In order to further understand some information of Apis cerana and provide a basis for studying its function, the genes and full-length transcripts associated with phenoloxidases (PO) and serine proteases (SP) in Apis cerana cerana were explored and analyzed using previously gained Nanopore long-read sequencing data. All full-length transcripts in Apis cerana cerana were aligned to KEGG and Nr databases with Blast tool to screen genes and full-length transcripts relevant to PO and SP. Structures of annotated genes were optimized by comparing PO and SP-associated full-length transcripts with annotated transcripts in the Apis cerana reference genome (ACSNU-2. 0) utilizing gffcompare software. Types of AS events in genes relative to PO and SP were identified by using Astalavista software, followed by visualization with IGV browser. The authenticity of AS events was confirmed by PCR. Predic-tion and investigation of APA sites were performed using TAPIS pipeline, and motifs at upstream of APA sites were then identified using TBtool software. Totally, 42 genes and 146 full-length transcripts relative to PO and SP in Apis cerana cerana were identified. Structures of 16 annotated genes were optimized, among these 5′ ends and 3′ ends of seven genes were prolonged, and both 5′ ends and 3′ ends of two genes were prolonged. Additionally, 389 AS events occurred in 10 genes were discovered, among these the most abundant type was alternative 3′ splice site. PCR result validated the authenticity of randomly selected two AS events. Furthermore, 34 genes associated with PO and SP were identified to include one or more APA sites, among which those genes containing three APA sites were in the largest group; multiple motifs at upstream of APA sites were detected, with the consistent sequence: GGHKSYW SHHTRATWTCNBHDMRRYWYRTNYTVACNGCKGCDCAYTGYR. This study identified 42 genes and 146 full-length transcripts related to Apis cerana cerana PO and SP, optimized the structures of 16 annotated PO and SPgenes in the reference genome of Apis cerana, and explored 389 AS events and 237 APA sites within genes rela-tive to PO and SP.
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