Fig 1.
Distribution of identified lncRNAs on each chromosome.
The outer ring represents the chicken genome labeled with chromosome number and position. The green circle shows the distribution of identified lncRNAs in G20W, and the orange circle shows the distribution in G55W.
Table 1.
Quality control results and high-quality clean reads obtained for each sample.
Fig 2.
(A) Computational pipeline for the systematic identification of lncRNAs. (B) Venn diagram illustrating the overlap of lncRNAs in breast muscle tissue libraries from G20W and G55W chickens. G20W: 20 weeks of age; G55W: 55 weeks of age. Length (C) and chromosomal (D) distribution of Gushi chicken lncRNAs.
Fig 3.
Analysis of differentially expressed lncRNAs.
(A) Representative of the degree of similarity between samples. The correlation coefficient is represented by color; deeper color represents a stronger correlation. (B) Clustering analysis of differentially expressed lncRNAs in G20W and G55W. (C) Volcano plot of differentially expressed lncRNAs in G20W and G55W. Green and red represent downregulated and upregulated expression, respectively.
Table 2.
The top 10 most abundantly expressed lncRNAs in breast muscle from G20W and G55W chickens.
Fig 4.
GO analyses of differentially expressed lncRNAs and mRNAs.
(A) Categories of biological processes, cellular components and molecular functions of the target genes of differentially expressed lncRNAs and mRNAs (cis). (B) Categories of the biological processes, cellular components and molecular functions of the target genes of differentially expressed lncRNAs and mRNAs (trans).
Fig 5.
KEGG analyses of differentially expressed lncRNAs and mRNAs.
(A) Scatter plot of the top 20 pathways enriched for differentially expressed lncRNAs and mRNAs in breast tissue from G20W and G55W chickens (cis). The abscissa represents the richness factor, and the ordinate represents the enriched pathway terms. The Q-value represents the corrected P (B) Scatter plot of the top 20 pathways enriched for differentially expressed lncRNAs and mRNAs in breast tissue from G20W and G55W chickens (trans). The abscissa represents the richness factor, and the ordinate represents the enriched pathway terms. The Q-value represents the corrected P.
Fig 6.
Differentially expressed lncRNA-mRNA interaction network analysis.
Circles represent coding genes, and arrows represent lncRNAs. Red nodes represent upregulated nodes, and green nodes represent downregulated nodes. Yellow nodes represent pathway terms. The node size represents -logP; the smaller the P value is, the greater is the node size. Lines between lncRNA-mRNA represent interactions between them.
Fig 7.
Validation of lncRNAs using RT-qPCR.
Data were analyzed by the 2-ΔΔCt method using β-actin as a reference gene. Each column represents the mean ±SE. Different letters indicate significant differences in expression levels between the two stages (P ≤ 0.05). Black bars represent read from RNA-Seq. Gray bars represent the results of qRT-PCR.