Identification of tissue-specific and cold-responsive lncRNAs in Medicago truncatula by high-throughput RNA sequencing

BMC Plant Biology
Min-Gui ZhaoWen-Hao Zhang

Abstract

Long non-coding RNAs (lncRNAs) play important roles in the regulation of plant responses to environmental stress by acting as essential regulators of gene expression. However, whether and how lncRNAs are involved in cold acclimation-dependent freezing tolerance in plants remains largely unknown. Medicago truncatula is a prominent model for studies of legume genomics, and distinguished by its cold-acclimation characteristics. To determine the roles of lncRNAs in plant cold stress response, we conducted genome-wide high-throughput sequencing in the legume model plant M. truncatula. RNA-seq data were generated from twelve samples for the four treatments, i.e., non-cold treated leaves and roots, cold-treated leaves and roots of M. truncatula Jemalong A17 seedlings. A total of 1204 million raw reads were generated. Of them, 1150 million filtered reads after quality control (QC) were subjected to downstream analysis. A large number of 24,368 unique lncRNAs were identified from the twelve samples. Among these lncRNAs, 983 and 1288 were responsive to cold treatment in the leaves and roots, respectively. We further found that the intronic-lncRNAs were most sensitive to the cold treatment. The cold-responsive lncRNAs were unevenly distri...Continue Reading

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Methods Mentioned

BETA
nuclear translocation
environmental stress
RNA-Seq
RNAseq
PCR
dissection
RNA Assay
Assay

Software Mentioned

StringTie
PhyloCSF ( frequency )
Pfam Scan
bowtie2
CNCI ( Coding - Non - Coding - Index )
CPC ( Coding Potential Calculator )
Cytoscape
SPSS17
GOseq R package
FastQC

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