Integrated mRNA, sRNA, and degradome sequencing reveal oilseed rape complex responses to Sclerotinia sclerotiorum (Lib.) infection

Jian, Hongju; Ma, Jinqi; Wei, Lijuan; Zhang, Aoxiang; Yang, Bo; Li, Jiana; Xu, Xinhua; Liu, Liezhao

doi:10.1038/s41598-018-29365-y

Cited by 23 publications

(17 citation statements)

References 77 publications

(67 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…MiRBase20.0 was used as reference; modified software mirdeep2 (Friedländer et al, 2012) and srna-tools-cli were used to obtain the potential miRNA and draw the secondary structures. Custom scripts were used to obtain the miRNA counts as well as base bias on the first position of identified miRNA with certain length and on each position of all identified miRNA, respectively (Jian et al, 2018). The characteristics of hairpin structure of miRNA precursor can be used to predict novel miRNA.…”

Section: Methodsmentioning

confidence: 99%

Identification of Potential Immune-Related circRNA–miRNA–mRNA Regulatory Network in Intestine of Paralichthys olivaceus During Edwardsiella tarda Infection

et al. 2019

View full text Add to dashboard Cite

Olive flounder ( Paralichthys olivaceus ) is an important economical flatfish in Japan, Korea, and China, but its production has been greatly threatened by disease outbreaks. In this research, we aimed to explore the immune responsive mechanism of P. olivaceus against Edwardsiella tarda infection by profiling the expression of circRNA, miRNA, and mRNA by RNA-seq and constructing a regulatory circular circRNA–miRNA–mRNA network. Illumina sequencing of samples from normal control (H0), 2 h (H2), 8 h (H8), and 12 h (H12) post-challenge was conducted. Differentially expressed (DE) circRNA (DE–circRNAs), miRNAs (DE–miRNAs), and mRNAs [differential expression genes (DEGs)] between challenge and control groups were identified, resulting in a total of 62 DE–circRNAs, 39 DE–miRNAs, and 3,011 DEGs. Based on the differentially expressed gene results, miRNA target interactions (circRNA–miRNA pairs and miRNA–mRNA pairs) were predicted by MiRanda software. Once these paired were combined, a preliminary circRNA–miRNA–mRNA network was generated with 198 circRNA–miRNA edges and 3,873 miRNA–mRNA edges, including 44 DE–circRNAs, 32 DE–miRNAs, and 1,774 DEGs. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis was performed to evaluate the function of the DEGs in this network, and we focused and identified two important intestinal immune pathways (herpes simplex infection and intestinal immune network for IgA production) that showed statistical significance between the challenge and control groups. Furthermore, three critical DEGs (nectin2, MHC II α-chain, and MHC II β-chain) were identified, mapped into the preliminary circRNA–miRNA–mRNA network, and new circRNA–miRNA–mRNA regulatory networks were constructed. In conclusion, we, for the first time, identified circRNA–miRNA–mRNA network from P. olivaceus in the pathogenesis of E. tarda and provided valuable resources for further analyses of the molecular mechanisms and signaling networks.

show abstract

Section: Methodsmentioning

confidence: 99%

Identification of Potential Immune-Related circRNA–miRNA–mRNA Regulatory Network in Intestine of Paralichthys olivaceus During Edwardsiella tarda Infection

et al. 2019

View full text Add to dashboard Cite

show abstract

“…Two degradome libraries were constructed according to the manufacturer's instructions and then sequenced on an Illumina HiSeq 2500 platform at LC-BIO (Hangzhou, China). Subsequent data analysis, including data processing, prediction of miRNA cleavage sites and target plot (t-plots) figure drawings, was based on previous reports [60,61]. The sesame genome v.1.0 (https://www.ncbi.nlm.nih.…”

Section: Degradome Library Sequencing and Target Identificationmentioning

confidence: 99%

Integrated small RNA and Degradome sequencing provide insights into salt tolerance in sesame (Sesamum indicum L.)

