Genome-wide identification and differentially expression analysis of lncRNAs in tilapia

Abstract

BackgroundLong noncoding RNAs (LncRNAs) play important roles in fundamental biological processes. However, knowledge about the genome-wide distribution and stress-related expression of lncRNAs in tilapia is still limited.ResultsGenome-wide identification of lncRNAs in the tilapia genome was carried out in this study using bioinformatics tools. 103 RNAseq datasets that generated in our laboratory or collected from NCBI database were analyzed. In total, 72,276 high-confidence lncRNAs were identified. The averaged positive correlation coefficient (r_mean = 0.286) between overlapped lncRNA and mRNA pairs showed significant differences with the values for all lncRNA-mRNA pairs (r_mean = 0.176, z statistics = − 2.45, p value = 0.00071) and mRNA-mRNA pairs (r_mean = 0.186, z statistics = − 2.23, p value = 0.0129). Weighted correlation network analysis of the lncRNA and mRNA datasets from 12 tissues identified 21 modules and many interesting mRNA genes that clustered with lncRNAs. Overrepresentation test indicated that these mRNAs enriched in many biological processes, such as meiosis (p = 0.00164), DNA replication (p = 0.00246), metabolic process (p = 0.000838) and in molecular function, e.g., helicase activity (p = 0.000102) and catalytic activity (p = 0.0000612). Differential expression (DE) analysis identified 99 stress-related lncRNA genes and 1955 tissue-specific DE lncRNA genes. MiRNA-lncRNA interaction analysis detected 72,267 lncRNAs containing motifs with sequence complementary to 458 miRNAs.ConclusionsThis study provides an invaluable resource for further studies on molecular bases of lncRNAs in tilapia genomes. Further function analysis of the lncRNAs will help to elucidate their roles in regulating stress-related adaptation in tilapia.Electronic supplementary materialThe online version of this article (10.1186/s12864-018-5115-x) contains supplementary material, which is available to authorized users.

Identification and characterization of immune-related lncRNAs and lncRNA-miRNA-mRNA networks of Paralichthys olivaceus involved in Vibrio anguillarum infection

“…Compared with mRNAs, lncRNAs exhibited lower MFE values, suggesting a flexibility in their secondary structures, which may facilitate their binding to miRNAs and mRNAs [ 33 ]. Other characteristics of flounder lncRNAs, including exon number, GC content, and expression level, were similar to that observed in the lncRNAs of yellow croaker, rainbow trout, Atlantic salmon, tilapia, and tongue sole [ 16 , 17 , 19 , 34 , 35 ]. However, the average length of founder lncRNAs (1861 bp) was longer than that of the lncRNAs of zebrafish (1113 bp), tilapia (764 bp), rainbow trout (400 bp), and Atlantic salmon (400 bp) [ 19 , 34 , 36 , 37 ].…”

Biological Network Approach for the Identification of Regulatory Long Non-Coding RNAs Associated With Metabolic Efficiency in Cattle

“…Recently, Sun et al (2019) applied this method for mining regulatory signatures of divergent feed efficiency in beef cattle investigating a multi-tissue transcriptome data set. WGCNA has also been used to find hub lncRNAs in a transcriptomic landscape in multiple studies in humans as well as animals (Miao et al, 2016; Tang et al, 2017; Li et al, 2018; Weikard et al, 2018; Wang et al, 2019). To mine for the functional role of lncRNAs of interest via WGCNA, one might select lncRNAs that are strongly correlated with coding neighbor genes (Li et al, 2018) or lncRNAs that were differentially expressed between conditions or phenotypes (Weikard et al, 2018; Wang et al, 2019).…”

Genome-wide analysis of long non-coding RNAs in adult tissues of the melon fly, Zeugodacus cucurbitae (Coquillett)

“…Systematic identification and analyses of lncRNAs have been investigated in various species, such as goat [13], mouse [14], zebrafish [15], tilapia [4], chicken [16], and fungus [17]. Many studies have provided data enabling lncRNA identification in insects.…”

“…These provide valuable information for gene annotation [ 2 ]. As the member of the non-coding RNA families, long non-coding RNA (lncRNA) is defined as transcript longer than 200 nt (nucleotides) without protein-coding potential [ 3 , 4 ]. Non-coding RNAs play essential roles in many biological processes, such as genomic imprinting, dosage compensation, and post-transcription regulation [ 5 , 6 ].…”