Transcriptome Complexities Across Eukaryotes

TL;DR

This study introduces new metrics to quantify transcriptome complexity across diverse eukaryotic species, enabling more precise evolutionary comparisons and insights into genome structure variations over deep timescales.

Contribution

It develops and applies novel complexity metrics, including TpG, EpT, EpG, and EEN, for evaluating transcriptome structural complexity across genomes, orthologs, and novel genes.

Findings

Complexity metrics reveal diversity in transcriptome structures across lineages.

Ortholog and novel gene analyses show biases towards low complexity genes.

Metrics improve cross-species complexity comparisons with greater accuracy.

Abstract

Genomic complexity is a growing field of evolution, with case studies for comparative evolutionary analyses in model and emerging non-model systems. Understanding complexity and the functional components of the genome is an untapped wealth of knowledge ripe for exploration. With the "remarkable lack of correspondence" between genome size and complexity, there needs to be a way to quantify complexity across organisms. In this study we use a set of complexity metrics that allow for evaluation of changes in complexity using TranD. We ascertain if complexity is increasing or decreasing across transcriptomes and at what structural level, as complexity is varied. We define three metrics -- TpG, EpT, and EpG in this study to quantify the complexity of the transcriptome that encapsulate the dynamics of alternative splicing. Here we compare complexity metrics across 1) whole genome annotations, 2) a filtered subset of orthologs, and 3) novel genes to elucidate the impacts of ortholog and novel genes in transcriptome analysis. We also derive a metric from Hong et al., 2006, Effective Exon Number (EEN), to compare the distribution of exon sizes within transcripts against random expectations of uniform exon placement. EEN accounts for differences in exon size, which is important because novel genes differences in complexity for orthologs and whole transcriptome analyses are biased towards low complexity genes with few exons and few alternative transcripts. With our metric analyses, we are able to implement changes in complexity across diverse lineages with greater precision and accuracy than previous cross-species comparisons under ortholog conditioning. These analyses represent a step forward toward whole transcriptome analysis in the emerging field of non-model evolutionary genomics, with key insights for evolutionary inference of complexity changes on deep timescales across the tree of life. We suggest a means to quantify biases generated in ortholog calling and correct complexity analysis for lineage-specific effects. With these metrics, we directly assay the quantitative properties of newly formed lineage-specific genes as they lower complexity in transcriptomes.