Abstract
The Andean bear is the only extant member of the Tremarctine subfamily and the only extant ursid species to inhabit South America. Here, we present an annotated de novo assembly of a nuclear genome from a captive-born female Andean bear, Mischief, generated using a combination of short and long DNA and RNA reads. Our final assembly has a length of 2.23 Gb, and a scaffold N50 of 21.12 Mb, contig N50 of 23.5 kb, and BUSCO score of 88%. The Andean bear genome will be a useful resource for exploring the complex phylogenetic history of extinct and extant bear species and for future population genetics studies of Andean bears.
Highlights
Bears of the family Ursidae are a geographically widespread lineage of large mammals that are important to cultures around the world, from providing sustenance to inspiring stories and mythologies
HiRise slightly improved the contig N50, from 20.1kb to 20.3kb. While this was an improvement in contiguity, the short read length of Illumina reads still resulted in a fragmented assembly at the contig level
The Andean bear genome assembly we present here is highly contiguous and complete, with low error
Summary
Bears of the family Ursidae are a geographically widespread lineage of large mammals that are important to cultures around the world, from providing sustenance to inspiring stories and mythologies. Ursinae is sister to the monophyletic subfamily Tremarctinae, which includes Tremarctos ornatus, the Andean bear or spectacled bear. Outgroup to these subfamilies is the monophyletic Aliuropodinae, which includes the giant panda Ailuropoda melanoleuca. Species within Ursidae represent an enormous range of physiologies, dietary and behavioral strategies, and ecological adaptations. Comparative analyses of their genomes promise to improve our understanding of the genomic underpinnings of these traits. A high-quality de novo assembly of an Andean bear genome enables the application of a range of new molecular approaches in the study of this species and of other bears. Our final genome has a length of 2.23 Gb across 12 402 scaffolds, with a scaffold N50 of 21.12 Mb, BUSCO score of 88%, and QV score of 34.36, making it of similar to or better quality than other Ursidae genome assemblies in terms of completeness and contiguity (Miller et al 2012; Taylor et al 2018; Fan et al 2019; Srivastava et al 2019), and provides an important resource for future research
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