Plant Biotechnology Reports

, Volume 9, Issue 5, pp 279–286

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

  • M. Muthusamy
  • S. Uma
  • S. Backiyarani
  • M. S. Saraswathi
Original Article

DOI: 10.1007/s11816-015-0363-6

Cite this article as:
Muthusamy, M., Uma, S., Backiyarani, S. et al. Plant Biotechnol Rep (2015) 9: 279. doi:10.1007/s11816-015-0363-6

Abstract

Long non-coding RNAs (LncRNAs) are one of the many layers of transcription in higher plants. LncRNAs are responsive to biotic and abiotic stresses and regulate genes. In our study, we have identified 905 novel lncRNAs from 8471 drought-responsive, novel transcripts of RNA-Seq reads from two banana cultivars, a drought-tolerant cv. ‘Saba’ (ABB) and -susceptible cv. ‘Grand Naine’ (AAA). Of these 905 lncRNAs, 75 (8.3 %) transcripts were natural antisense RNAs (NATs) and 2 transcripts identified as precursors of microRNA-miR156 and miR166. Among the 905 identified lncRNAs, 216, 150 and 279, 164 lncRNAs were induced and reduced to drought stress, respectively, in tolerant and susceptible in comparison to their equivalent controls. The remaining 22 lncRNA of tolerant cultivars was not regulated by drought stress. Of the 882 drought-responsive lncRNAs, 44 new lncRNAs were identified as induced. Musa lncRNAs were unevenly distributed in 11 chromosomes of Musa acuminata and no lncRNAs were found in chromosome-9 of drought-tolerant cultivar. The average lengths of lncRNAs were 683 nucleotides (nt). Drought-responsive differential expression of lncRNAs was found between +8.11585- and −4.04311-fold. Around 7.9 % of the identified lncRNAs were decoys of 85 conserved microRNAs. These findings will lay a basic platform for effective strategic planning of developing drought-resilient crop varieties.

Keywords

Banana lncRNA Drought stress-responsive lncRNA Natural antisense RNAs microRNA decoys Genome-wide screening for novel lncRNA 

Supplementary material

11816_2015_363_MOESM1_ESM.txt (646 kb)
Supplementary data. 1 A total of 905 predicted banana long non-coding RNA sequences (TXT 646 kb)
11816_2015_363_MOESM2_ESM.xlsx (136 kb)
Supplementary data. 2 Musa drought-responsive, novel lncRNA expression and coding potential from RNA-Seq data (XLSX 136 kb)
11816_2015_363_MOESM3_ESM.xlsx (35 kb)
Supplementary data. 3 Banana lncRNAs predicted as Natural Antisense RNAs (XLSX 35 kb)
11816_2015_363_MOESM4_ESM.xlsx (131 kb)
Supplementary data. 4 Banana LncRNAs predicted as microRNA target mimics (XLSX 130 kb)

Copyright information

© Korean Society for Plant Biotechnology and Springer Japan 2015

Authors and Affiliations

  1. 1.ICAR-National Research Centre for BananaTiruchirapalliIndia

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