Abstract
The silk gland of the silkworm Bombyx mori is a specialized organ where silk proteins are efficiently synthesized under precise regulation that largely determines the properties of silk fibers. To understand the genes involved in the regulation of silk protein synthesis, considerable research has focused on the transcripts expressed in silk glands; however, the complete transcriptome profile of this organ has yet to be elucidated. Here, we report a full-length silk gland transcriptome obtained by PacBio single-molecule long-read sequencing technology. In total, 11,697 non-redundant transcripts were identified in mixed samples of silk glands dissected from larvae at five developmental stages. When compared with the published reference, the full-length transcripts optimized the structures of 3002 known genes, and a total of 9061 novel transcripts with an average length of 2171 bp were detected. Among these, 1403 (15.5%) novel transcripts were computationally revealed to be lncRNAs, 8135 (89.8%) novel transcripts were annotated to different protein and nucleotide databases, and 5655 (62.4%) novel transcripts were predicted to have complete ORFs. Furthermore, we found 1867 alternative splicing events, 2529 alternative polyadenylation events, 784 fusion events and 6596 SSRs. This study provides a comprehensive set of reference transcripts and greatly revises and expands the available silkworm transcript data. In addition, these data will be very useful for studying the regulatory mechanisms of silk protein synthesis.
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Acknowledgements
This work was supported by a grant (31872291) from the National Natural Science Foundation of China and a grant (cstc2017jcyjBX0041) from the Chongqing Research Program of Basic Research and Frontier Technology. American Journal Experts performed English language editing on this manuscript.
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All authors conceived and designed the experiments. TC, QS, YM and WZ performed the experiments and analyzed the data. LH, QS and HX wrote the manuscript. All authors read and approved the final manuscript.
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438_2020_1691_MOESM1_ESM.tif
Supplementary file1 (TIF 2897 kb) Bioinformatics analysis process. (A) PacBio data processing pipeline. (B) Transcriptome analysis pipeline
438_2020_1691_MOESM2_ESM.tif
Supplementary file2 (TIF 410 kb) AS events in major silk gland TFs. Sashimi plot of ES and truncation events in the ASG, MMSG, PMSG and PSG. The RNA coverage is given as the log-transformed RPKM value, and junction reads are plotted as arcs whose width is proportional to the number of reads aligned to the junction spanning the exons connected by the arc. Genomic coordinates are shown on the x-axis. Quantified mRNA isoforms identified from the MergedSet are shown on bottom (exons in black, introns as lines with arrowheads)
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Chen, T., Sun, Q., Ma, Y. et al. A transcriptome atlas of silkworm silk glands revealed by PacBio single-molecule long-read sequencing. Mol Genet Genomics 295, 1227–1237 (2020). https://doi.org/10.1007/s00438-020-01691-9
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DOI: https://doi.org/10.1007/s00438-020-01691-9