Abstract

Introns exist not only in coding sequences (CDSs) but also in untranslated regions (UTRs) of a gene. Recent studies in animals and model plants such as Arabidopsis have revealed that the UTR-introns (UIs) are widely presented in most genomes and involved in regulation of gene expression or RNA stability. In the present study, we identified introns at both 5′UTRs (5UIs) and 3′UTRs (3UIs) of sweet orange genes, investigated their size and nucleotide distribution characteristics, and explored the distribution of cis-elements in the UI sequences. Functional category of genes with predicted UIs were further analyzed using GO, KEGG, and PageMan enrichment. In addition, the organ-dependent splicing and abundance of selected UI-containing genes in root, leaf, and stem were experimentally determined. Totally, we identified 825 UI- and 570 3UI-containing transcripts, corresponding to 617 and 469 genes, respectively. Among them, 74 genes contain both 5UI and 3UI. Nucleotide distribution analysis showed that 5UI distribution is biased at both ends of 5′UTR whiles 3UI distribution is biased close to the start site of 3′UTR. Cis- elements analysis revealed that 5UI and 3UI sequences were rich of promoter-enhancing related elements, indicating that they might function in regulating the expression through them. Function enrichment analysis revealed that genes containing 5UI are significantly enriched in the RNA transport pathway. While, genes containing 3UI are significantly enriched in splicesome. Notably, many pentatricopeptide repeat-containing protein genes and the disease resistance genes were identified to be 3UI-containing. RT-PCR result confirmed the existence of UIs in the eight selected gene transcripts whereas alternative splicing events were found in some of them. Meanwhile, qRT-PCR result showed that UIs were differentially expressed among organs, and significant correlation was found between some genes and their UIs, for example: The expression of VPS28 and its 3UI was significantly negative correlated. This is the first report about the UIs in sweet orange from genome-wide level, which could provide evidence for further understanding of the role of UIs in gene expression regulation.

Highlights

  • The existence of intron in genes was initially discovered in late 1970 [1]

  • The high 5 untranslated regions (UTRs) intron density might be due to the fact that the Arabidopsis genome is better sequenced and annotated with less unknown sequences (Ns)

  • We identified a total of 965 5 UTR intron (5UI) sequences and 745 3 UTR intron (3UI) sequences from 825 5UI-Ts and 570 3UI-Ts (469 genes)

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Summary

Introduction

It has come to be identified as a common event in all eukaryotic genomes. In the past, it was recognized as an important gene structure that was eliminated from transcripts by a complex molecular mechanism called a spliceosome [2,3,4]. The Sh1 intron 1 enhances chimeric gene expression in rice and maize protoplasts approximately 100-fold [8]. These have revealed that the introns in the transcripts showed positive effect on gene expression, i.e., intron-mediated enhancement (IME) [9,10,11]

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