Honeybee caste differentiation is a prime example of phenotypic plasticity in eusocial insects and serves as a valuable model for epigenetic studies. Various epigenetic modifications such as non-coding RNAs and histone modifications, have been implicated in caste differentiation. However, the role of some epigenetic modifications such as DNA methylation still remains controversial. Similarly, mRNA m6A modification has been suggested to participate in honeybee caste differentiation. Here we used Oxford Nanopore technology to compare m6A modifications in 2d, 4d, and 6d queen and worker larvae. Our data indicated that m6A modification is unlikely to exert a direct role in the caste differentiation at the developmental stages examed in this study. We identified 363, 1074, and 1000 differentially expressed transcripts (DETs) in 2d, 4d, and 6d queen-worker larval comparisons, respectively, 74 of which were mapped in seven key KEGG pathways (e.g., mTOR, Notch, FoxO, MAPK, Wnt, Hippo, Hedgehog) associated with honeybee caste differentiation. In contrast, only 16, 39, and 11 differentially m6A-modified transcripts (m6A-DMTs) were found in the 2d, 4d and 6d comparisons, with very few m6A-DMTs involved in key pathways for caste differentiation. Notably, no correlation was observed between m6A modification levels and transcript expression, including DETs and m6A-DMTs. The motifs of m6A modifications remained unchanged across all three developmental time points. When the original samples were randomly regrouped, the number of m6A-DMTs did not change significantly, but the DETs related to caste differentiation were dramatically altered. Therefore, the functional relevance of m6A in honeybee caste differentiation is still under debate and requires more comprehensive studies.
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