Biology subjects

Groenvold, L.

Publications and source records attributed to Groenvold, L..

3 recordsLinked to original sources

bioRxiv2020

Comparative regulomics reveals pervasive selection on gene dosage following whole genome duplication

Whole genome duplication (WGD) events have played a major role in eukaryotic genome evolution, but the consequence of these extreme events in adaptive genome evolution is still not well understood. To address this knowledge gap we used a comparative phylogenetic model and transcriptomic data from seven species to infer selection on gene expression in duplicated genes (ohnologs) following the salmonid WGD 80-100 million years ago. We find rare cases of tissue-specific expression evolution but pervasive expression evolution affecting many tissues, reflecting strong selection on maintenance of genome stability following genome doubling. Although ohnolog expression levels have evolved mostly asymmetrically, by diverting one ohnolog copy down a path towards pseudogenization, strong evolutionary constraints have frequently also favoured symmetric shifts in gene dosage of both copies, likely to achieve gene dose reduction while avoiding accumulation of toxic mutations. Mechanistically, ohnolog regulatory divergence is dictated by the number of bound transcription factors in promoters, with transposable elements being one source of novel binding sites driving tissue-specific gains in expression. Our results imply pervasive adaptive expression evolution following WGD to overcome the immediate challenges posed by genome doubling and to exploit the long-term genetic opportunities for novel phenotype evolution.

evolutionary biology↗

bioRxiv2017

Evolution of cold acclimation in temperate grasses (Pooideae)

In the past 50 million years climate cooling has triggered the expansion of temperate biomes. During this period, many extant plant lineages in temperate biomes evolved from tropical ancestors and adapted to seasonality and cool conditions. Among the Poaceae (grass family), one of the subfamilies that successfully shifted from tropical to temperate biomes is the Pooideae (temperate grasses). Subfamily Pooideae contains the most important crops cultivated in the temperate regions including wheat (Triticum aestivum) and barley (Hordeum vulgare). Due to the need of well-adapted cultivars, extensive research has produced a large body of knowledge about the mechanisms underlying cold adaptation in cultivated Pooideae species. Especially cold acclimation, a process which increases the frost tolerance during a period of non-freezing cold, plays an important role. Because cold adaptation is largely unexplored in lineages that diverged early in the evolution of the Pooideae, little is known about the evolutionary history of cold acclimation in the Pooideae. Here we test if several species of early diverging lineages exhibit increased frost tolerance after a period of cold acclimation. We further investigate the conservation of five well-studied gene families that are known to be involved in the cold acclimation of Pooideae crop species. Our results indicate that cold acclimation exists in early diverging lineages, but that genes involved in regulation of cold acclimation are not conserved. The investigated gene families show signs of lineage-specific evolution and support the hypothesis that gene family expansion is an important mechanism in adaptive evolution.

evolutionary biology↗

bioRxiv2017

Comparative transcriptomics reveals lineage specific evolution of cold response in Pooideae

BackgroundUnderstanding how complex traits evolve through adaptive changes in gene regulation remains a major challenge in evolutionary biology. Over the last ~50 million years, Earth has experienced climate cooling and ancestrally tropical plants have adapted to expanding temperate environments. The grass subfamily Pooideae dominates the grass flora of the temperate regions, but the role of cold-response gene regulation in the transitioning from tropical to temperate climate remains unexplored.\n\nResultsTo establish if molecular responses to cold are conserved throughout the phylogeny, we assembled the transcriptomes of five Pooideae species spanning early to later diverging lineages, and compared short- and long-term cold responsive genes using 8633 high confidence ortholog groups with resolved gene tree topologies. We found that a majority of cold responsive genes were specific to one or two lineages, an observation that we deem incompatible with a cold adapted Pooideae ancestor. However, all five species shared short-term cold response in a small set of general stress genes as well as the ability to down-regulate the photosynthetic machinery during cold temperatures.\n\nConclusionsOur observations indicate that the different Pooideae lineages have assembled cold response programs in parallel by taking advantage of a common potential for cold adaptation.

evolutionary biology↗