Abstract: 【Aim】The Chinese honey bee (Apis cerana cerana) is the most widely distributed subspecies of the eastern honey bee (Apis cerana) in China, with significant advantages in geographic adaptation and ecological diversity. The cold resistance of A. c. cerana is superior to that of the western bee (A. mellifera) and can be used for beekeeping at high altitudes and collecting winter honey sources, this performance plays an important role in production. Exploring the low temperature tolerance of A. c. cerana can help to select excellent strains and create greater value for agricultural economy. 【Methods】 Samples of six groups of A. c. cerana workers of the 3-, 10- and 21-day-old subjected to normal temperature ［(25.0±0.2) ℃］ treatment (the control group) and low temperature ［(4.0±0.2) ℃］ treatment, respectively, for 6 h were collected and used for transcriptome sequencing by Illumina RNA-Seq and for full-length transcriptome sequencing by PacBio Iso-Seq. The Illumina RNA-Seq data were used to correct the PacBio Iso-Seq data. Based on the high-quality sequencing data, functional annotation of novel transcripts and genes were conducted using NR, NT, Pfam, KOG/COG, Swiss-Prot, KEGG and GO databases. 【Results】 A total of 71.17, 42.76, 58.82, 53.45, 40.33 and 42.79 Gb reads of the full-length transcriptome sequencing of A. c. cerana workers in six groups were obtained, respectively, with an average N₅₀ of 205 895 bp, yielding 164 194 consistent sequences after quality control. A total of 21 519 novel transcripts were obtained by alignment to the A. cerana reference genome, and were closely related to the material metabolism, nervous system, and signal transduction of A. c. cerana. The material metabolism, cell development, lifespan, and neural development of A. c. cerana at different day-old were affected by low temperature stress. Furthermore, 28 647 long non-coding RNAs (LncRNAs) were identified, among them lincRNA and sense_intronic were the most abundant lncRNAs, accounting for 35% and 45%, respectively.【Conclusion】This study identified a large number of unannotated novel genes and transcripts using the corrected the PacBio Iso-Seq data and conducted functional annotation of A. c. cerana workers. The quantity and types of LncRNA were also analyzed. These results complement the reference genome of A. cerana and provide a good data background for exploring the cold resistance mechanism of A. c. cerana.

Key words: Apis cerana cerana, low temperature, transcriptome, reference genome, developmental stage, PacBio Iso-Seq