PMID- 30866814 OWN - NLM STAT- MEDLINE DCOM- 20190701 LR - 20200225 IS - 1471-2164 (Electronic) IS - 1471-2164 (Linking) VI - 20 IP - 1 DP - 2019 Mar 13 TI - Strand-specific RNA-seq based identification and functional prediction of drought-responsive lncRNAs in cassava. PG - 214 LID - 10.1186/s12864-019-5585-5 [doi] LID - 214 AB - BACKGROUND: Long noncoding RNAs (lncRNAs) have emerged as playing crucial roles in abiotic stress responsive regulation, however, the mechanism of lncRNAs underlying drought-tolerance remains largely unknown in cassava, an important tropical and sub-tropical root crop of remarkable drought tolerance. RESULTS: In this study, a total of 833 high-confidence lncRNAs, including 652 intergenic and 181 anti-sense lncRNAs, were identified in cassava leaves and root using strand-specific RNA-seq technology, of which 124 were drought-responsive. Trans-regulatory co-expression network revealed that lncRNAs exhibited tissue-specific expression patterns and they preferred to function differently in distinct tissues: e.g., cell-related metabolism, cell wall, and RNA regulation of transcription in folded leaf (FL); degradation of major carbohydrate (CHO) metabolism, calvin cycle and light reaction, light signaling, and tetrapyrrole synthesis in full expanded leaf (FEL); synthesis of major CHO metabolism, nitrogen-metabolism, photosynthesis, and redox in bottom leaf (BL); and hormone metabolism, secondary metabolism, calcium signaling, and abiotic stress in root (RT). In addition, 27 lncRNA-mRNA pairs referred to cis-acting regulation were identified, and these lncRNAs regulated the expression of their neighboring genes mainly through hormone metabolism, RNA regulation of transcription, and signaling of receptor kinase. Besides, 11 lncRNAs were identified acting as putative target mimics of known miRNAs in cassava. Finally, five drought-responsive lncRNAs and 13 co-expressed genes involved in trans-acting, cis-acting, or target mimic regulation were selected and confirmed by qRT-PCR. CONCLUSIONS: These findings provide a comprehensive view of cassava lncRNAs in response to drought stress, which will enable in-depth functional analysis in the future. FAU - Ding, Zehong AU - Ding Z AD - Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Xueyuan Road 4, Haikou, Hainan, China. dingzehong@itbb.org.cn. FAU - Tie, Weiwei AU - Tie W AD - Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Xueyuan Road 4, Haikou, Hainan, China. FAU - Fu, Lili AU - Fu L AD - Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Xueyuan Road 4, Haikou, Hainan, China. FAU - Yan, Yan AU - Yan Y AD - Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Xueyuan Road 4, Haikou, Hainan, China. FAU - Liu, Guanghua AU - Liu G AD - Institute of Tropical and Sub-tropical Cash Crops, Yunnan Academy of Agricultural Sciences, Baoshan, Yunnan, China. FAU - Yan, Wei AU - Yan W AD - Institute of Tropical and Sub-tropical Cash Crops, Yunnan Academy of Agricultural Sciences, Baoshan, Yunnan, China. FAU - Li, Yanan AU - Li Y AD - Institute of Tropical and Sub-tropical Cash Crops, Yunnan Academy of Agricultural Sciences, Baoshan, Yunnan, China. FAU - Wu, Chunlai AU - Wu C AD - Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Xueyuan Road 4, Haikou, Hainan, China. AD - Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, Chinese National Center of Plant Gene Research (Wuhan) HUST Part, Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology (HUST), Wuhan, China. FAU - Zhang, Jiaming AU - Zhang J AD - Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Xueyuan Road 4, Haikou, Hainan, China. FAU - Hu, Wei AU - Hu W AD - Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Xueyuan Road 4, Haikou, Hainan, China. huwei2013@itbb.org.cn. LA - eng GR - 31600198/National Natural Science Foundation of China/ GR - 17CXTD-28, 1630052017017/the Central Public-Interest Scientific Institution Basal Research Fund for Innovative Research Team Program of CATAS/ GR - 1630052016005, 1630052016006, 1630052017021/the Central Public-Interest Scientific Institution Basal Research Fund for Chinese Academy of Tropical Agricultural Sciences/ PT - Journal Article DEP - 20190313 PL - England TA - BMC Genomics JT - BMC genomics JID - 100965258 RN - 0 (Plant Proteins) RN - 0 (RNA, Long Noncoding) RN - 0 (RNA, Plant) SB - IM MH - *Adaptation, Physiological MH - Droughts MH - Gene Expression Profiling MH - Gene Expression Regulation, Plant MH - *Gene Regulatory Networks MH - Manihot/genetics/*growth & development MH - Organ Specificity MH - Plant Leaves/genetics/growth & development MH - Plant Proteins MH - RNA, Long Noncoding/*genetics MH - RNA, Plant/genetics MH - Sequence Analysis, RNA/*methods PMC - PMC6417064 OTO - NOTNLM OT - Cassava OT - PEG treatment OT - Tissue-specific expression OT - lncRNA OT - ssRNA-Seq COIS- ETHICS APPROVAL AND CONSENT TO PARTICIPATE: Not applicable. CONSENT FOR PUBLICATION: Not applicable. COMPETING INTERESTS: The authors declare that they have no competing interests. PUBLISHER'S NOTE: Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations. EDAT- 2019/03/15 06:00 MHDA- 2019/07/02 06:00 PMCR- 2019/03/13 CRDT- 2019/03/15 06:00 PHST- 2018/09/21 00:00 [received] PHST- 2019/03/05 00:00 [accepted] PHST- 2019/03/15 06:00 [entrez] PHST- 2019/03/15 06:00 [pubmed] PHST- 2019/07/02 06:00 [medline] PHST- 2019/03/13 00:00 [pmc-release] AID - 10.1186/s12864-019-5585-5 [pii] AID - 5585 [pii] AID - 10.1186/s12864-019-5585-5 [doi] PST - epublish SO - BMC Genomics. 2019 Mar 13;20(1):214. doi: 10.1186/s12864-019-5585-5.