Genome assembly and gene expression in the American black bear provides new insights into the renal response to hibernation

Abstract

The prevalence of chronic kidney disease (CKD) is rising worldwide and 10–15% of the global population currently suffers from CKD and its complications. Given the increasing prevalence of CKD there is an urgent need to find novel treatment options. The American black bear (Ursus americanus) copes with months of lowered kidney function and metabolism during hibernation without the devastating effects on metabolism and other consequences observed in humans. In a biomimetic approach to better understand kidney adaptations and physiology in hibernating black bears, we established a high-quality genome assembly. Subsequent RNA-Seq analysis of kidneys comparing gene expression profiles in black bears entering (late fall) and emerging (early spring) from hibernation identified 169 protein-coding genes that were differentially expressed. Of these, 101 genes were downregulated and 68 genes were upregulated after hibernation. Fold changes ranged from 1.8-fold downregulation (RTN4RL2) to 2.4-fold upregulation (CISH). Most notable was the upregulation of cytokine suppression genes (SOCS2, CISH, and SERPINC1) and the lack of increased expression of cytokines and genes involved in inflammation. The identification of these differences in gene expression in the black bear kidney may provide new insights in the prevention and treatment of CKD.

A Beary Good Genome: Haplotype-Resolved, Chromosome-Level Assembly of the Brown Bear (Ursus arctos)

“…1 B ). Consistent with previous results, we found that long interspersed nuclear elements (LINEs) represented the largest percentage of repetitive elements in the Ursidae family ( Srivastava et al 2019 ; Zhu et al 2020 ), however, one study reported fewer total repeats in the American black bear ( Ursus americanus ) and a greater number of repeats overall in the giant panda ( Ailuropoda melanoleuca ) ( Srivastava et al 2019 ). Interestingly, while most Ursid species contain a relatively low percent of small RNA repetitive elements, we find expansions of this repetitive element class in the Andean bear ( Tremarctos ornatus ) and the Japanese black bear ( Ursus thibetanus japonicus ) ( Fig.…”

Conservation of chromatin conformation in carnivores

“…Chromosome or scaffold-level assemblies of the following species were used for this study: Neofelis nebulosa , clouded leopard; Panthera pardus , leopard ( 46 ); Panthera tigris , tiger ( 47 ); Acinonyx jubatus, cheetah ( 48 ); Puma concolor, puma ( https://www.ncbi.nlm.nih.gov/nuccore/QAVW00000000.1 ); Canis lupus dingo , dingo ( https://www.ncbi.nlm.nih.gov/nuccore/QKWQ00000000.1 ); Lycaon pictus , African wild dog ( 49 ); Vulpes vulpes , red fox ( 50 ); Ursus americanus , black bear ( 51 ); and Ursus arctos , grizzly bear ( 52 ); Ursus maritimus , polar bear ( 53 ) ( Dataset S1 ). All assemblies were obtained from the DNA Zoo database ( https://www.dnazoo.org/assemblies , cutoff date, July 2019).…”

Draft Genome Assembly for the Tibetan Black Bear (Ursus thibetanus thibetanus)

“…The gene sets from nine species-human, mouse, dog, giant panda, polar bear, tiger (Panthera tigris, GCF_000464555.1) 6 , brown bear (Ursus arctos, GCF_003584765.1) 7 , American black bear (Ursus americanus, GCA_003344425.1) 8 (Srivastava et al, 2019), and Tibetan black bear-were used for gene clustering. We identified clusters for all protein-coding genes using OrthoFinder v2.3.4 (Emms and Kelly, 2015) with default parameters.…”