Conservation of chromatin conformation in carnivores.

High throughput chromatin conformation capture (Hi-C) of leukocyte DNA was used to investigate the evolutionary stability of chromatin conformation at the chromosomal level in 11 species from three carnivore families: Felidae, Canidae, and Ursidae. Chromosome-scale scaffolds (C-scaffolds) of each species were initially used for whole-genome alignment to a reference genome within each family. This approach established putative orthologous relationships between C-scaffolds among the different species. Hi-C contact maps for all C-scaffolds were then visually compared and found to be distinct for a given reference chromosome or C-scaffold within a species and indistinguishable for orthologous C-scaffolds having a 1:1 relationship within a family. The visual patterns within families were strongly supported by eigenvectors from the Hi-C contact maps. Analysis of Hi-C contact maps and eigenvectors across the three carnivore families revealed that most cross-family orthologous subchromosomal fragments have a conserved three-dimensional (3D) chromatin structure and thus have been under strong evolutionary constraint for ∼54 My of carnivore evolution. The most pronounced differences in chromatin conformation were observed for the X chromosome and the red fox genome, whose chromosomes have undergone extensive rearrangements relative to other canids. We also demonstrate that Hi-C contact map pattern analysis can be used to accurately identify orthologous relationships between C-scaffolds and chromosomes, a method we termed "3D comparative scaffotyping." This method provides a powerful means for estimating karyotypes in de novo sequenced species that have unknown karyotype and no physical mapping information.

Whole genome analysis of clouded leopard species reveals an ancient divergence and distinct demographic histories.

Similar to other apex predator species, populations of mainland (Neofelis nebulosa) and Sunda (Neofelis diardi) clouded leopards are declining. Understanding their patterns of genetic variation can provide critical insights on past genetic erosion and a baseline for understanding their long-term conservation needs. As a step toward this goal, we present draft genome assemblies for the two clouded leopard species to quantify their phylogenetic divergence, genome-wide diversity, and historical population trends. We estimate that the two species diverged 5.1 Mya, much earlier than previous estimates of 1.41 Mya and 2.86 Mya, suggesting they separated when Sundaland was becoming increasingly isolated from mainland Southeast Asia. The Sunda clouded leopard displays a distinct and reduced effective population size trajectory, consistent with a lower genome-wide heterozygosity and SNP density, relative to the mainland clouded leopard. Our results provide new insights into the evolutionary history and genetic health of this unique lineage of felids.

Exploring the underwater silken architectures of caddisworms: comparative silkomics across two caddisfly suborders.

Caddisfly (Trichoptera) larvae assemble a variety of underwater structures using bioadhesive silk. The order is divided into two primary sub-orders distinguished by how the larvae deploy their silk. Foraging Integripalpia larvae construct portable tube cases. Annulipalpia larvae construct stationary retreats, some with suspended nets to capture food. To identify silk molecular adaptations that may have contributed to caddisfly diversification, we report initial characterization of silk from a net-spinner genus, Parapsyche, for comparison with the silk of a tube case-maker genus, Hesperophylax. Overall, general features of silk structure and processing are conserved across the sub-orders despite approximately 200 Ma of divergence: the H-fibroin proteins comprise repeating phosphoserine-rich motifs, naturally spun silk fibres contain approximately 1 : 1 molar ratios of divalent metal ions to phosphate, silk fibre precursors are stored as complex fluids of at least two types of complexes, and silk gland proteins contain only traces of divalent metal ions, suggesting metal ions that solidify the fibres are absorbed from the aqueous environment after silk extrusion. However, the number and arrangement of the repeating phosphoserine blocks differ between genera, suggesting molecular adaptation of H-fibroin through duplication and shuffling of conserved structural modules may correspond with the radiation of caddisflies into diverse environments. This article is part of the theme issue 'Transdisciplinary approaches to the study of adhesion and adhesives in biological systems'.