Table 1.
Result of the genome assembly of P. b. seulensis.
Table 2.
Annotation of genes of the P. b. seulensis.
Fig 1.
Quality assessment of P. b. seulensis RNA-sequencing (RNA-seq) data.
(a) 4 development stages of P. b. seulensis for RNA-seq. (b) Grouping of samples via principal component analysis based on the P. b. seulensis transcriptome expression abundance. (c) Venn diagram shows the unique and shared unigenes during P. b. seulensis development.
Table 3.
Number of differentially expressed genes in P. b. seulensis.
Fig 2.
Trend analysis based on gene expression abundance.
(a) Heatmap shows 23,552 transcripts. The gene counts were normalized into Fragments Per Kilobase of transcript per Million mapped reads (FPKM), then averaged by life stage. The FPKM values for each gene were transformed and then hierarchically clustered using Pearson correlation. Clustering was performed based on similarities between gene expression profiles throughout the developmental stages. The mean expression values for each gene at each of the four developmental stages were normalized to the mean expression values in the former developmental stages to represent expression levels. Groups were chosen based on similar expression patterns over 0.7 of the Pearson correlation coefficient. After clustering the expression profiles, the number in the top left-hand corner of a profile box is the profile ID number. We assigned the number of genes on the right side of each cluster. Nonwhite profiles of the same color represent profiles grouped into a single cluster. White profiles represent the statically non-significant profiles of gene expression. (b) Detailed expression profiles of the genes in each cluster. Selected profiles were statically significant. (c) Likelihood score and gene count analysis of each cluster’s wing development-related genes. The likelihood score is calculated based on the observation values divided by the expectation values. (d) Likelihood score and gene count analysis of the metamorphosis-related genes in each cluster.
Fig 3.
Comparison of P. b.seulensis transcriptome profiles of the genes related to development, early development, hox, and metamorphosis.
The heatmap of gene expression profiles of 10 major wing development and metamorphosis functional categories. Each column stands for a developmental stage, for example, Egg, Larva, Pupa, and Adult, respectively, and each row represents a transcript. Red stands for high expression abundance, whereas blue represents low expression abundance.
Fig 4.
Histogram presentation of the Gene Ontology and KEGG enrichment of the P. b.seulensis genes in cluster 4.
A total of 1,598 unigenes were allocated to three specific GO categories. 1,183 Unigene sequences were specifically assigned to 236 KEGG pathways. The top 10 enrichment function lists and their p-value.
Fig 5.
Functional association network analysis. (a) Functional association network in P. b. seulensis. Nodes in the same group are coded with the same color. Cyan, yellow, blue, and red nodes represent P. b. seulensis, cluster 4, wing development and metamorphosis-related, and both cluster 4 and wing development and metamorphosis-related genes, respectively. (a, c) The average number of interacting partners and betweenness centrality score of the P. b. seulensis, cluster 4, wing development and metamorphosis-related, and both cluster 4 and wing development and metamorphosis-related genes. Statistical analysis was performed using the Mann-Whitney U test.
Table 4.
List of genes with wing development and metamorphosis-related genes and topological network parameters (Number of interaction partner and betweenness centrality).
Fig 6.
Genome comparison among representatives of coleoptera groups and coleoptera phylogeny.
(a) 2,686,932 aa from 9,608 conserved orthologues, (b) 35,555 aa sites from 269 wing development orthologous, and (c)1,952 aa sites from 19 metamorphosis orthologous. The tree was reconstructed by IQ-Tree 1.5.1 with the best fit model (LG+F+G4). The D. melanogaster was used as outgroups, Branch lengths were optimized and node ages were estimated from 100 trees.