Identification, Characterization and Comparison of the Genome-Scale UTR Introns from Six Citrus Species

Abstract

Ever since their discovery, introns within the coding sequence (CDS) of transcripts have been paid great attention. However, the introns located in the untranslated regions (UTRs) are often ignored. Here, we identified, characterized and compared the UTR introns (UIs) from six citrus species. Results showed that the average intron number of UTRs is greatly lower than that of CDSs. Among all six citrus species, the number and density of 5′UTR introns (5UIs) are higher than those of 3′UTR introns (3UIs). The UI densities varied greatly among different citrus species. There are 11 and 9 types of splice site (SS) pairs for the UIs of C. sinensis and C. medica, respectively. However, the UIs of the other four citrus species all own only three kinds of SS pairs. The ‘GT-AG’, accounting for more than 95% of both 5UIs and 3UIs SS pairs for all the six species, is the most popular type. Moreover, 81 5UIs and 26 3UIs were identified as common UIs among the six citrus species, and the transcripts containing these common UIs were mostly involved in gene expression or gene expression regulation. Our study revealed that the UIs’ length, abundance, density and SS pair types varied among different citrus species and that many UI-containing genes play important roles in gene expression regulation. Our findings have great implications for future citrus UI function research.

DNA and coding/non‐coding RNA methylation analysis provide insights into tomato fruit ripening

“…The latter of which is related to metal-binding (Dagar et al, 2010) and was also found with m5C modification (Appendix S10). In addition, we identified several different methylated lncRNAs and cir-cRNAs, for which the target genes were F-box/ketch-repeat protein SKIP11, wall-associated receptor kinase, and paired amphipathic helix protein (Appendix S10), etc., all of which may be involved in the response to abiotic stress and lipid transport (Cheng et al, 2022). The Plant Journal, (2022), 112, 399-413 biogenesis and oxidation-reduction processes.…”