Transposable element annotation in non-model species: The benefits of species-specific repeat libraries using semi-automated EDTA and DeepTE de novo pipelines

Transposable elements (TEs) are significant genomic components which can be detected either through sequence homology against existing databases or de novo, with the latter potentially reducing the risk of underestimating TE abundance. Here, we describe the semi-automated generation of a de novo TE library using the newly developed EDTA pipeline and DeepTE classifier in a non-model teleost (Corydoras fulleri). Using both genomic and transcriptomic data, we assess this de novo pipeline's performance across four TE based metrics: (i) abundance, (ii) composition, (iii) fragmentation, and (iv) age distributions. We then compare the results to those found when using a curated teleost library (Danio rerio). We identify quantitative differences in these metrics and highlight how TE library choice can have major impacts on TE-based estimates in non-model species.

Interspecific introgression mediates adaptation to whole genome duplication

Adaptive gene flow is a consequential phenomenon across all kingdoms. Although recognition is increasing, there is no study showing that bidirectional gene flow mediates adaptation at loci that manage core processes. We previously discovered concerted molecular changes among interacting members of the meiotic machinery controlling crossover number upon adaptation to whole-genome duplication (WGD) in Arabidopsis arenosa. Here we conduct a population genomic study to test the hypothesis that adaptation to WGD has been mediated by adaptive gene flow between A. arenosa and A. lyrata. We find that A. lyrata underwent WGD more recently than A. arenosa, suggesting that pre-adapted alleles have rescued nascent A. lyrata, but we also detect gene flow in the opposite direction at functionally interacting loci under the most extreme levels of selection. These data indicate that bidirectional gene flow allowed for survival after WGD, and that the merger of these species is greater than the sum of their parts.

Whole genome duplication (WGD) presents new challenges to the establishment of optimal allelic combinations and to the meiotic machinery. Here, the authors show that adaptive gene flow from Arabidopsis arenosa could rescue the nascent A. lyrata from extinction following WGD.

Whole genome duplication and transposable element proliferation drive genome expansion in Corydoradinae catfishes

Genome size varies significantly across eukaryotic taxa and the largest changes are typically driven by macro-mutations such as whole genome duplications (WGDs) and proliferation of repetitive elements. These two processes may affect the evolutionary potential of lineages by increasing genetic variation and changing gene expression. Here, we elucidate the evolutionary history and mechanisms underpinning genome size variation in a species-rich group of Neotropical catfishes (Corydoradinae) with extreme variation in genome size—0.6 to 4.4 pg per haploid cell. First, genome size was quantified in 65 species and mapped onto a novel fossil-calibrated phylogeny. Two evolutionary shifts in genome size were identified across the tree—the first between 43 and 49 Ma (95% highest posterior density (HPD) 36.2–68.1 Ma) and the second at approximately 19 Ma (95% HPD 15.3–30.14 Ma). Second, restriction-site-associated DNA (RAD) sequencing was used to identify potential WGD events and quantify transposable element (TE) abundance in different lineages. Evidence of two lineage-scale WGDs was identified across the phylogeny, the first event occurring between 54 and 66 Ma (95% HPD 42.56–99.5 Ma) and the second at 20–30 Ma (95% HPD 15.3–45 Ma) based on haplotype numbers per contig and between 35 and 44 Ma (95% HPD 30.29–64.51 Ma) and 20–30 Ma (95% HPD 15.3–45 Ma) based on SNP read ratios. TE abundance increased considerably in parallel with genome size, with a single TE-family (TC1-IS630-Pogo) showing several increases across the Corydoradinae, with the most recent at 20–30 Ma (95% HPD 15.3–45 Ma) and an older event at 35–44 Ma (95% HPD 30.29–64.51 Ma). We identified signals congruent with two WGD duplication events, as well as an increase in TE abundance across different lineages, making the Corydoradinae an excellent model system to study the effects of WGD and TEs on genome and organismal evolution.

Hybrids and horizontal transfer: introgression allows adaptive allele discovery

Evolution has devised countless remarkable solutions to diverse challenges. Understanding the mechanistic basis of these solutions provides insights into how biological systems can be subtly tweaked without maladaptive consequences. The knowledge gained from illuminating these mechanisms is equally important to our understanding of fundamental evolutionary mechanisms as it is to our hopes of developing truly rational plant breeding and synthetic biology. In particular, modern population genomic approaches are proving very powerful in the detection of candidate alleles for mediating consequential adaptations that can be tested functionally. Especially striking are signals gained from contexts involving genetic transfers between populations, closely related species, or indeed between kingdoms. Here we discuss two major classes of these scenarios, adaptive introgression and horizontal gene flow, illustrating discoveries made across kingdoms.

Observation of resonant interatomic coulombic decay in Ne clusters

We have measured the electron spectra of Ne clusters after excitation with photon energies around the 2s inner valence threshold. At two photon energies below threshold, a resonantly enhanced surplus of low kinetic-energy electrons is observed. The kinetic energy of the peak does not vary with the photon energy and is slightly larger than the transition energy of Interatomic Coulombic Decay (ICD) above threshold. This leads us to assume that an ICD-like process is present. In analogy to the Auger and the resonant Auger decay this new phenomenon is termed resonant ICD.

Femtosecond interatomic Coulombic decay in free neon clusters: large lifetime differences between surface and bulk

A quantitative determination of 2s vacancy lifetimes in surface and bulk atoms of free Ne clusters has been made. While for free atoms the 2s inner-valence hole has a ps lifetime, it reduces to 6+/-1 fs for cluster bulk atoms. For surface atoms, the lifetime is on average longer than 30 fs. The lifetime estimate was obtained from fits of high-resolution photoelectron spectra of Ne clusters. The shortening of the lifetime is attributed to the coordination dependent interatomic Coulombic decay, which is extremely sensitive to internuclear distances.

Intramolecular electron scattering and electron transfer following autoionization in dissociating molecules

Resonant Auger decay of core-excited molecules during ultrafast dissociation leads to a Doppler shift of the emitted electrons depending on the direction of the electron emission relative to the dissociation axis. We have investigated this process by angle-resolved electron-fragment ion coincidence spectroscopy. Electron energy spectra for selected emission angles for the electron relative to the molecular axis reveal the occurrence of intermolecular electron scattering and electron transfer following the primary emission. These processes amount to approximately 25% of the resonant atomic Auger intensity emitted in the studied transition.

Experimental evidence for interatomic coulombic decay in Ne clusters

Electron spectra of photoexcited Ne clusters are shown to display a signal at low kinetic energies that is neither present in the Ne monomer nor at photon energies below the inner-valence 2s threshold. These findings are strong evidence for the existence of interatomic Coulombic decays (ICD), a mechanism that was recently predicted theoretically [Phys. Rev. Lett. 79, 4778 (1997)]]. In ICD, an inner-valence hole state in a weakly bonded system can undergo ultrafast relaxation due to energy transfer to a neighboring atom, followed by electron emission from this neighboring site.