Hi‐C scaffolded short‐ and long‐read genome assemblies of the California sea lion are broadly consistent for syntenic inference across 45 million years of evolution

• DOI: 10.1111/1755-0998.13443
• Publication Date: 2021-06-08T20:52:37Z
• Authors: Claire R. Peart; Christina Williams; Saurabh D. Pophaly; Benjamin A. Neely; Frances M. D. Gul...; David J. Adams; Bee Ling Ng; William Cheng; Michael E. Goebel; Olivier Fedrigo; Bettina Haase; Jacquelyn Mountca...; Arkarachai Fungta...; Giulio Formenti; Joanna Collins; Jonathan Wood; Ying Sims; James Torrance; Alan Tracey; Kerstin Howe; Arang Rhie; Joseph I. Hoffman; Jeremy Johnson; Erich D. Jarvis; Matthew Breen; Jochen B. W. Wolf
• Keywords: Synteny

With the advent of chromatin-interaction maps, chromosome-level genome assemblies have become a reality for wide range organisms. Scaffolding quality is, however, difficult to judge. To explore this gap, we generated multiple chromosome-scale an emerging wild animal model carcinogenesis, California sea lion (Zalophus californianus). Short-read were scaffolded with two independent chromatin interaction mapping data sets (Hi-C and Chicago), long-read three types (Hi-C, optical maps 10X linked reads) following "Vertebrate Genomes Project (VGP)" pipeline. In both approaches, 18 major scaffolds recovered karyotype (2n = 36), scaffold N50s 138 147 Mb, respectively. Synteny relationships at chromosome level other pinniped genomes 32-36), ferret 34), red panda 36) domestic dog 78) consistent across approaches known fissions fusions. Comparative painting multicolour tiling panel 264 genome-integrated single-locus canine bacterial artificial probes provided evaluation organization. Broad-scale discrepancies between observed within chromosomes, most commonly in translocations centred around centromeres telomeres, which better resolved VGP assembly. Genomic cytological agreed on near-perfect synteny X chromosome, combination allowed detailed investigation autosomal rearrangements lion. This study presents high-quality cancer highlights that even highly fragmented short-read Hi-C can yield reliable suitable comparative genomic analyses.