| Summary: | 碩士 === 國立臺灣大學 === 農藝學研究所 === 105 === Transposable elements (TE) are the mobile and replicable sequences within the genome. Particularly, 85% of maize genome is composed of TEs. It has been demonstrated that a TE insertion can possibly introduce alternative splicing (AS) junction sites in the intron of a gene and result in new isoforms. AS events in plants have also been reported to be responsive to environmental stresses. To understand the roles of alternative splicing caused by insertions of the Ds elements, a family of well-studied DNA TE, during abiotic stresses, we assembled and analyzed 53 stress-related RNA-Seq libraries of maize under drought, osmotic, salt, heat, cold, water flooding, and UV stresses.
Among all assembled transcripts, 68% are known transcripts, 25% are novel isoforms of known genes, and 7% are intergenic transcripts. In most stressed samples, the total transcripts would be greater than those in the corresponding controlled samples. The functional annotations of the genes differentially expressing known transcripts were distinct from those of novel isoforms, together, highlighting the importance of AS in enhancing transcriptomic diversity during abiotic stresses. The identification of partial Ds sequences in the isoforms of 8 annotated and 1 putative intergenic genes suggested that the Ds elements can affect the splicing of inserted genes through 4 mechanisms including intron retention, exonization, alt-transcription start site, and alt-polyadenylation site. Several Ds-related isoforms appeared to be induced by a specific abiotic stress. In conclusion, our results implied that the AS isoforms resulted from TE insertion may contribute to the transcriptomic responses to diverse abiotic stresses in maize.
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