Identification and analysis of MAPK signaling pathway-related genes and full-length transcripts in Apis mellifera ligustica
Author of the article:FAN Xiao-Xue, JING Xin, KANG Jing, GAO Xu-Ze, ZHANG Yi-Qiong, YAO Yu-Tong, MAO Yu-Li, NIU Qing-Sheng
Author's Workplace：College of Bee Science and Biomedicine, Fujian Agriculture and Forestry University
Key Words：Apis mellifera ligustica; MAPK signaling pathway; full-length transcript; alternative splicing; alternative polyadenylation
Abstract：
Abstract [Aim] To identify genes and full-length transcripts associated with the mitogen activated protein kinase (MAPK) signaling pathway in Apis mellifera ligustica, and explore alternative polyadenylation (APA) sites and alternative splicing (AS) events in MAPK signaling pathway-related genes. [Methods] All full-length transcripts were aligned to the Nr and KEGG databases, after which MAPK signaling pathway-associated genes and full-length transcripts were screened out. MAPK signaling pathway-associated full-length transcripts were compared with those annotated in the reference genome of A. mellifera (Amel_HAv3.1) to optimize the structures of annotated genes. APA sites were predicted using the TAPIS pipeline, followed by identification of motifs 50 bp upstream of all APA sites. AS events were identified using Astalavista software followed by statistics on the number of various kinds of AS events. PCR was used to validate AS events in genes related to the MAPK signaling pathway. [Results] In total, 83 genes and 443 full-length transcripts relevant to the MAPK signaling pathway were identified. 5′ UTR and 3′ UTR of one gene were prolonged, and 5′ UTR of 12 genes and 3′ UTR of 10 genes were prolonged, respectively. 52 genes associated with the MAPK signaling pathway contained one or more APA sites and there were two motifs upstream of the APA sites. Twenty-one AS events in 13 genes related to the MAPK signaling pathway were identified, of which the most abundant was exon skipping (ES). PCR confirmed the authenticity of four ES events in the Bone morphogenetic protein receptor type-1B gene and one ES event in the Ets DNA-binding protein pokkuri gene. [Conclusion] Eighty-three genes and 446 full-length transcripts associated with the MAPK signaling pathway in A. m. ligustica were identified for the first time, structures of 21 annotated genes in the A. mellifera reference genome were optimized, 406 APA sites and 52 AS events of genes related to MAPK signaling pathway were discovered, and the authenticity of AS events in MAPK signaling pathway-associated genes was verified.