The hidden structural variability in avian genomes

Structural variants (SVs) are DNA mutations that can have relevant effects at micro- and macro-evolutionary scales. The detection of SVs is largely limited by the type and quality of sequencing technologies adopted, therefore genetic variability linked to SVs may remain undiscovered, especially in complex repetitive genomic regions. In this study, we used a combination of long-read and linked-read genome assemblies to investigate the occurrence of insertions and dele-tions across the chromosomes of 14 species of birds-of-paradise and two species of estrildid finches including highly repetitive W chro-mosomes. The species sampling encompasses most genera and representatives from all major clades of birds-of-paradise, allowing comparisons between individuals of the same species, genus, and family. We found the highest densities of SVs to be located on the microchromosomes and on the female-specific W chromosome. Genome assemblies of multiple individuals from the same species allowed us to compare the levels of genetic variability linked to SVs and single nucleotide polymorphisms (SNPs) on the W and other chromosomes. Our results demonstrate that the avian W chromosome harbours more genetic variability than previously thought and that its structure is shaped by the continuous accumulation and turn-over of transposable element insertions, especially endogenous retroviruses.

Bioinspired Microstructured Polymer Surfaces with Antireflective Properties

Over the years, different approaches to obtaining antireflective surfaces have been explored, such as using index-matching, interference, or micro- and nanostructures. Structural super black colors are ubiquitous in nature, and biomimicry thus constitutes an interesting way to develop antireflective surfaces. Moth-eye nanostructures, for example, are well known and have been successfully replicated using micro- and nanofabrication. However, other animal species, such as birds of paradise and peacock spiders, have evolved to display larger structures with antireflective features. In peacock spiders, the antireflective properties of their super black patches arise from relatively simple microstructures with lens-like shapes organized in tightly packed hexagonal arrays, which makes them a good candidate for cheap mass replication techniques. In this paper, we present the fabrication and characterization of antireflective microarrays inspired by the peacock spider’s super black structures encountered in nature. Firstly, different microarrays 3D models are generated from a surface equation. Secondly, the arrays are fabricated in a polyacrylate resin by super-resolution 3D printing using two-photon polymerization. Thirdly, the resulting structures are inspected using a scanning electron microscope. Finally, the reflectance and transmittance of the printed structures are characterized at normal incidence with a dedicated optical setup. The bioinspired microlens arrays display excellent antireflective properties, with a measured reflectance as low as 0.042 ± 0.004% for normal incidence, a wavelength of 550 nm, and a collection angle of 14.5°. These values were obtained using a tightly-packed array of slightly pyramidal lenses with a radius of 5 µm and a height of 10 µm.

Sequence Transpositions Restore Genes on the Highly Degenerated W Chromosomes of Songbirds

The female-specific W chromosomes of most Neognathae birds are highly degenerated and gene-poor. Previous studies have demonstrated that the gene repertoires of the Neognathae bird W chromosomes, despite being in small numbers, are conserved across bird species, likely due to purifying selection maintaining the regulatory and dosage-sensitive genes. Here we report the discovery of DNA-based sequence duplications from the Z to the W chromosome in birds-of-paradise (Paradisaeidae, Passeriformes), through sequence transposition. The original transposition involved nine genes, but only two of them (ANXA1 and ALDH1A1) survived on the W chromosomes. Both ANXA1 and ALDH1A1 are predicted to be dosage-sensitive, and the expression of ANXA1 is restricted to ovaries in all the investigated birds. These analyses suggest the newly transposed gene onto the W chromosomes can be favored for their role in restoring dosage imbalance or through female-specific selection. After examining seven additional songbird genomes, we further identified five other transposed genes on the W chromosomes of Darwin’s finches and one in the great tit, expanding the observation of the Z-to-W transpositions to a larger range of bird species, but not all transposed genes exhibit dosage-sensitivity or ovary-biased expression We demonstrate a new mechanism by which the highly degenerated W chromosomes of songbirds can acquire genes from the homologous Z chromosomes, but further functional investigations are needed to validate the evolutionary forces underlying the transpositions.