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Updated: Jan 25, 2026

Identification of Alternative Splicing and Polyadenylation in RNA-seq Data
Published on: June 24, 2021
Ascosphaera apis invasion alters the expression pattern, alternative splicing and alternative polyadenylation of
Jianfeng Qiu1, Fangji Wang2, Xiang Li2
1College of Bee Science and Biomedicine, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China; National & Local United Engineering Laboratory of Natural Biotoxin, 350002 Fuzhou, Fujian, China; Apitherapy Research Institute of Fujian Province, 350002 Fuzhou, Fujian, China.
Abstract:
The Ascosphaera apis infects the honeybee larval gut and causes chalkbrood disease, which impacts colony health and beekeeping production. Currently, the innate immune mechanisms by which honeybee larvae resist A. apis infection remain unclear. This study utilized nanopore sequencing technology to analyze differentially expressed transcripts (DETs) in A. apis-infected and uninfected Apis cerana cerana larval guts, and identified alternative splicing (AS) and alternative polyadenylation (APA) in honeybee genes. The results showed that 1,642, 1,281, and 1,377 DETs were detected on 1-3 days post-infection, respectively. Ten DETs were randomly selected from each group for RT-qPCR validation, and 26 DETs exhibited expression trends consistent with the nanopore sequencing results. A total of 5,476 AS events from 2,430 genes were identified in the larval guts during 1-3 days post-infection, with the number of AS events in the A. apis-infected group being higher than in the control group. Five randomly validated AS events matched the sequencing results. Additionally, 7,310 genes containing APA sites were identified, with the majority having more than five APA sites. Three genes were randomly selected, and their APA sites were validated. These findings provide preliminary insights into the roles of AS and APA at the transcript level in honeybee responses to A. apis infection.
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