Abstract
Main conclusion
Comprehensive transcriptome profiling uncovers extensive intraspecific variation of circular RNAs in maize, shedding light on genomic and phenotypic variation among maize inbred lines.
Circular RNAs (circRNAs) are single-strand, covalently closed transcripts. A substantial number of circRNAs have been identified and shown to be associated with phenotypic variation in various species. However, little is known about the intraspecific variation of circRNAs in maize (Zea mays L.). Here, we collected a large transcriptomic dataset (by circRNA-seq and mRNA-seq) from seedling leaves of the reference maize inbred lines B73 and Mo17. We identified over 1500 circRNAs in these lines using two circRNA detection methods, CIRCexplorer2 and CIRI. Notably, a substantial proportion of circRNAs varied in terms of sequence or expression level between lines, pointing to extensive intraspecific variation of circRNAs in maize. GO and KEGG analyses showed that genes producing circRNAs with intraspecific variation were more likely to be enriched in multiple functional groups, compared with those that did not produce circRNAs. These findings suggest that circRNAs could be utilized as an indicator of genomic and phenotypic variation among maize inbred lines. Ribosomal profiling revealed that several circRNAs might have translational capacity in maize. These results uncover the extensive intraspecific variation of circRNAs and pave the way for further understanding the molecular mechanisms underlying phenotypic variation at the circRNA level in maize.
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Funding
This research was supported by the National Key Research and Development Program of China (2016YFD0100802) and Huazhong Agricultural University Scientific & Technological Self-innovation Foundation (Program No. 2015RC016). The authors declare no conflict of interest.
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Supplementary material 2 Table S1 Summary of circRNA-seq data obtained for B73 and Mo17. Table S2 Detailed information about circRNAs detected in B73 and Mo17. Table S3 Parental gene IDs of circRNAs in B73 and Mo17. Table S4 Overlapped circRNAs in B73 and Mo17. Table S5 Differentially expressed circRNAs in B73 and Mo17. Table S6 qRT-PCR validation of differentially expressed circRNAs in B73 and Mo17. Table S7 Enriched GO terms for the parental genes of B73- and Mo17-specific circRNAs. Table S8 Number of circRNAs with junction sites covered by Ribo-seq data in B73 and Mo17. Table S9 Enriched GO terms for the parental genes of circRNAs with junction sites covered by Ribo-seq data. Table S10 Sequences of validated translatable circRNAs in B73 and Mo17. Table S11 Primer information for the validation of translatable circRNAs and differentially expressed circRNAs (XLSX 263 kb)
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Luo, Z., Han, L., Qian, J. et al. Circular RNAs exhibit extensive intraspecific variation in maize. Planta 250, 69–78 (2019). https://doi.org/10.1007/s00425-019-03145-y
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DOI: https://doi.org/10.1007/s00425-019-03145-y
Keywords
- Maize
- Circular RNAs
- Intraspecific variation
- Phenotypic variation