Meta-Analysis of the Public RNA-Seq Data of the Western Honeybee Apis mellifera to Construct Reference Transcriptome Data

Abstract

The Western honeybee (Apis mellifera) is valuable in biological research and agriculture. Its genome sequence was published before those for other insect species. RNA-Seq data for A. mellifera have been applied in several recently published studies. Nevertheless, these data have not been prepared for use in subsequent meta-analyses. To promote A. mellifera transcriptome analysis, we constructed reference transcriptome data using the reference genome sequence and RNA-Seq data curated from about 1,000 runs of public databases. The new reference transcriptome data construct comprised 149,685 transcripts, and 194,174 protein sequences were predicted. Approximately 50–60% of the predicted protein sequences were functionally annotated using the protein sequence data for several model and insect species. Novel candidate immune-related transcripts were searched by meta-analysis using immune-response-related RNA-Seq and reference transcriptome data. Three to twenty candidate transcripts including autophagy-related protein 3 were upregulated or downregulated in response to both viral and bacterial infections. The constructed reference transcriptome data may facilitate future transcriptome analyses of A. mellifera.

A Global Survey of the Full-Length Transcriptome of Apis mellifera by Single-Molecule Long-Read Sequencing

“…The first version of the A. mellifera complete genome sequence was published in 2006 [ 2 ]; since then, several versions of genome sequences have been released on Genbank. So far, the genomic sequences [ 2 , 3 ], transcriptome [ 4 , 5 ] and genetic linkage map [ 6 , 7 , 8 ] of A. mellifera have been studied extensively.…”

Meta-analysis of public RNA sequencing data revealed potential key genes associated with reproductive division of labor in social Hymenoptera and termites

“…The 212 identified genes were ranked based on their QW-score values (Table S4: https://doi.org/10.6084/m9.figshare.21524286.v4). These genes were annotated by the corresponding homologs of other species ( D. melanogaster, H. sapiens, Mus musculu s, Bombyx mori, Bombus terrestis , and Nasonia vitripennis ) using the annotation table created by Yokoi et al 2022 [67] (Table S4: https://doi.org/10.6084/m9.figshare.21524286.v4). We focused on the top 10 and bottom 10 genes in Table S4 because they showed abrupt score changes (Figure 2 and Table 1).…”

“…As a result of the above processes, the transcript IDs of all species were converted to the protein IDs of A. mellifera . The protein IDs of A. mellifera were then converted to those of other species using the annotation table for transcripts of A. mellifera [67]. Transcripts and amino acid sequences created in this study can be downloaded from figshare (Supplemental File S1).…”

Meta-Analysis of Public RNA Sequencing Data Revealed Potential Key Genes Associated with Reproductive Division of Labor in Social Hymenoptera and Termites

“…The 212 identified genes were ranked based on their QW score values (Table S4: https://doi.org/10.6084/m9.figshare.21524286.v6, accessed on 6 April 2023). These genes were annotated based on the corresponding homologs of other species (D. melanogaster, H. sapiens, Mus musculus, Bombyx mori, Bombus terrestis, and Nasonia vitripennis) using the annotation table created by Yokoi et al 2022 [60] (Table S4: https://doi.org/10.6084/m9.figshare.21524286.v6, accessed on 6 April 2023). We focused on the top 10 and bottom 10 genes in Table S4 because they showed abrupt score changes (Figure 2 and Table 1).…”

“…As a result of the above processes, the transcript IDs of all species were converted to the protein IDs of A. mellifera. The protein IDs of A. mellifera were then converted to those of other species using the annotation table for transcripts of A. mellifera [60]. Transcripts and amino acid sequences created in this study can be downloaded from figshare (Supplemental File S1).…”