RESEARCH ARTICLE


De Novo Assembly and Transcriptome Profiling of Ethiopian Lowland Bamboo Oxytenanthera Abyssinica (A. rich) Munro Under Drought and Salt Stresses



Muhamed Adem1, 2, *, Dereje Beyene2, Tileye Feyissa2, 3, Kai Zhao4, Tingbo Jiang4
1 Department of Forestry, School of Agriculture and Natural Resources, Madawalabu University, P.O. Box 247 Bale Robe, Oromia, Ethiopia
2 Department of Microbial, Cellular and Molecular Biology, College of Natural and Computational Sciences, Addis Ababa University, P.O. Box 1176 Addis Ababa, Ethiopia
3 Institute of Biotechnology, College of Natural and Computational Sciences, Addis Ababa University, P.O. Box 1176 Addis Ababa, Ethiopia
4 State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China


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© 2019 Adem et al.

open-access license: This is an open access article distributed under the terms of the Creative Commons Attribution 4.0 International Public License (CC-BY 4.0), a copy of which is available at: (https://creativecommons.org/licenses/by/4.0/legalcode). This license permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

* Address correspondence to this author at the Department of Forestry, School of Agriculture and Natural Resources, Madawalabu University, P.O. Box 247 Bale Robe, Oromia, Ethiopia; E-mail: muhamed.adem@aau.edu.et


Abstract

Background:

Bamboos are perennial grasses classified under family Poaceae and subfamily Bambusoideae and are among the fastest growing plants on earth. Despite ecological and economic significances, Ethiopian lowland bamboo (O. abyssinica) lacks global gene expression under abiotic stress.

Methods:

Plastic pot germinated seedlings of O. abyssinica were subjected to 200 µm NaCl and 25% PEG-6000 (Poly Ethylene glycol) to induce salt and drought stress, respectively. Using the Illumina sequencing platform, fifteen cDNA libraries were constructed and sequenced to generate the first drought and salt stress transcriptome profiling of the species so as to elucidate genome-wide transcriptome changes in response to such stresses.

Results:

Following quality control, 754,444,646 clean paired-ends reads were generated, and then de novo assembled into 406,181 unigenes. Functional annotation against the public databases presented annotation of 217,067 (53.4%) unigenes, where NCBI-Nr 203,777, Swissport 115,741, COG 81,632 and KEGG 80,587. Prediction of Transcripts Factors (TFs) have generated 4,332 TFs organized into 64 TF families. Analysis of Differentially Expressed Genes (DEGs) provided 65,471 genes where 569 genes belong to all stresses. Protein families with a higher number of differentially expressed genes include bZIP (49), WRKY (43), MYB (38), AP2/ERF (30), HD-ZIP (25) and MYB related (21).

Conclusion:

In addition to revealing the genome-wide level appraisal of transcriptome resources of the species, this study also uncovered the comprehensive understanding of key stress responsive protein-coding genes, protein families and pathways which could be used as the basis for further studies.

Keywords: RNA-Seq, Transcriptome profiling, Differential expressed genes, Drought and salt stress, Transcription factors, O. abyssinica.