Trio‐binned genomes of the woodrats Neotoma bryanti and Neotoma lepida reveal novel gene islands and rapid copy number evolution of xenobiotic metabolizing genes

Abstract

The genomic architecture underlying the origins and maintenance of biodiversity is an increasingly accessible feature of species, due in large part to third‐generation sequencing and novel analytical toolsets. Applying these techniques to woodrats (Neotoma spp.) provides a unique opportunity to study how herbivores respond to environmental change. Neotoma bryanti and N. lepida independently achieved a major dietary feat in the aftermath of a natural climate change event: switching to the novel, toxic food source creosote bush (Larrea tridentata). To better understand the genetic mechanisms underlying this ability, we employed a trio binning sequencing approach with a N. bryanti × N. lepida F1 hybrid, allowing the simultaneous assembly of genomes representing each parental species. The resulting phased, chromosome‐level, highly complete haploid references enabled us to explore the genomic architecture of several gene families—cytochromes P450, UDP‐glucuronosyltransferases (UGTs), and ATP‐binding cassette (ABC) transporters—known to play key roles in the metabolism of naturally occurring toxic dietary compounds. In addition to duplication events in the ABCG and UGT2B subfamilies, we found expansions in three P450 gene families (2A, 2B, 3A), including the evolution of multiple novel gene islands within the 2B and 3A subfamilies, which may have provided the crucial substrate for dietary adaptation. Our assemblies demonstrate that trio binning from an F1 hybrid rodent effectively recovers parental genomes from species that diverged more than a million years ago.

Specific Gene Duplication and Loss of Cytochrome P450 in Families 1-3 in Carnivora (Mammalia, Laurasiatheria)

“…Recently, a koala genome project revealed that a huge expansion of CYP2Cs was possibly an adaptation to a diet of eucalypts [ 11 ]. Further, among woodrat genomes, especially juniper-eating species, several reports have found higher gene copy numbers of CYP2As, 2Bs, and 3As compared to other rodents [ 12 , 28 , 29 ], and studies have also suggested that the woodrat’s CYP2Bs gene expansion might contribute to their high metabolic capacity for terpenes from juniper plants. In this study, we found specific duplication of CYP2Cs and CYP2As in the brown bear, CYP2Cs in the black bear, CYP2Cs and 3As in the badger, and CYP3As in the dog.…”

“…Such an evolutionary history is essential for characterizing isoform-specific substrate-specificity and further characterizing species-specific metabolism in animals [ 10 ]. Reports suggest that CYP genetic duplication or loss affects the xenobiotic metabolism capacity in several animals and that these evolutionary consequences might be due to the need of some insects, birds, and herbivorous mammals to manage constant exposure to phytochemicals [ 11 , 12 , 13 , 14 ]. This “plant-arms race” concept may explain the necessity of CYP duplication events in herbivorous species: it hones detoxification systems in response to phytochemicals or toxins originating in plants.…”

Four Decades of Cytochrome P450 2B Research: From Protein Adducts to Protein Structures and Beyond

“…Intriguingly, the biggest recent surprise regarding CYP2B enzymes came not from studies of protein structure but of genome structures from the laboratory of my collaborator Dr. Denise Dearing. Her group has discovered a novel CYP2B gene island in the woodrat N. lepida, which is comprised solely of variable numbers of duplicated genes most (Greenhalgh et al, 2022), and which may play an important role in allowing the animals to ingest diets high in toxic monoterpenes.…”

Duplication, Loss, and Evolutionary Features of Specific UDP-Glucuronosyltransferase Genes in Carnivora (Mammalia, Laurasiatheria)

“…The generally accepted “animal-plant warfare” hypothesis considers the evolution of the xenobiotic metabolism as one of major defense mechanisms in animals against daily exposure to xenobiotics; in this regard, plant secondary metabolites are likely among the major sources of evolutionary pressure [ 13 , 24 , 25 , 26 ]. Several studies have shown that herbivorous mammals and birds have experienced a huge expansion of UGT families [ 27 , 28 , 29 , 30 ]. In placental mammals, Kawai et al (2021) [ 31 ] recently demonstrated a relationship of herbivorous diet with a large number of UGT2B genes but not with UGT1A genes.…”

“…This strongly suggests that UGT2Bs might be important for the daily metabolism of plant secondary metabolites. Moreover, a recent genomic analysis in woodrats (highly herbivorous) indicated significant duplication of UGT2Bs, in contrast to closely related omnivorous rats and deer mice [ 28 ]. Similarly, sika deer genomic analysis [ 29 ] suggested that genes in the UGT2B subfamily have a strong correlation with the adaptation of the species to a high-tannin diet.…”