Integration of small <scp>RNA</scp>s, degradome and transcriptome sequencing in hyperaccumulator <i>Sedum alfredii</i> uncovers a complex regulatory network and provides insights into cadmium phytoremediation

Han, Xiaojiao; Yin, Hengfu; Song, Xixi; Zhang, Yunxing; Liu, Mingying; Sang, Jiang; Jiang, Jing; Li, Jihong; Zhuo, Renying

doi:10.1111/pbi.12512

Cited by 101 publications

(88 citation statements)

References 75 publications

(78 reference statements)

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“…The physiological mechanisms underlying this species' resistance and hyperaccumulation of different metal ions have been investigated (Lu et al, 2008;Jin et al, 2008;Li et al, 2016;Tian et al, 2016;Tian et al, 2017). Analyses of the transcriptome, small RNAs, degradome and proteome have been carried out under Cd stress (Li et al, 2016;Han et al, 2016;. Furthermore, many g e n e s a s s o c i a t e d w i t h C d u p t a k e , r e s i s t a n c e a n d hyperaccumulation, such as SpHMA3, SpMTL, SaREF, SaMT2, SaCAX2 and SaCu/ZnSOD, have been characterized from S. plumbizincicola and S. alfredii (Zhang et al, 2014;Liu et al, 2016;Zhang et al, 2016;.…”

Section: Introductionmentioning

confidence: 99%

SaHsfA4c From Sedum alfredii Hance Enhances Cadmium Tolerance by Regulating ROS-Scavenger Activities and Heat Shock Proteins Expression

Chen

et al. 2020

Front. Plant Sci.

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The heat shock transcription factor (Hsf) family, an important member in plant stress response, affects cadmium (Cd) tolerance in plants. In this study, we identified and functionally characterized a transcript of the Hsf A4 subgroup from Sedum alfredii. Designated as SaHsfA4c, the open reading frame was 1,302 bp long and encoded a putative protein of 433 amino acids containing a complete DNA-binding domain (DBD). Heterologous expression of SaHsfA4c in yeast enhanced Cd stress tolerance and accumulation, whereas expression of the alternatively spliced transcript InSaHsfA4c which contained an intron and harbored an incomplete DBD, resulted in relatively poor Cd stress tolerance and low Cd accumulation in transgenic yeast. The function of SaHsfA4c under Cd stress was characterized in transgenic Arabidopsis and nonhyperaccumulation ecotype S. alfredii. SaHsfA4c was able to rescue the Cd sensitivity of the Arabidopsis athsfa4c mutant. SaHsfA4c reduced reactive oxygen species (ROS) accumulation and increased the expression of ROS-scavenging enzyme genes and Hsps in transgenic lines. The present results suggest that SaHsfA4c increases plant resistance to stress by up-regulating the activities of ROS-scavenging enzyme and the expression of Hsps.

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Section: Introductionmentioning

confidence: 99%

SaHsfA4c From Sedum alfredii Hance Enhances Cadmium Tolerance by Regulating ROS-Scavenger Activities and Heat Shock Proteins Expression

Chen

et al. 2020

Front. Plant Sci.

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“…In order to identify the targets of the miRNA and predict their functions, we performed a degradome sequencing analysis (Han et al 2016; Wei et al 2013). A total of 356 targets and 773 cleavage sites were identified.…”

Section: Resultsmentioning

confidence: 99%

Drought stress-induced changes of microRNAs in diploid and autotetraploid Paulownia tomentosa

et al. 2016

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Drought stress adversely affects plant productivity. Growth and timber production of Paulownia trees are limited under drought stress. Changes in gene expression patterns and miRNA in different ploidy of Paulownia tomentosa have been investigated. However, the responses of P. tomentosa to drought stress at the microRNA (miRNA) level have not been reported so far. To identify miRNA candidates and their target genes involved in the drought stress response in diploid and tetraploid P. tomentosa, four small RNA and four degradome libraries from diploid and autotetraploid P. tomentosa under normal and drought stress conditions were constructed and sequenced. A total of 41 conserved and 90 novel miRNAs were identified. Among these miRNAs, 67 (26 conserved and 41 novel) and 53 (six conserved and 47 novel) were significantly differentially expressed in response to drought stress in diploid and autotetraploid P. tomentosa, respectively. Degradome analysis identified 356 candidate miRNA target genes that encoded proteins with functions that included plant defense, transcriptional regulation, and hormone metabolism. In particular, miR4 and miR156 were identified only in autotetraploid P. tomentosa under drought stress. These results will help us build a foundation for future studies of the biological functions of miRNA-mediated gene regulation in P. tomentosa.Electronic supplementary materialThe online version of this article (doi:10.1007/s13258-016-0473-8) contains supplementary material, which is available to authorized users.

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“…DERs were predicted as Han et al described [41]. To better understand the molecular function of the miRNAs that related to PaWB, TargetFinder software (Copyright: 2007-2010, http://jcclab.…”

Section: Ders Identification and Target Genes Predictionmentioning

confidence: 99%

Transcriptome and Small RNA Sequencing Analysis Revealed Roles of PaWB-Related miRNAs and Genes in Paulownia fortunei

Zhai

Cao

et al. 2018

Forests

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Paulownia witches' broom (PaWB) is an epidemic disease caused by phytoplasmas infection, which is responsible for large production and economic losses. The study of PaWB has made significant progress, but the specific molecular mechanisms associated with PaWB remain unclear. To clearly know the gene expression profiles of plantlets infected with phytoplasmas, in this study, we used high-throughput sequencing technology to generate an integrated analysis of the transcriptome and microRNAs (miRNAs) of Paulownia fortunei (seem.) Hemsl. plantlets, and to obtain a comprehensive resource for the relationship between vital miRNA-target gene pairs and PaWB. A total of 756 genes, and 45 conserved and 22 new miRNAs were identified associated with PaWB. In addition, 635 target genes were predicted for the 67 DERs (Differentially expressed miRNAs). An interaction network of these miRNAs and their target genes was constructed. Gene ontology (GO) and KEGG pathway analysis of these target genes indicated that genes encoding transcription factors (TFs), including auxin response factors (ARF), WRKY, NAC (NAM, ATAF1/2 and CUC2), and MYB (v-myb avian myeloblastosis viral oncogene homolog), and genes encoding superoxide dismutase (SOD), as well as alternative splicing were related directly or indirectly to PaWB. Our results shed light on the possible roles of genes and miRNAs in PaWB-infected plantlets, which will enhance the understanding of the PaWB mechanism in Paulownia plants.

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Integration of small RNAs, degradome and transcriptome sequencing in hyperaccumulator Sedum alfredii uncovers a complex regulatory network and provides insights into cadmium phytoremediation

Cited by 101 publications

References 75 publications

SaHsfA4c From Sedum alfredii Hance Enhances Cadmium Tolerance by Regulating ROS-Scavenger Activities and Heat Shock Proteins Expression

SaHsfA4c From Sedum alfredii Hance Enhances Cadmium Tolerance by Regulating ROS-Scavenger Activities and Heat Shock Proteins Expression

Drought stress-induced changes of microRNAs in diploid and autotetraploid Paulownia tomentosa

Transcriptome and Small RNA Sequencing Analysis Revealed Roles of PaWB-Related miRNAs and Genes in Paulownia fortunei

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