Alternative splicing level related to intron size and organism complexity

Abstract

Background Alternative splicing is the process of selecting different combinations of splice sites to produce variably spliced mRNAs. However, the relationships between alternative splicing prevalence and level (ASP/L) and variations of intron size and organism complexity (OC) remain vague. Here, we developed a robust protocol to analyze the relationships between ASP/L and variations of intron size and OC. Approximately 8 Tb raw RNA-Seq data from 37 eumetazoan species were divided into three sets of species based on variations in intron size and OC. Results We found a strong positive correlation between ASP/L and OC, but no correlation between ASP/L and intron size across species. Surprisingly, ASP/L displayed a positive correlation with mean intron size of genes within individual genomes. Moreover, our results revealed that four ASP/L-related pathways contributed to the differences in ASP/L that were associated with OC. In particular, the spliceosome pathway displayed distinct genomic features, such as the highest gene expression level, conservation level, and fraction of disordered regions. Interestingly, lower or no obvious correlations were observed among these genomic features. Conclusions The positive correlation between ASP/L and OC ubiquitously exists in eukaryotes, and this correlation is not affected by the mean intron size of these species. ASP/L-related splicing factors may play an important role in the evolution of OC.

Evolutionary genomics of the emergence of brown algae as key components of coastal ecosystems

“…Increased intron density may have facilitated some of the genome-wide tendencies that will be described below, such as increased reorganisation of composite genes for example. Even if the mechanisms that initially led to an increased prevalence of introns are likely to have been neutral 19 , this increase will have provided scope for alternative splicing and domain reorganisation that may have played an important role in the acquisition of developmental complexity 17,20–22 .…”

The evolutionary dynamics that retain long neutral genomic sequences in face of indel deletion bias: a model and its application to human introns

“…Moreover, the authors also showed that almost all introns longer than 10 000 bp harbour conserved sequences, emphasizing the important role conserved segments play in generating the heavy tail of the intron length distribution. Second, Yang et al [36] have recently shown that within a genome, the intron size is correlated to the alternative splicing level and prevalence. Sironi et al [37] showed a correlation between the logarithm of intron length and the number of conserved sequences within the intron.…”

“…Second, Yang et al . [36] have recently shown that within a genome, the intron size is correlated to the alternative splicing level and prevalence. Sironi et al .…”

The evolutionary dynamics that retain long neutral genomic sequences in face of indel deletion bias: a model and its application to human introns

“…Moreover, the authors also showed that almost all introns longer than 10,000 bp harbor conserved sequences, emphasizing the important role conserved segments play in generating the heavy tail of the intron length distribution. Second, Yang et al (2021) have recently showed that within a genome, the intron size is correlated to the alternative splicing level and prevalence. Sironi et al (2005) showed a correlation between the logarithm of intron length and the number of conserved sequences within the intron.…”