ArticlePlant biotechnology journal2016
Integration of small RNAs, degradome and transcriptome sequencing in hyperaccumulator Sedum alfredii uncovers a complex regulatory network and provides insights into cadmium phytoremediation.
Article in Plant biotechnology journal, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 53 papers.
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Who cites it
53 citing papers in PubMed.
- MicroRNA regulation and physiological adaptation of Brassica juncea to cadmium toxicity.Molecular biology reports · 2026Article
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- Molecular mechanism of nano-vitamin A-mediated regulation of intramuscular fat deposition involving noncoding RNAs in pigs.BMC genomics · 2025Article
- Identification of miRNAs and Their Targets inInternational journal of molecular sciences · 2025Article
- A 24-nt miR9560 modulates the transporter gene BrpHMA2 expression in Brassica parachinensis.The plant genome · 2025Article
- Interfamily Grafted HybridsPlants (Basel, Switzerland) · 2024Article
- Cytological observation and RNA-seq analysis reveal novel miRNAs high expression associated with the pollen fertility of neo-tetraploid rice.BMC plant biology · 2023Article
- Endoplasmic reticulum stress-responsive microRNAs are involved in the regulation of abiotic stresses in wheat.Plant cell reports · 2023Article
- microRNA regulation of skin pigmentation in golden-back mutant of crucian carp from a rice-fish integrated farming system.BMC genomics · 2023Article
- Integration of transcriptome and metabolome analyses reveals sorghum roots responding to cadmium stress through regulation of the flavonoid biosynthesis pathway.Frontiers in plant science · 2023Article
- Transcriptional multiomics reveals the mechanism of seed deterioration in Nicotiana tabacum L. and Oryza sativa L.Journal of advanced research · 2022Article
- Parallel analysis of RNA ends reveals global microRNA-mediated target RNA cleavage in maize.The Plant journal : for cell and molecular biology · 2022Article
- microRNAs: Key Players in Plant Response to Metal Toxicity.International journal of molecular sciences · 2022Review
- Genome-Wide Characterization, Evolutionary Analysis ofPlants (Basel, Switzerland) · 2022Article
- Identification and expression analysis of the3 Biotech · 2022Article
- Genome-Wide Characterization ofPlants (Basel, Switzerland) · 2022Article
- Integration of small RNA, degradome, and transcriptome sequencing data illustrates the mechanism of low phosphorus adaptation inFrontiers in plant science · 2022Article
- Arsenic perception and signaling: The yet unexplored world.Frontiers in plant science · 2022Review
- Integrated analysis of small RNAs, transcriptome and degradome sequencing reveal the drought stress network inFrontiers in plant science · 2022Article
- Identification and Analysis of bZIP Family Genes inFrontiers in plant science · 2022Article
Corrections and comments
- Erratum issuedCorrigendum.2021
Authors and funding
9 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The hyperaccumulating ecotype of Sedum alfredii Hance is a cadmium (Cd)/zinc/lead co-hyperaccumulating species of Crassulaceae. It is a promising phytoremediation candidate accumulating substantial heavy metal ions without obvious signs of poisoning. However, few studies have focused on the regulatory roles of miRNAs and their targets in the hyperaccumulating ecotype of S. alfredii. Here, we combined analyses of the transcriptomics, sRNAs and the degradome to generate a comprehensive resource focused on identifying key regulatory miRNA-target circuits under Cd stress. A total of 87 721 unigenes and 356 miRNAs were identified by deep sequencing, and 79 miRNAs were differentially expressed under Cd stress. Furthermore, 754 target genes of 194 miRNAs were validated by degradome sequencing. A gene ontology (GO) enrichment analysis of differential miRNA targets revealed that auxin, redox-related secondary metabolism and metal transport pathways responded to Cd stress. An integrated analysis uncovered 39 pairs of miRNA targets that displayed negatively correlated expression profiles. Ten miRNA-target pairs also exhibited negative correlations according to a real-time quantitative PCR analysis. Moreover, a coexpression regulatory network was constructed based on profiles of differentially expressed genes. Two hub genes, ARF4 (auxin response factor 4) and AAP3 (amino acid permease 3), which might play central roles in the regulation of Cd-responsive genes, were uncovered. These results suggest that comprehensive analyses of the transcriptomics, sRNAs and the degradome provided a useful platform for investigating Cd hyperaccumulation in S. alfredii, and may provide new insights into the genetic engineering of phytoremediation.
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