The emergence and evolution of intron‐poor and intronless genes in intron‐rich plant gene families

Abstract

Eukaryotic genes can be classified into intronless (no introns), intron-poor (three or fewer introns per gene) or intron-rich. Early eukaryotic genes were mostly intron-rich, and their alternative splicing into multiple transcripts, giving rise to different proteins, might have played pivotal roles in adaptation and evolution. Interestingly, extant plant genomes contain many gene families with one or sometimes few sub-families with genes that are intron-poor or intronless, and it remains unknown when and how these intron-poor or intronless genes have originated and evolved, and what their possible functions are. In this study, we identified 33 such gene families that contained intronless and intron-poor sub-families. Intronless genes seemed to have first emerged in early land plant evolution, while intron-poor sub-families seemed first to have appeared in green algae. In contrast to intron-rich genes, intronless genes in intron-poor sub-families occurred later, and were subject to stronger functional constraints. Based on RNA-seq analyses in Arabidopsis and rice, intronless or intron-poor genes in AP2, EF-hand_7, bZIP, FAD_binding_4, STE_STE11, CAMK_-CAMKL-CHK1 and C2 gene families were more likely to play a role in response to drought and salt stress, compared with intron-rich genes in the same gene families, whereas intronless genes in the B_lectin and S_locus_glycop gene family were more likely to participate in epigenetic processes and plant development. Understanding the origin and evolutionary trajectory, as well as the potential functions, of intronless and intron-poor sub-families provides further insight into plant genome evolution and the functional divergence of genes.

Genome-Wide Identification and Evolutionary Analysis of the SRO Gene Family in Tomato

“…The SRO genes in the same group showed similar numbers of exons and conserved structures in a variety of tomatoes, especially the SRO genes in group I, which had a highly consistent exon distribution and the largest number of motifs and were likely the core gene cluster in the tomato SRO family. However, compared with wild tomatoes, SRO genes in cultivated tomato often have longer gene structures and more introns than other genes in the same group, which means that SolySROs can achieve transcriptional diversification through alternative splicing and other processes, thus regulating more complex and extensive functions ( Liu et al, 2021 ). This was obviously not available in the SRO gene in wild tomatoes.…”

Identification and Analysis of GhEXO Gene Family Indicated That GhEXO7_At Promotes Plant Growth and Development Through Brassinosteroid Signaling in Cotton (Gossypium hirsutum L.)

“…This corresponds to the last two motifs in the analysis of upland cotton conserved motifs, which are contained in all GhEXO protein sequences. Moreover, it has been found that the structure of a gene permits its evolutionary analysis, and the pattern of exon/intron distribution is useful for its function ( Roy and Gilbert, 2006 ; Liu et al, 2021 ). In our study, exon/intron analysis indicated that most of the GhEXO genes have no introns, only 25% or fewer contain introns.…”

Cytokinin glucosyl transferases, key regulators of cytokinin homeostasis, have potential value for wheat improvement

“…The 48 genes with reliable structures show consistent phylogenetic patterns (Figure S5). However, in all cases the CGTs could be described as intron‐less or intron poor (Liu et al ., 2021). In contrast, many of the putative TaUGTs , with low E value, are intron‐rich (Figure S6).…”

“…Liu et al . (2021) speculate that loss of introns may be a factor in early land plant evolution allowing fast response to stress conditions and also may have facilitated faster developmental adaptations to life on land. Indeed, Vyroubalová et al .…”

“…In contrast, many of the putative TaUGTs, with low E value, are intron-rich (Figure S6). Liu et al (2021) speculate that loss of introns may be a factor in early land plant evolution allowing fast response to stress conditions and also may have facilitated faster developmental adaptations to life on land. Indeed, Vyroubalov a et al (2009) commented that O-glucosylation 'is a mechanism by which the plant cell could react very fast to the disturbed homeostasis induced by physiological stimuli'.…”