Comparative de novo transcriptomics and untargeted metabolomic analyses elucidate complicated mechanisms regulating celery (Apium graveolens L.) responses to selenium stimuli

Abstract

Presently, concern regarding the effects of selenium (Se) on the environment and organisms worldwide is increasing. Too much Se in the soil is harmful to plants. In this study, Illumina RNA sequencing and the untargeted metabolome of control and Se-treated celery seedlings were analyzed. In total, 297,911,046 clean reads were obtained and assembled into 150,218 transcripts (50,876 unigenes). A total of 36,287 unigenes were annotated using different databases. Additionally, 8,907 differentially expressed genes, including 5,319 up- and 3,588 downregulated genes, were identified between mock and Se-treated plants. “Phenylpropanoid biosynthesis” was the most enriched KEGG pathway. A total of 24 sulfur and selenocompound metabolic unigenes were differentially expressed. Furthermore, 1,774 metabolites and 237 significant differentially accumulated metabolites were identified using the untargeted metabolomic approach. We conducted correlation analyses of enriched KEGG pathways of differentially expressed genes and accumulated metabolites. Our findings suggested that candidate genes and metabolites involved in important biological pathways may regulate Se tolerance in celery. The results increase our understanding of the molecular mechanism responsible for celery’s adaptation to Se stress.

Comparative physiological and full-length transcriptome analyses reveal the molecular mechanism of melatonin-mediated salt tolerance in okra (Abelmoschus esculentus L.)

“…A total amount of 3 μg RNA per sample was used for the library preparation [ 25 ]. The NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) was used to generate sequencing libraries as described by the manufacturer.…”

“…Differential expression analysis was performed using the DESeq R package (1.10.1). Genes with an adjusted P -value < 0.05 found by DESeq were assigned as differentially expressed [ 25 ].…”

“…Transcriptomics provides an important basis for systematically revealing gene transcription maps and their regulation, clarifying the molecular mechanism of complex biological traits, and understanding the interaction mechanism between genetic and environmental factors [ 24 , 25 ]. The second-generation high-throughput sequencing technology is easy to produce many fragments and overlapping groups that can not be spliced, and to lose important information such as variable splicing [ 26 – 28 ].…”

Advances in “Omics” Approaches for Improving Toxic Metals/Metalloids Tolerance in Plants

“…In soil, excess Se may appear destructive to plants. Zhang et al (2019b) carried out an untargeted metabolome analysis of Se-treated and control celery seedlings and identified 24 sulfur and seleno-compound metabolic unigenes to be differentially expressed. Moreover, 1,774 metabolites and 237 SDMs were found through UHPLC-MS/MS.…”

Impact of Genomic and Transcriptomic Resources on Apiaceae Crop Breeding Strategies

“…In Notopterygium incisum , 21 transcripts were related to cold tolerance [ 86 ] and among them, stand out the genes homologous to COR47 ( COLD-REGULATED GENE ), GIF2 ( GRF1-INTERACTING FACTOR 2 ) PGP20 ( P-GLYCOPROTEIN 20 ), RECQ4A (a DNA helicase from the RecQ family) and UGT80B1 ( UDP-GLYCOSYLTRANSFERASE 80B1 ). In Apium graveolens , 24 genes associated with sulfur and selenium compound metabolism, including four ATP-sulfurylases, resulted in differential expression with selenium treatment [ 132 ]. Since heat is one of the most detrimental stresses, major efforts are underway to identify heat-responsive genes in several species.…”