Profiling Alternative 3' Untranslated Regions in Sorghum using RNA-seq Data.

Min Tu,Yin Li

doi:10.3389/fgene.2020.556749

Abstract

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 N6-methyladenosine (m6A) modification, suggesting a clear indication between alternative 3′UTR and m6A 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.

Highlights

Sorghum bicolor is a crop globally used for food, fodder, and fuel
We focus on analyzing the features of the alternative 3 untranslated regions (3 UTR) genes in terms of their 3 UTR lengths, gene order, and functions rather than the 3 UTR dynamics over the time points
The read depth within a mRNA tends to drop rapidly when reaching to its 3 end in RNA-seq data, which is known as the 3 bias of RNA-seq (Li et al, 2015)

Summary

Introduction

Sorghum bicolor is a crop globally used for food, fodder, and fuel. The importance of sorghum in agriculture and bioenergy is due to its advantages in diversity, genetics, and genomics (Calvino and Messing, 2012; Boyles et al, 2019; Xie and Xu, 2019). Grain sorghum ranks 5th in global cereal production (Boyles et al, 2019); grain sorghum and forage sorghum serve as significant sources for animal feed; sweet sorghum and energy sorghum are promising bioenergy crops for sugar- and lignocellulosic-based biofuels (Mullet et al, 2014; Mathur et al, 2017; Li et al, 2018; Yang et al, 2020). Like in model species and major crops, RNA-seq has recently been widely employed in sorghum research and advanced our understanding in many aspects of sorghum including development (Davidson et al, 2012; Kebrom et al, 2017; Turco et al, 2017; Leiboff and Hake, 2019), accumulation of sugar/biomass M. et al, 2018 Li et al, 2019a,b; Zhang et al, 2019; Hennet et al, 2020), stress responses and tolerance (Dugas et al, 2011; Gelli et al, 2014; Sui et al, 2015; Fracasso et al, 2016; Yang et al, 2018; Varoquaux et al, 2019), senescence (Johnson et al, 2015; Wu et al, 2016a), and regulation of miRNA and long non-coding RNA (Calvino et al, 2011; Sun et al, 2020)

Methods

Results

Conclusion