Zhang

Gong

et al. 2020

BMC Genomics

View full text Add to dashboard Cite

Background: MicroRNAs (miRNAs) exhibit important regulatory roles in the response to abiotic stresses by posttranscriptionally regulating the target gene expression in plants. However, their functions in sesame response to salt stress are poorly known. To dissect the complex mechanisms underlying salt stress response in sesame, miRNAs and their targets were identified from two contrasting sesame genotypes by a combined analysis of small RNAs and degradome sequencing. Results: A total of 351 previously known and 91 novel miRNAs were identified from 18 sesame libraries. Comparison of miRNA expressions between salt-treated and control groups revealed that 116 miRNAs were involved in salt stress response. Using degradome sequencing, potential target genes for some miRNAs were also identified. The combined analysis of all the differentially expressed miRNAs and their targets identified miRNA-mRNA regulatory networks and 21 miRNA-mRNA interaction pairs that exhibited contrasting expressions in sesame under salt stress. Conclusions: This comprehensive integrated analysis may provide new insights into the genetic regulation mechanism of miRNAs underlying the adaptation of sesame to salt stress.

show abstract

“…Therefore, we believe that the pathways controlling these processes deserve intensive research focus. The commonly used NGS technique allows for comprehensive analyses of sRNAoms, transcriptoms, and degradomes, as well as identification of sRNAs and their target genes in both model and non-model plants, for example: tomato [58], soybean [59], Arabidopsis [60,61], oilseed rape [62], Brassica juncea [63], lily [64,65], peanut [66], orchardgrass [67] or wheat [68,69].…”

Section: Discussionmentioning

confidence: 99%

Integrated analysis of small RNA, transcriptome and degradome sequencing provides new insights into floral development and abscission in yellow lupine (Lupines luteus L.)

Glazińska

Kulasek

Glinkowski

et al. 2019

Preprint

View full text Add to dashboard Cite

Background Yellow lupine (Lupinus luteus L., Taper c.) is an important legume crop. However, its flower development and pod formation are often affected by excessive abscission. Organ detachment occurs within the abscission zone (AZ) and in L. luteus primarily affects flowers formed at the top of the inflorescence. The top flowers’ fate appears determined before anthesis. The organ development and abscission mechanisms utilize a complex molecular network, not yet not fully understood, especially as to the role of miRNAs and siRNAs. We aimed at identifying differentially expressed (DE) small ncRNAs in lupine by comparing small RNA-seq libraries generated from developing upper and lower raceme flowers, and flower pedicels with active and inactive AZs. Their target genes were also identified using transcriptome and degradome sequencing. Results Within all the libraries, 394 known and 28 novel miRNAs and 316 phased siRNAs were identified. In flowers at different stages of development, 30 miRNAs displayed DE in the upper and 29 in the lower parts of the raceme. In comparisons between upper and lower raceme flowers, a total of 46 DE miRNAs were identified. miR393 and miR160 were related to the upper and miR396 to the lower flowers and pedicels of non-abscising flowers. In flower pedicels we identified 34 DE miRNAs, with miR167 being the most abundant of all. Most siRNAs seem to play a marginal role in the processes studied herein, with the exception of tasiR-ARFs, which were DE in the developing flowers. The target genes of these miRNAs were predominantly categorized into the following Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways: ‘Metabolism’ (15,856), ‘Genetic information processing’ (5,267), and ‘Environmental information processing’ (1,517). Over 700 putative targets were categorized as belonging to the ‘Plant Hormone Signal Transduction pathway’. 26,230 target genes exhibited Gene Ontology (GO) terms: 23,092 genes were categorized into the ‘Cellular component’, 23,501 into the ‘Molecular function’, and 22,939 into the ’Biological process’. Conclusion Our results indicate that miRNAs and siRNAs in yellow lupine may influence the development of flowers and, consequently, their fate by repressing their target genes, particularly those associated with the homeostasis of phytohormones, mainly auxins.

show abstract

Integrated mRNA, sRNA, and degradome sequencing reveal oilseed rape complex responses to Sclerotinia sclerotiorum (Lib.) infection

Cited by 23 publications

References 77 publications

Identification of Potential Immune-Related circRNA–miRNA–mRNA Regulatory Network in Intestine of Paralichthys olivaceus During Edwardsiella tarda Infection

Identification of Potential Immune-Related circRNA–miRNA–mRNA Regulatory Network in Intestine of Paralichthys olivaceus During Edwardsiella tarda Infection

Integrated small RNA and Degradome sequencing provide insights into salt tolerance in sesame (Sesamum indicum L.)

Integrated analysis of small RNA, transcriptome and degradome sequencing provides new insights into floral development and abscission in yellow lupine (Lupines luteus L.)

Contact Info

Product

Resources

About