Fumagalli, M. R. | bioRxiv Science

bioRxiv2023

Gene regulatory programs in the life history of Salpingoeca rosetta

The choanoflagellate Salpingoeca rosetta can differentiate into at least five morphologically and behaviorally distinct cell types during its lifetime, going from individual motile cells to linear and rosette-shaped colonies. Due to the capability to form colonies and its close relationship with Metazoa, this organism is considered a model for studying multicellular evolution. The gene regulatory programs underlying these transformations are, however, unknown. Here we analyze transcriptomic data obtained from Salpingoeca rosetta in different states to identify a core of genes associated with the formation of multicellular colonies. We then compare the results with other organisms which display simple forms of multicellularity, highlighting commonalities and differences.

evolutionary biology↗

bioRxiv2019

Genomic duplications shaped current retrotransposon position distribution in human

Retrotransposons, DNA sequences capable of creating copies of themselves, compose about half of the human genome and played a central role in the evolution of mammals. Their current position in the host genome is the result of the retrotranscription process and of the following host genome evolution. We apply a model from statistical physics to show that the genomic distribution of the two most populated classes of retrotransposons in human deviates from random placement, and that this deviation increases with time. The time dependence suggests a major role of the host genome dynamics in shaping the current retrotransposon distributions. In fact, these distributions can be explained by a stochastic process of random placement due to retrotranscription followed by genome expansion and sequence duplications. Besides the inherent interest in understanding the origin of current retrotransposon distributions, this work sets a general analytical framework to analyze quantitatively the effects of genome evolutionary dynamics on the distribution of genomic elements.

biophysics↗