Shedding light upon the complex net of genome size, genome composition and environment in chordates

Abstract

The nucleotype theory has been advanced on the basis of studies regarding genome size and composition in various plant and animal species, i.e. the influence that genome can have on the phenotype independently of the informational content of DNA. It has also been noted that during evolution various interactions between different environmental factors and genome structural and functional parameters would have occurred. In this review, changes in genome size, transposon content, and base composition occurred during the evolution of chordates were examined. Many environmental stresses, such as temperature, can act on transposons and through these on genome size. Temperature is also one of the most important elements of natural selection able to interact both with base composition and genome size. It has been evidenced that temperature exerts a direct influence on base composition and its increase would have led to an higher content of genome GC-rich components during the evolution of chordates, in particular in endotherms. Temperature would have controlled the rate of biosynthesis in G1 phase and consequently the cell cycle duration which in turn would have interacted with genome size. The combined action of temperature, base composition, and genome size would also have been very important in controlling the metabolic rate. Finally, another important aspect of the nucleotypic effect is the influence that genome size and cell cycle duration, in correlation with environmental temperature, would have exert on embryo and larval development, very important for environmental adaptation. In conclusion, studies here reviewed to confirm the existence in chordates of a mutual influence between environment and genome non-coding components that would have played an important role in the evolution of these animals especially in environmental adaptation processes.

Investigation of the activity of transposable elements and genes involved in their silencing in the newt Cynops orientalis, a species with a giant genome

“…Overall, the activity of TEs can increase due to environmental stressors such as temperature 22 . In particular, the beginning of Carboniferous and the transition from Permian to Triassic were characterized by severe environmental changes 56 that might have provoked a reduction of the efficiency of silencing mechanisms in gonads, leading to a mobilization of TEs and thus to an increase of genome size in lungfish and newts 17 .…”

“…Even though several factors, such as metabolic rate and cell cycle duration, have been associated with amphibian genome size 8 , 16 , 17 , the molecular mechanisms favouring the persistence of extreme repetitive DNA contents in salamander genomes remain to be addressed.…”

A high-quality carabid genome provides insights into beetle genome evolution and cold adaptation

“…Despite many attempts to find abiotic and biotic factors that contribute to the enormous natural variation in genome size, it remains an open question which evolutionary and ecological variables drive genome size changes (Blommaert 2020). The main challenges to resolving this question arise from the complexity of genome composition, decoupling the role of selection (if present) from many different environmental factors, and the dependence of genome size on phylogenetic relatedness (Alfsneset al 2017;Canapa et al 2020;Ritchie et al2017). Recent studies have shown that the genome size is positively correlated with the size of repetitive DNA in insects (Quesneville 2015), but repetitive DNA has been linked to both adaptive and non-adaptive evolutionary processes (Canapa et al 2015;Loweret al 2017).…”

Mobile Elements in Ray-Finned Fish Genomes

“…Moreover, transposons can be co-opted and exapted, creating regulatory sequences, coding exons, or entirely new genes useful for the host genome [ 22 , 23 , 37 , 205 ]. Indeed, a great number of reports have suggested the responsiveness and susceptibility of TEs to environmental changes or stressful conditions [ 206 , 207 , 208 , 209 , 210 , 211 , 212 , 213 , 214 ]. Yuan and colleagues [ 31 ] analyzed 52 fishes and reported an increase in the DNA transposons in bony fish living in freshwaters and an abundance of tandem repeats in marine species that was not explained by phylogenetic relationships.…”