Identification and characterization of miRNA169 family members in banana (Musa acuminata L.) that respond to fusarium oxysporum f. sp. cubense infection in banana cultivars
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Abstract
MicroRNAs (miRNAs) play an important role in plant resistance to pathogen infections. However, little is known about the role of miRNAs in banana Fusarium wilt, which is the most economically devastating disease in banana production. In the present study, we identified and characterized a total of 18 miR169 family members in banana (Musa acuminata L.) based on small RNA sequencing. The banana miR169 family clustered into 2 groups based on miRNA evolutionary analysis. Multiple sequence alignment indicated a high degree of sequence conservation in miRNA169 family members across 28 plant species. Computational target prediction algorithms were used to identify 25 targets of miR169 family members in banana. These targets were enriched in various metabolic pathways that include the following molecules: glycine, serine, threonine, pentose, glycerolipids, nucleotide sugars, starch, and sucrose. Through miRNA transcriptomic analysis, we found that ma-miR169a and ma-miR169b displayed high expression levels, whereas the other 16 ma-miR169 members exhibited low expression in the HG and BX banana cultivars. Further experiments indicate that there were negative relationships between ma-miR169a, ma-miR169b and their targets basing on their expression levels to Foc4(Fusarium oxysporum f. sp. cubense tropical race 4) infection in resistant cultivars. but they were low expressed in susceptive cultivars. These results suggested that the expression levels of ma-miR169a and ma-miR169b were consistent with the resistance degree of the banana cultivars to Foc4. The analysis presented here constitutes a starting point to understand ma-miR169-mediated Fusarium wilt resistance at the transcriptional level in banana and predicts possible candidate targets for the genetic improvement of banana resistance to Foc4.
Cite this as
2018. Identification and characterization of miRNA169 family members in banana (Musa acuminata L.) that respond to fusarium oxysporum f. sp. cubense infection in banana cultivars. PeerJ Preprints 6:e27369v1 https://doi.org/10.7287/peerj.preprints.27369v1note This preprint is not peer-reviewed. You may wish to reference the subsequent peer-reviewed version of this article.
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This is a submission to PeerJ for review.
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Supplemental Information
Additional Files1,3,4,6,7,8
Additional file 1: MiR169 family mature sequences of all crops
Additional file 3: The targets of ma-miR169 family
Additional file 4: KEGG Pathway of the targets
Additional file 6: The FPKM values expressed of HG and BX cultivars(Reads per Kilo bases per Million reads values)
Additional file 7: The primer pairs for miRNAs and targets comfirmation and quantitative detection
Additional file 8: Expression profiles of mature ma-miR169a, ma-miR169b and their targets in root in response to Fusarium wilt
The sequences of the miR169 family members
Evolutionary analysis clustered the miR169 family.
The pathways of target genes
The pathways of target genes. 1)Glycine, serine and threonine metabolism, 2)Pentose and glucuronate interconversions, 3)Glycerolipid metabolism, 4)Amino sugar and nucleotide sugar metabolism, 5)Starch and sucrose metabolism
Additional Information
Competing Interests
The authors declare that they have no competing interests.
Author Contributions
Shun Song conceived and designed the experiments, performed the experiments, contributed reagents/materials/analysis tools, prepared figures and/or tables, approved the final draft.
Yi Xu performed the experiments, analyzed the data, contributed reagents/materials/analysis tools, prepared figures and/or tables, approved the final draft.
Dongmei Huang performed the experiments, analyzed the data, contributed reagents/materials/analysis tools, approved the final draft.
Muhammad Aleem Ashraf analyzed the data, contributed reagents/materials/analysis tools, prepared figures and/or tables, authored or reviewed drafts of the paper, approved the final draft.
Jingyang Li contributed reagents/materials/analysis tools, authored or reviewed drafts of the paper, approved the final draft.
Wei Hu contributed reagents/materials/analysis tools, approved the final draft.
Zhiqiang Jin contributed reagents/materials/analysis tools, authored or reviewed drafts of the paper, approved the final draft.
Changying Zeng conceived and designed the experiments, contributed reagents/materials/analysis tools, authored or reviewed drafts of the paper, approved the final draft.
Fenling Tang contributed reagents/materials/analysis tools, approved the final draft.
Biyu Xu contributed reagents/materials/analysis tools, approved the final draft.
Huicai Zeng contributed reagents/materials/analysis tools, approved the final draft.
Yujia Li contributed reagents/materials/analysis tools, approved the final draft.
Jianghui Xie conceived and designed the experiments, authored or reviewed drafts of the paper, approved the final draft.
Data Deposition
The following information was supplied regarding data availability:
1. miRBase: the microRNA database.
http://www.mirbase.org/cgi-bin/mirna_summary.pl?fam=MIPF0000012
2. GSMUA_Achr8G16690_001: https://phytozome.jgi.doe.gov/pz/portal.html#!gene?search=1&detail=1&method=4987&searchText=transcriptid:32311987
GSMUA_Achr4G12800_001: https://phytozome.jgi.doe.gov/pz/portal.html#!gene?search=1&detail=1&method=4987&searchText=transcriptid:32297417
3. Designed primers for target genes in the Banana Genome Hub, http://banana-genome-hub.southgreen.fr/primer_designer, after got the RT reverse primer, RT forward primer, and PCR forward primer. After setting relevant parameters, all primers designed were verified experimentally, and then the ones with good specificity are available in Additional File 7.
Funding
This work was supported by the National Natural Science Foundation of China (NSFC, No. 31501371), the Commonwealth Industry (Agriculture) Specific Fund (201503110), the National Key Research and Development Program of China (2016YFD0200104) and the Central Public-interest Scientific Institution Basal Research Fund for Chinese Academy of Tropical Agricultural Sciences (No. 1630092017011). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
