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Publication Type J
Authors Xiao, XR; Hong, YH; Xia, W; Feng, SP; Zhou, X; Fu, XM; Zang, J; Xiao, Y; Niu, XL; Li, CX; Chen, YH
Author Full Name Xiao, Xiaorong; Hong, Yuhui; Xia, Wei; Feng, Shipeng; Zhou, Xi; Fu, Xiumei; Zang, Jian; Xiao, Yong; Niu, Xiaolei; Li, Chunxia; Chen, Yinhua
Title Transcriptome Analysis of Ceriops tagal in Saline Environments Using RNA-Sequencing
Source PLOS ONE
Language English
Document Type Article
Keywords Plus SALT STRESS; MESEMBRYANTHEMUM-CRYSTALLINUM; ARABIDOPSIS-THALIANA; ABIOTIC STRESS; H+-ATPASE; TOLERANCE; PROLINE; ACID; EXPRESSION; MANGROVES
Abstract Identification of genes involved in mangrove species' adaptation to salt stress can provide valuable information for developing salt-tolerant crops and understanding the molecular evolution of salt tolerance in halophiles. Ceriops tagal is a salt-tolerant mangrove tree growing in mudflats and marshes in tropical and subtropical areas, without any prior genome information. In this study, we assessed the biochemical and transcriptional responses of C. tagal to high salt treatment (500 mmol/L NaCl) by hydroponic experiments and RNA-seq. In C. tagal root tissues under salt stress, proline accumulated strongly from 3 to 12 h of treatment; meanwhile, malondialdehyde content progressively increased from 0 to 9 h, then dropped to lower than control levels by 24 h. These implied that C. tagal plants could survive salt stress through biochemical modification. Using the Illumina sequencing platform, approximately 27.39 million RNA-seq reads were obtained from three salt-treated and control (untreated) root samples. These reads were assembled into 47,111 transcripts with an average length of 514 bp and an N50 of 632 bp. Approximately 78% of the transcripts were annotated, and a total of 437 genes were putative transcription factors. Digital gene expression analysis was conducted by comparing transcripts from the untreated control to the three salt treated samples, and 7,330 differentially expressed transcripts were identified. Using k-means clustering, these transcripts were divided into six clusters that differed in their expression patterns across four treatment time points. The genes identified as being up-or downregulated are involved in salt stress responses, signal transduction, and DNA repair. Our study shows the main adaptive pathway of C. tagal in saline environments, under short-term and long-term treatments of salt stress. This provides vital clues as to which genes may be candidates for breeding salt-tolerant crops and clarifying molecular mechanisms of salt tolerance in C. tagal. The expression levels of 20 candidate genes measured by RNA-Seq were validated via qRT-PCR. Eighteen genes showed consistent expression patterns in RNA-Seq and qRT-PCR results, suggesting that the RNA-seq dataset was dependable for gene expression pattern analysis.
Author Address [Xiao, Xiaorong; Hong, Yuhui; Xia, Wei; Feng, Shipeng; Zhou, Xi; Fu, Xiumei; Zang, Jian; Xiao, Yong; Niu, Xiaolei; Li, Chunxia; Chen, Yinhua] Hainan Univ, Hainan Key Lab Sustainable Utilizat Trop Bioresou, Haikou, Peoples R China; [Xiao, Xiaorong; Hong, Yuhui; Xia, Wei; Feng, Shipeng; Zhou, Xi; Fu, Xiumei; Zang, Jian; Xiao, Yong; Niu, Xiaolei; Li, Chunxia; Chen, Yinhua] Hainan Univ, Coll Agr, Haikou, Peoples R China
Reprint Address Li, CX; Chen, YH (reprint author), Hainan Univ, Hainan Key Lab Sustainable Utilizat Trop Bioresou, Haikou, Peoples R China.; Li, CX; Chen, YH (reprint author), Hainan Univ, Coll Agr, Haikou, Peoples R China.
E-mail Address chun_xia_li@126.com; yhchen@hainu.edu.cn
Funding Agency and Grant Number National Natural Science foundation of China [31260345, 31060040]; Special Fund for Agro-scientific Research in the Public Interest of the People's Republic of China [201403075]
Funding Text The study was supported by a grant from National Natural Science foundation of China (31260345, 31060040) and the Special Fund for Agro-scientific Research in the Public Interest of the People's Republic of China (Grant No. 201403075). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.; This work was supported by the National Natural Science Foundation of China (31260345, 31060040). We thank Beidong Liu for manuscript revision and our thanks also go to Beijing Genomics Institute at Shenzhen for technical assistance in data analysis. The authors have no conflicts of interest to declare
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Cited Reference Count 42
Publisher PUBLIC LIBRARY SCIENCE
Publisher City SAN FRANCISCO
Publisher Address 1160 BATTERY STREET, STE 100, SAN FRANCISCO, CA 94111 USA
ISSN 1932-6203
29-Character Source Abbreviation PLOS ONE
ISO Source Abbreviation PLoS One
Publication Date DEC 9
Year Published 2016
Volume 11
Issue 12
Article Number e0167551
Digital Object Identifier (DOI) 10.1371/journal.pone.0167551
Page Count 19
Web of Science Category Multidisciplinary Sciences
Subject Category Science & Technology - Other Topics
Document Delivery Number EE4PU
Unique Article Identifier WOS:000389587100122
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