title: Integration of small RNAs, degradome and transcriptome sequencing in hyperaccumulator Sedum alfredii uncovers a complex regulatory network and provides insights into cadmium phytoremediation.
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.
authors.affiliation: State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China.|Key Laboratory of Tree Breeding of Zhejiang Province, The Research Institute of Subtropical of Forestry, Chinese Academy of Forestry, Hangzhou, Zhejiang, China.
authors.forename: Xiaojiao
authors.initials: X
authors.lastname: Han
authors.affiliation: Key Laboratory of Tree Breeding of Zhejiang Province, The Research Institute of Subtropical of Forestry, Chinese Academy of Forestry, Hangzhou, Zhejiang, China.
authors.forename: Hengfu
authors.initials: H
authors.lastname: Yin
authors.affiliation: State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China.|Key Laboratory of Tree Breeding of Zhejiang Province, The Research Institute of Subtropical of Forestry, Chinese Academy of Forestry, Hangzhou, Zhejiang, China.
authors.forename: Xixi
authors.initials: X
authors.lastname: Song
authors.affiliation: State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China.|Key Laboratory of Tree Breeding of Zhejiang Province, The Research Institute of Subtropical of Forestry, Chinese Academy of Forestry, Hangzhou, Zhejiang, China.
authors.forename: Yunxing
authors.initials: Y
authors.lastname: Zhang
authors.affiliation: State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China.|Key Laboratory of Tree Breeding of Zhejiang Province, The Research Institute of Subtropical of Forestry, Chinese Academy of Forestry, Hangzhou, Zhejiang, China.
authors.forename: Mingying
authors.initials: M
authors.lastname: Liu
authors.affiliation: State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China.|Key Laboratory of Tree Breeding of Zhejiang Province, The Research Institute of Subtropical of Forestry, Chinese Academy of Forestry, Hangzhou, Zhejiang, China.
authors.forename: Jiang
authors.initials: J
authors.lastname: Sang
authors.affiliation: State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China.|Key Laboratory of Tree Breeding of Zhejiang Province, The Research Institute of Subtropical of Forestry, Chinese Academy of Forestry, Hangzhou, Zhejiang, China.
authors.forename: Jing
authors.initials: J
authors.lastname: Jiang
authors.affiliation: Key Laboratory of Agricultural Ecology and Environment, College of Forestry, Shandong Agricultural University, Tai'an, Shandong, China.
authors.forename: Jihong
authors.initials: J
authors.lastname: Li
authors.affiliation: State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China.|Key Laboratory of Tree Breeding of Zhejiang Province, The Research Institute of Subtropical of Forestry, Chinese Academy of Forestry, Hangzhou, Zhejiang, China.
authors.forename: Renying
authors.initials: R
authors.lastname: Zhuo
mesh_terms: D001673:Biodegradation, Environmental; D001692:Biological Transport / Q000235:genetics; D002104:Cadmium / Q000378:metabolism* / Q000494:pharmacology; D018506:Gene Expression Regulation, Plant / Q000187:drug effects; D053263:Gene Regulatory Networks; D035683:MicroRNAs / Q000737:chemistry; D031963:Sedum / Q000187:drug effects / Q000235:genetics / Q000378:metabolism*; D017423:Sequence Analysis, RNA; D015398:Signal Transduction / Q000187:drug effects / Q000235:genetics; D059467:Transcriptome / Q000187:drug effects*
chemical_list: D035683:MicroRNAs; D002104:Cadmium
keywords: Sedum alfredii Hance; cadmium stress; coexpression network; integration analysis; phytoremediation