Genome-Wide Identification and Stage-Specific Expression Profile Analysis Reveal the Function of Ribosomal Proteins for Oogenesis of Spodoptera litura

Abstract

Ribosomal proteins (Rps) are indispensable in ribosome biogenesis and protein synthesis, which tightly correlate with cell growth and proliferation in different physiological processes across species. Up to now, genes coding for Rps have been identified and studied in many species, however, their information still remains elusive in many insect species, especially in Spodoptera litura. In this study, 81 Rp genes were identified from S. litura genome and were mapped to their positions on the chromosomes. In addition, their physical and chemical properties, gene structure, phylogenetic relationships, targeted microRNAs were also analyzed. Gene ontology analysis disclosed that Rp genes were closely associated with processes related to ribosome biosynthesis, proteins translation processing, molecular binding activities. The quantitative real-time PCR (qRT-PCR) revealed expression profiles of Rp genes varied in different stages of oogenesis, and found that most Rp genes accumulated in previtellogenesis stage. This study described the comprehensive genome-wide analysis of Rp gene family in agricultural pests, which provided foundation for further characterizing the roles of Rps in oogenesis of insects, and some Rp genes may further serve as targets for innovative pest control.

Keywords: Spodoptera litura; gene expression; oogenesis; phylogenetic relationships; ribosomal proteins.

FIGURE 1

Chromosomal distribution of SlRp genes.

FIGURE 2

Synteny analysis of Rp genes in S. litura and B. mori. The red and yellow fronts in the blocks represented the chromosome labels in S. litura (Sl) and B. mori (Bm), respectively, and the green lines refer to the orthologous Rp genes in S. litura and B. mori.

FIGURE 3

The GO enrichment terms of SlRps.

FIGURE 4

Phylogenetic relationship, motifs analysis, and gene structure of SlRp genes. (A), the ML phylogenetic tree based on SlRps; (B), Exon-intron structure of SlRp genes. Blackish-grey lines indicate introns and green boxes indicate UTR regions, and yellow rectangles indicate the position of SlRp CDS domains; (C), Conserved domains of SlRps were predicted in smart database, and different-colored squares represent different domains of Rps.

FIGURE 5

The heatmap for the expression patterns of Rp genes in oogenesis of S. litura, including previtellogenesis stage (PS), vitellogenesis stage (VS.) and choriogenesis stage (CS). (A–D) represented four different expression types of Rp genes among these three stages. The mean expression values were calculated from three independent biological replicates, and significance was determined using one-way ANOVA. p value < 0.05 represents significant difference. The heatmap was performed using Tbtools (V 1.098669) software based on the relative mRNA expression level of SlR_p genes.