Genome-wide discovery and functional prediction of salt-responsive lncRNAs in duckweed

BMC Genomics
Lili FuJiaming Zhang

Abstract

Salt significantly depresses the growth and development of the greater duckweed, Spirodela polyrhiza, a model species of floating aquatic plants. Physiological responses of this plant to salt stress have been characterized, however, the roles of long noncoding RNAs (lncRNAs) remain unknown. In this work, totally 2815 novel lncRNAs were discovered in S. polyrhiza by strand-specific RNA sequencing, of which 185 (6.6%) were expressed differentially under salinity condition. Co-expression analysis indicated that the trans-acting lncRNAs regulated their co-expressed genes functioning in amino acid metabolism, cell- and cell wall-related metabolism, hormone metabolism, photosynthesis, RNA transcription, secondary metabolism, and transport. In total, 42 lncRNA-mRNA pairs that might participate in cis-acting regulation were found, and these adjacent genes were involved in cell wall, cell cycle, carbon metabolism, ROS regulation, hormone metabolism, and transcription factor. In addition, the lncRNAs probably functioning as miRNA targets were also investigated. Specifically, TCONS_00033722, TCONS_00044328, and TCONS_00059333 were targeted by a few well-studied salt-responsive miRNAs, supporting the involvement of miRNA and lncRNA interac...Continue Reading

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Methods Mentioned

BETA
salt stress
salt treatment
ssRNA-seq
RNA-seq

Software Mentioned

Coding - Potential Assessment Tool ( CPAT )
Coding Potential Calculator ( CPC ) Coding Index ( )
MapMan
Cytoscape
WGCNA
Tophat
edgeR
psRNATarget
Cufflinks
DESeq

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