Genome-wide identification of novel, long non-coding RNAs responsive to Mycosphaerella eumusae and Pratylenchus coffeae infections and their differential expression patterns in disease-resistant and sensitive banana cultivars
- 36 Downloads
Long non-coding RNAs (lncRNAs) are important regulators of gene expression in plant response to biotic and abiotic stresses. The participation of lncRNAs in plant disease resistance in bananas is largely unknown. Therefore, we attempted to identify novel lncRNAs responsive to Mycosphaerella eumusae, a causative agent of Eumusae leaf spot disease and root lesion nematode, Pratylenchus coffeae and their differential expression patterns during stress and normal conditions in respective resistant and sensitive banana genotypes. Illumina paired-end transcriptome sequencing of control and infected samples of resistant and sensitive banana cultivars was performed and the sequence reads assembled into 172434, 201256 transcriptional units (TUs) for M. eumusae and P. coffeae, respectively. The genome-wide analysis for ELSD-responsive lncRNAs led to identification of 5142 novel lncRNAs including 3031-intergenic, 1672-intragenic, and 440 antisense lncRNAs classes collectively from ELSD-resistant and sensitive cultivars. Similarly, 5615 lncRNAs comprised of 3283 intergenic, 1878-intragenic, and 454 antisense classes were identified from P. coffeae-infected resistant and sensitive banana cultivars. Most of the lncRNAs were stress specific, evenly distributed among banana chromosomes and the average length is ranging from 620 to 684 nucleotides. In addition, 1250 and 1284 lncRNAs were differentially expressed to M. eumusae and P. coffeae infections, respectively. The LncRNA–mRNA interaction-based functional role showed lncRNA-mediated downregulation of horcolin, an antifungal protein is likely responsible for ELSD sensitivity in banana cultivars. Furthermore, we identified 100 of these lncRNAs also play a role in drought stress response of banana indicating a possible crosstalk between biotic and abiotic stresses.
KeywordsBanana lncRNA Eumusae leaf spot disease Root lesion nematode RNA seq Leaf spot resistant cultivars Fungi
This work was supported by the NPTC-Functional Genomics component of the Indian Council of Agricultural Research (ICAR), India. The authors thank the Director of the ICAR-National Research Centre for Banana for providing technical support.
Conflict of interest
The authors declare that no competing interests.
- Muthusamy M, Uma S, Backiyarani S, Saraswathi MS (2015) Genome-wide screening for novel, drought stress-responsive long non-coding RNAs in drought-stressed leaf transcriptome of drought-tolerant and -susceptible banana (Musa spp) cultivars using Illumina high-throughput sequencing. Plant Biotechnol Rep 9:279–286CrossRefGoogle Scholar
- Nejat N, Mantri N (2017) Emerging roles of long non-coding RNAs in plant response to biotic and abiotic stresses. Crit Rev Biotechnol 1–13. https://doi.org/10.1080/07388551.2017.1312270
- Tang W, Zheng Y, Dong J et al (2016) Comprehensive transcriptome profiling reveals long noncoding RNA expression and alternative splicing regulation during fruit development and ripening in kiwifruit (Actinidia chinensis). Front Plant Sci 7:1–15. https://doi.org/10.3389/fpls.2016.00335 Google Scholar
- Wang KC, Chang HY (2012) Molecular mechanisms of long noncoding RNAs. Mol Cell 43:904–914. https://doi.org/10.1016/j.molcel.2011.08.018.Molecular CrossRefGoogle Scholar