Abstract
Numerous instances of presence/absence variations for introns have been documented in eukaryotes, and some cases of recurrent loss of the same intron have been suggested. However, there has been no comprehensive or phylogenetically deep analysis of recurrent intron loss. Of 883 cases of intron presence/absence variation that we detected in five sequenced grass genomes, 93 were confirmed as recurrent losses and the rest could be explained by single losses (652) or single gains (118). No case of recurrent intron gain was observed. Deep phylogenetic analysis often indicated that apparent intron gains were actually numerous independent losses of the same intron. Recurrent loss exhibited extreme non-randomness, in that some introns were removed independently in many lineages. The two larger genomes, maize and sorghum, were found to have a higher rate of both recurrent loss and overall loss and/or gain than foxtail millet, rice or Brachypodium. Adjacent introns and small introns were found to be preferentially lost. Intron loss genes exhibited a high frequency of germ line or early embryogenesis expression. In addition, flanking exon A+T-richness and intron TG/CG ratios were higher in retained introns. This last result suggests that epigenetic status, as evidenced by a loss of methylated CG dinucleotides, may play a role in the process of intron loss. This study provides the first comprehensive analysis of recurrent intron loss, makes a series of novel findings on the patterns of recurrent intron loss during the evolution of the grass family, and provides insight into the molecular mechanism(s) underlying intron loss.
Highlights
Spliceosomal introns are noncoding DNA segments within eukaryotic genes that are removed after transcription
Accumulating evidence suggests that the common ancestors of at least several eukaryotic supergroups were intron rich [1,2,7,8] and the great interspecies difference in intron density was caused by considerably different rates of lineage-specific intron loss and/or gain [3,5]
We provide results for the first comprehensive analysis of recurrent intron turnover within a plant family and show that recurrent intron loss represents a considerable portion of all intron losses identified and intron loss events far outnumber intron gain events
Summary
Spliceosomal introns (called introns hereafter) are noncoding DNA segments within eukaryotic genes that are removed after transcription. Patterns of intron loss and gain have been investigated extensively in numerous subclades of the eukaryotic tree of life with different levels of taxon sampling (see review in [3]). Vast numbers of single loss and gain events (events inferred as occurring only once in the phylogeny investigated (Fig. 1, top) have been well-documented. Some studies document cases of recurrent loss [9,10,11] and/or recurrent gain (otherwise called parallel gain) [12,13,14], terms describing introns that are independently removed from or inserted into the identical sites more than once in an investigated phylogeny (Fig. 1, middle)
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