoderma . Recent advancements in transcriptome analysis, which integrates multiple types of morphological, physiological and molecular analyses, has been rapidly widely accepted as a powerful tool for uncovering the underlying mechanism of action (Huang et al 2022 ). Therefore, we conducted an RNA-sequencing analysis to compare the transcriptomes of T .…”