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Tropical Plant Biology

, Volume 12, Issue 1, pp 44–54 | Cite as

Analysis of Small RNAs from Solanum torvum Swartz by Deep Sequencing

  • Xu Yang
  • Yu Zhang
  • Jinyan Xue
  • Fei Liu
  • Yufu ChengEmail author
Article
  • 86 Downloads

Abstract

Verticillium wilt causes substantial economic losses in eggplant by reducing its yield and quality. However, the relationship between the host and fungal pathogen is poorly understood. Large amounts of high quality clean reads were obtained from our samples. We used bioinformatics analysis to detect 373 differentially expressed miRNAs and 18 differentially expressed novel miRNAs. Eleven highly enriched MIRNA families were found to be involved in the resistance to Verticillium Wilt in eggplant. We identified the differentially expressed miRNAs among samples and analyzed their 78 target genes. These target genes were annotated with GO function enrichment and KEGG pathway association. The target genes included transcription factors such as TCP, E3 and FEX6 etc. Functional categorization of those target genes reflected a number of important pathways, which are involved in the plant’s resistance to various pathogens. These differentially expressed miRNAs and their target genes will provide a theoretical basis for the further study of Verticillium wilt-related miRNAs and the regulation of disease resistance mechanisms of eggplant at the miRNA level.

Keywords

Verticillium wilt Solanum torvum Swartz Verticillium dahlia Klep Small RNA 

Abbreviations

COG

Clusters of Orthologous Groups

FDR

False Discovery Rate

GO

Gene Ontology

KEGG

Kyoto Encyclopedia of Genes and Genomes

miRNAs

microRNAs

NGS

next-generation sequencing

RISC

RNA-induced silencing complex

siRNAs

small interfering RNAs

sRNAs

small RNAs

TPM

tags per Million reads

U

uridine

Notes

Acknowledgements

The work presented here was supported by the National Natural Science Foundation of China (Grant No.NSFC31171954), the Natural Science Foundation of Jiangsu Province (Grant No. BK2010320), China Postdoctoral Science Foundation (Grant No. 20110491463) and Jiangsu Postdoctoral Science Foundation (Grant No. 1002001C).

Author’s Contributions

All authors contributed experimental design oversight. XY and Y-f C designed the experiments. YZ performed the experiments. YZ, FL and J-y X analyzed the data. YZ and FL wrote the paper. All authors read and approved the final manuscript.

Compliance with Ethical Standards

Ethics Approval and Consent to Participate

Before the sampling phase of the study, the approval for handling and sampling of eggplant samples were obtained from school of Horticulture and Plant Protection, yangzhou university.

Competing Interests

The authors declare that they have no competing interests.

Supplementary material

12042_2018_9216_MOESM1_ESM.xls (414 kb)
ESM 1 (XLS 414 kb)
12042_2018_9216_MOESM2_ESM.doc (284 kb)
ESM 2 (DOC 284 kb)

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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2019

Authors and Affiliations

  1. 1.College of Horticulture and Plant ProtectionYangzhou UniversityYangzhouChina
  2. 2.Jiangsu Key Laboratory for Horticultural Crop Genetic ImprovementJiangsu Academy of Agricultural SciencesNanjingChina

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