GC content of vertebrate exome landscapes reveal areas of accelerated protein evolution

Abstract

Background Rapid accumulation of vertebrate genome sequences render comparative genomics a powerful approach to study macro-evolutionary events. The assessment of phylogenic relationships between species routinely depends on the analysis of sequence homology at the nucleotide or protein level. Results We analyzed mRNA GC content, codon usage and divergence of orthologous proteins in 55 vertebrate genomes. Data were visualized in genome-wide landscapes using a sliding window approach. Landscapes of GC content reveal both evolutionary conservation of clustered genes, and lineage-specific changes, so that it was possible to construct a phylogenetic tree that closely matched the classic “tree of life”. Landscapes of GC content also strongly correlated to landscapes of amino acid usage: positive correlation with glycine, alanine, arginine and proline and negative correlation with phenylalanine, tyrosine, methionine, isoleucine, asparagine and lysine. Peaks of GC content correlated strongly with increased protein divergence. Conclusions Landscapes of base- and amino acid composition of the coding genome opens a new approach in comparative genomics, allowing identification of discrete regions in which protein evolution accelerated over deep evolutionary time. Insight in the evolution of genome structure may spur novel studies assessing the evolutionary benefit of genes in particular genomic regions. Electronic supplementary material The online version of this article (10.1186/s12862-019-1469-1) contains supplementary material, which is available to authorized users.

Quantitative Approach to Fish Cytogenetics in the Context of Vertebrate Genome Evolution

“…The currently most plausible findings link the genome GC content with the chromosome size and with life history traits, where the effective population size (Ne) is the most important indicator of the strength of the gBGC [ 18 , 20 ]. For fish, there is no systematic analysis of GC% based on purely genomic data as are available for mammals [ 20 , 21 , 22 ], birds [ 23 , 24 ], and reptiles [ 25 , 26 ]. One study assessing GC% based on non-genomic determination showed a slightly higher GC% in marine and migrating marine fish species [ 58 ].…”

“…Here, the chromosome or chromosome arm size plays an important role as there is at least one crossing-over (i.e., one recombination event) per one chromosome arm in bi-armed chromosomes and per chromosome in mono-armed chromosomes [ 18 , 19 ]. Among vertebrates, the efficiency of gBGC on the GC% has been investigated in great detail mostly in the coding (i.e., exonic) regions and above all in mammals [ 20 , 21 , 22 ] and birds [ 23 , 24 ], but also in reptiles [ 25 , 26 ]. The same applies for the online available GCevobase, an evolution-based database for the GC content in eukaryotic genomes displaying GC contents for all the annotated coding sequences from Ensembl [ 27 ].…”

A computational exploration of resilience and evolvability of protein–protein interaction networks

“…An extensive amount of research has been dedicated to our understanding of protein sequence evolution, and what may enable adaptation without disrupting already present biological functions. The functional divergence of genomes has been explored by studying gene duplication 2 – 4 , de novo gene emergence 5 – 10 , open reading frame extension 11 – 13 , and sequence properties 14 , 15 , i.e., GC-content 16 and codon usage 17 – 19 . While there has been much focus on addressing wherefrom and how novel sequence features emerge (e.g., gene duplication, de novo gene emergence), limited attention has been given to how novelty may become integrated into the cellular apparatus from a systems-level perspective and what systems-level processes facilitate the incorporation of novel interactions.…”

Regional effect on the molecular clock rate of protein evolution in Eutherian and Metatherian genomes

“…Recently we proposed a method that facilitates genome-wide analysis of macro-evolutionary events in vertebrates [1]. We used a sliding window approach, which integrates information of a centered gene and its 100 neighbors, smoothening the known erratic behavior of individual genes that vary greatly in nucleotide composition, intron size and rate of evolution of encoded proteins [1]. Such integration visualizes strong region-specific events that apply to tens or hundreds of adjacent genes.…”