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Continuous salt stress-induced long non-coding RNAs and DNA methylation patterns in soybean roots

文献类型： 外文期刊

作者： Chen, Rui 1 ; Li, Ming 2 ; Zhang, Huiyuan 2 ; Duan, Lijin 1 ; Sun, Xianjun 2 ; Jiang, Qiyan 2 ; Zhang, Hui 2 ; Hu, Zheng 2 ;

作者机构： 1.Tianjin Acad Agr Sci, Tianjin Inst Agr Qual Stand & Testing Technol, Tianjin 300381, Peoples R China

2.Chinese Acad Agr Sci, Inst Crop Sci, Natl Key Facil Crop Genet Resources & Improvement, Beijing 100081, Peoples R China

3.Chinese Acad Agr Sci, Zhengzhou Fruit Res Inst, Zhengzhou 450009, Henan, Peoples R China

关键词： Whole transcriptome sequencing; DNA methylation; Continuous salt stress; Long non-coding RNAs; Soybean roots

期刊名称：BMC GENOMICS （ 影响因子：3.969； 五年影响因子：4.478 ）

ISSN： 1471-2164

年卷期： 2019 年 20 卷 1 期

页码：

收录情况： SCI

摘要： Background Environmental stimuli can activate a series of physiological and biochemical responses in plants accompanied by extensive transcriptional reprogramming. Long non-coding RNAs (lncRNAs), as versatile regulators, control gene expression in multiple ways and participate in the adaptation to biotic and abiotic stresses. Results In this study, soybean seedlings were continuously cultured for 15 days with high salinity solutions started from seed germination. Strand-specific whole transcriptome sequencing and stringent bioinformatic analysis led to the identification of 3030 long intergenic non-coding RNAs (lincRNAs) and 275 natural antisense transcripts (lncNATs) in soybean roots. In contrast to mRNAs, newly identified lncRNAs exhibited less exons, similar AU content to UTRs, even distribution across the genome and low evolutionary conservation. Remarkably, more than 75% of discovered lncRNAs that were activated or up-regulated by continuous salt stress mainly targeted proteins with binding and catalytic activities. Furthermore, two DNA methylation maps with single-base resolution were generated by using reduced representation bisulfite sequencing, offering a genome-wide perspective and important clues for epigenetic regulation of stress-associated lncRNAs and protein-coding genes. Conclusions Taken together, our findings systematically demonstrated the characteristics of continuous salt stress-induced lncRNAs and extended the knowledge of corresponding methylation profiling, providing valuable evidence for a better understanding of how plants cope with long-term salt stress circumstances.

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