Pippel, M. | bioRxiv Science

bioRxiv2019

Diversity, dynamics and effects of LTR retrotransposons in the model grass Brachypodium distachyon

O_LITransposable elements (TEs) are the main reason for the high plasticity of plant genomes, where they occur as communities of diverse evolutionary lineages. Because research has typically focused on single abundant families or summarized TEs at a coarse taxonomic level, our knowledge about how these lineages differ in their effects on genome evolution is still rudimentary.\nC_LIO_LIHere we investigate the community composition and dynamics of 32 long terminal repeat retrotransposon (LTR-RT) families in the 272 Mb genome of the Mediterranean grass Brachypodium distachyon.\nC_LIO_LIWe find that much of the recent transpositional activity in the B. distachyon genome is due to centromeric Gypsy families and Copia elements belonging to the Angela lineage. With a half-life as low as 66 ky, the latter are the most dynamic part of the genome and an important source of within-species polymorphisms. Second, GC-rich Gypsy elements of the Retand lineage are the most abundant TEs in the genome. Their presence explains more than 20 percent of the genome-wide variation in GC content and is associated to higher methylation levels.\nC_LIO_LIOur study shows how individual TE lineages change the genetic and epigenetic constitution of the host beyond simple changes in genome size.\nC_LI

genomics↗

bioRxiv2019

Evolved for success in novel environments: the round goby genome

Since the beginning of global trade, hundreds of species have colonized territories outside of their native range. Some of these species proliferate at the expense of native ecosystems, i.e., have become invasive. Invasive species constitute powerful in situ experimental systems to study fast adaptation and directional selection on short ecological timescales. They also present promising case studies for ecological and evolutionary success in novel environments.\n\nWe seize this unique opportunity to study genomic substrates for ecological success and adaptability to novel environments in a vertebrate. We report a highly contiguous long-read based genome assembly for the most successful temperate invasive fish, the benthic round goby (Neogobius melanostomus), and analyse gene families that may promote its impressive ecological success.\n\nOur approach provides novel insights from the large evolutionary scale to the small species-specific scale. We describe expansions in specific cytochrome P450 enzymes, a remarkably diverse innate immune system, an ancient duplication in red light vision accompanied by red skin fluorescence, evolutionary patterns in epigenetic regulators, and the presence of genes that may have contributed to the round gobys capacity to invade cold and salty waters.\n\nA recurring theme across all analyzed gene families are gene expansions. This suggests that gene duplications may promote ecological flexibility, superior performance in novel environments, and underlie the impressive colonization success of the round goby. Gobiidae generally feature fascinating adaptations and are excellent colonizers. Further long-read genome approaches across the goby family may reveal whether the ability to conquer new habitats relates more generally to gene copy number expansions.

ecology↗