Profiling Alternative 3 ' Untranslated Regions In Sorghum Using Rna-Seq Data

Sorghum is an important crop widely used for food, feed, and fuel. Transcriptome-wide studies of 3 ' untranslated regions (3 ' UTR) using regular RNA-seq remain scarce in sorghum, while transcriptomes have been characterized extensively using Illumina short-read sequencing platforms for many sorghum varieties under various conditions or developmental contexts. 3 ' UTR is a critical regulatory component of genes, controlling the translation, transport, and stability of messenger RNAs. In the present study, we profiled the alternative 3 ' UTRs at the transcriptome level in three genetically related but phenotypically contrasting lines of sorghum: Rio, BTx406, and R9188. A total of 1,197 transcripts with alternative 3 ' UTRs were detected using RNA-seq data. Their categorization identified 612 high-confidence alternative 3 ' UTRs. Importantly, the high-confidence alternative 3 ' UTR genes significantly overlapped with the genesets that are associated with RNA N-6-methyladenosine (m(6)A) modification, suggesting a clear indication between alternative 3 ' UTR and m(6)A methylation in sorghum. Moreover, taking advantage of sorghum genetics, we provided evidence of genotype specificity of alternative 3 ' UTR usage. In summary, our work exemplifies a transcriptome-wide profiling of alternative 3 ' UTRs using regular RNA-seq data in non-model crops and gains insights into alternative 3 ' UTRs and their genotype specificity.