Biology subjects

Bein, B.

Publications and source records attributed to Bein, B..

4 recordsLinked to original sources

bioRxiv2026

Integrated genomics and transcriptomics reveal mechanisms of extreme dietary adaptation in vampire bats

Vampire bats are the only tetrapods that feed exclusively on blood. To uncover the molecular basis of this extreme dietary specialization, we generated six new reference genomes, including genomes of all three vampire bat species, and integrated comparative analyses of gene sequence evolution (selection signatures, duplications, and losses) with transcriptomic data from six major organs to identify shifts in gene expression. Our integrative analyses reveal sequence or expression changes in 150 genes that illuminate the genetic mechanisms underlying sanguivory. Through comparative analyses and experiments, we show that the enlarged vampire bat stomach has increased connective tissue content enabling extreme expansion, is pH-neutral, and exhibits reduced mucus production, together providing molecular insights into its shift from a digestive to an absorptive organ for water, electrolytes, and vitamins. We further uncover pathway-level molecular changes underlying altered gastrointestinal motility; trypsin-dependent protein digestion; upregulated amino acid catabolism with key aspects diverging from other mammals; impaired dietary fat digestion counterbalanced by increased fatty acid synthesis; defective sugar metabolism and natural insulin deficiency; enhanced heme iron absorption; and adult splenic erythropoiesis. Together, these findings reveal the molecular adaptations that enable one of the most extreme dietary transitions among vertebrates.

evolutionary biology↗

bioRxiv2026

Accurate, comprehensive gene annotation and ortholog identification across thousands of vertebrate genomes with TOGA2

Inferring orthologs and annotating coding genes remain central challenges in genomics, evident by the growing gap between assembled and annotated genomes. TOGA (Tool to infer Orthologs from Genome Alignments) addresses this challenge by integrating gene annotation and orthology inference. Here, we present TOGA2, the next generation of TOGA, which substantially improves annotation completeness, accuracy, scalability, and orthology inference. TOGA2 leverages exon-level orthology and introduces an exon-wise annotation procedure that reduces memory usage 513-fold and runtime 6.1-fold. We show that human-trained deep learning models for splice site prediction generalize across vertebrates. Integrating these predictions enables robust handling of evolutionary changes in exon-intron structure, including splice site shifts, intron deletions, and exonization of introns. A new gene tree reconciliation step refines orthology inference, and UTR annotation improves gene model completeness. Across mammals, birds, turtles, and percomorph fishes, TOGA2 annotations generally achieve higher gene completeness than transcriptome-informed RefSeq annotations. TOGA2 identifies previously unannotated exons in mouse, assigns informative gene symbols, and annotates V(D)J segments of antigen receptors. TOGA2 scales to thousands of genomes, which we demonstrate by generating comprehensive comparative genomics resources for 2,162 vertebrate assemblies, including gene annotations, ortholog sets, gene losses and duplications, retrogene candidates, and outputs supporting downstream analyses. Together, TOGA2 provides a scalable and versatile framework for comparative genomics that bridges the genome annotation gap.

genomics↗

bioRxiv2025

Comparative genomics indicate multiple genetic routes to the evolution of torpor in placental mammals

Torpor is a key survival strategy that many avian and mammalian lineages evolved in response to challenging environmental conditions. Whether the independent evolution of torpor in different lineages involved changes in the same genes remains poorly understood. Here, we performed comparative screens across 190 placental mammal genomes to comprehensively examine associations between loss, positive selection and evolutionary rate shifts in individual protein-coding genes and evolutionary shifts in torpor use. We find that gene-torpor associations are highly clade-specific, with no gene being able to explain the majority of torpor shifts across the phylogeny of placental mammals. Instead, a relatively higher but limited extent of evolutionary convergence can be detected at the pathway level. Our results suggest that torpor emerged through several genetic routes in placental mammals, which likely explains the vast diversity of torpor use patterns that can be observed among torpor-capable species today. SignificanceA fundamental question in evolutionary genomics is whether independent gains and losses of a convergent trait may be achieved through similar or distinct genetic paths. Here, we address this question by focusing on the evolution of torpor across placental mammals, a key trait that likely emerged independently in several lineages. By conducting multiple comparative genomics screens across 190 placental mammal species, we find that individual protein-coding genes have a low explanatory power for evolutionary shifts in torpor. In contrast, there is slightly stronger evidence for pathway-level convergence. Our findings suggest that the wide diversity of patterns of torpor use across placental mammals may, in part, be due to the existence of multiple genetic paths to torpor.

evolutionary biology↗

bioRxiv2024

Long-read sequencing and genome assembly of natural history collection samples and challenging specimens

Museum collections harbor millions of samples, largely unutilized for long-read sequencing. Here, we use ethanol-preserved samples containing kilobase-sized DNA to show that amplification-free protocols can yield contiguous genome assemblies. Additionally, using a modified amplification-based protocol, employing an alternative polymerase to overcome PCR bias, we assembled the 3.1 Gb maned sloth genome, surpassing the previous 500 Mb protocol size limit. Our protocol also improves assemblies of other difficult-to-sequence molluscs and arthropods, including millimeter-sized organisms. By highlighting collections as valuable sample resources and facilitating genome assembly of tiny and challenging organisms, our study advances efforts to obtain reference genomes of all eukaryotes.

genomics↗