Integration analysis of PacBio SMRT- and Illumina RNA-seq reveals candidate genes and pathway involved in selenium metabolism in hyperaccumulator Cardamine violifolia

Abstract

Background Cardamine violifolia, native to China, is one of the selenium (Se) hyperaccumulators. The mechanism of Se metabolism and tolerance remains unclear, and only limited genetic information is currently available. Therefore, we combined a PacBio single-molecule real-time (SMRT) transcriptome library and the Illumina RNA-seq data of sodium selenate (Na2SeO4)-treated C. violifolia to further reveal the molecular mechanism of Se metabolism. Results The concentrations of the total, inorganic, and organic Se in C. violifolia seedlings significantly increased as the Na2SeO4 treatment concentration increased. From SMRT full-length transcriptome of C. violifolia, we obtained 26,745 annotated nonredundant transcripts, 14,269 simple sequence repeats, 283 alternative splices, and 3407 transcription factors. Fifty-one genes from 134 transcripts were identified to be involved in Se metabolism, including transporter, assimilatory enzyme, and several specific genes. Analysis of Illumina RNA-Seq data showed that a total of 948 differentially expressed genes (DEGs) were filtered from the four groups with Na2SeO4 treatment, among which 11 DEGs were related to Se metabolism. The enrichment analysis of KEGG pathways of all the DEGs showed that they were significantly enriched in five pathways, such as hormone signal transduction and plant-pathogen interaction pathways. Four genes related to Se metabolism, adenosine triphosphate sulfurase 1, adenosine 5′-phosphosulfate reductase 3, cysteine (Cys) desulfurase 1, and serine acetyltransferase 2, were regulated by lncRNAs. Twenty potential hub genes (e.g., sulfate transporter 1;1, Cys synthase, methionine gamma-lyase, and Se-binding protein 1) were screened and identified to play important roles in Se accumulation and tolerance in C. violifolia as concluded by weighted gene correlation network analysis. Based on combinative analysis of expression profiling and annotation of genes as well as Se speciation and concentration in C. violifolia under the treatments with different Na2SeO4 concentrations, a putative Se metabolism and assimilation pathway in C. violifolia was proposed. Conclusion Our data provide abundant information on putative gene transcriptions and pathway involved in Se metabolism of C. violifolia. The findings present a genetic resource and provide novel insights into the mechanism of Se hyperaccumulation in C. violifolia.

Comparative study of the effects of selenium yeast and sodium selenite on selenium content and nutrient quality in broccoli florets (Brassica oleracea L. var. italica)

“…The total Se content of broccoli florets was detected using the method of Rao et al 17 . through hydride‐generation atomic fluorescence spectrometry (HG‐AFS) (AFS8510; Beijing Haiguang Instrument Co., Beijing, China).…”

“…The total Se content of broccoli florets was detected using the method of Rao et al 17 through hydride-generation atomic fluorescence spectrometry (HG-AFS) (AFS8510; Beijing Haiguang Instrument Co., Beijing, China). In brief, 0.20 g of samples were weighed and placed in a digestion tube and subsequently digested with 10 mL of HNO 3 and 2 mL of H 2 O 2 in a microwavedigestion system.…”

Nanopore RNA Sequencing Revealed Long Non-Coding and LTR Retrotransposon-Related RNAs Expressed at Early Stages of Triticale SEED Development

“…The application of long-read technologies to the exploration of the lncRNA repertoire in plants has been demonstrated for several plant species, including Oryza sativa L. ssp. japonica [ 27 ], Populus simonii [ 28 ], P. qiongdaoensis [ 29 ], poplar “Nanlin 895” [ 30 ], Trifolium pratense [ 31 ], Cardamine violifolia [ 32 ], and Vigna angularis [ 33 ]. These studies demonstrated that long-read sequencing can be used to obtain a comprehensive catalogue of lncRNAs.…”

Comparative Transcriptomic Analyses Provide Insights into the Enzymatic Browning Mechanism of Fresh-Cut Sand Pear Fruit

“…Full length (FL) transcripts can significantly upgrade the accuracy of genome annotation and assembly, which help to identify full length isoforms of a gene, AS events, lncRNAs, and alternative polyadenylation (APA) sites [38]. Recent advances in comprehensive information with SMRT-seq and Illumina RNA-seq have been applied to detect more gene isoforms and expose functional variety [39,40]. SMRT sequencing was used to obtain diverse FL cDNA sequences and enhance gene annotation in birch-leaf pear (P. betulifolia Bunge) [41], but the error rate of these data was not overcome by correction of Illumina RNA-Seq.…”