Imprecise intron losses are less frequent than precise intron losses but are not rare in plants

Abstract

In this study, we identified 19 intron losses, including 11 precise intron losses (PILs), six imprecise intron losses (IILs), one de-exonization, and one exon deletion in tomato and potato, and 17 IILs in Arabidopsis thaliana. Comparative analysis of related genomes confirmed that all of the IILs have been fixed during evolution. Consistent with previous studies, our results indicate that PILs are a major type of intron loss. However, at least in plants, IILs are unlikely to be as rare as previously reported.

Reviewers: This article was reviewed by Jun Yu and Zhang Zhang. For complete reviews, see the Reviewers' Reports section.

Keywords: Arabidopsis thaliana; De-exonization; De-intronization; Deletion; Insertion; Intron loss; Solanum.

Figure 1

Two examples of imprecise intron losses. (A) The S. tuberosum gene PGSC0003DMG400000276 lost both an intron and a 21-bp-long downstream exon. The downstream intron was intact and did not lose any nucleotides; its splicing was supported by > 10 RNA-Seq reads. The splicing of the target intron in S. lycopersicum was also supported by > 10 RNA-Seq reads and by EST asmbl_392.tomatov23pasa_pasa4. The assembly of the variation site in S. tuberosum was supported by nine different Whole Genome Shotgun (WGS) reads. (B) The S. lycopersicum gene Solyc04g007270.2 lost a 204-bp-long intron, a 22-bp-long segment from an upstream exon and a 9-bp-long segment from a downstream exon. This deletion occurred in the 3'-UTR and did not inactivate the gene, as supported by >10 RNA-Seq reads. The successful splicing of the target intron in S. tuberosum was supported by > 10 RNA-Seq reads. The assembly of the variation site in S. lycopersicum was supported by > 10 WGS reads. For details of the RNA-Seq and WGS reads and other intron losses, see Additional file 2 and Additional file 3.