TephritidBase: a genome visualization and gene expression database for tephritid flies

Abstract

The fruit flies in Tephritidae include many severe fruits and vegetables pests. To date, the genomes and transcriptomes of tephritid flies are distributed in different major databases. However, the tephritid flies community lacks an integrated database. Here, we introduce the first release of TephritidBase, available online at https://tephritid.biodb.org. The database encompasses 12 tephritid genomes, 677 tephritid transcriptomes and nearly 7 million docking results. Transcripts Per Kilobase of exon model per Million mapped reads (TPM), Fragments Per Kilobase of exon model per Million mapped fragments (FPKM) or Reads Per Kilobase of exon model per Million mapped reads (RPKM) were evaluated, and transcriptome samples were grouped in detail so that users could analyze transcriptome results at various developmental stages, tissues, treatments and so on. In total, there were 2,694 predicted chemoreception genes with accessible three-dimensional (3D) protein structures simulated by AlphaFold2. Furthermore, TephritidBase provided molecular docking data for 2,074 insect pheromones and 794 natural ingredients of host plants with these proteins. In addition, TephritidBase provides evolutionary data for the genome, principal component analysis and co-expression network data for the transcriptome. TephritidBase provides useful information and guidance for screening of bioactive compounds against tephritid flies targeting the chemoreception proteins.