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.
California sea lion (Zalophus californianus)
Carnivora
Hi-C
cancer
chromatin interaction mapping
genome assembly
genome evolution
Journal
Molecular ecology resources
ISSN: 1755-0998
Titre abrégé: Mol Ecol Resour
Pays: England
ID NLM: 101465604
Informations de publication
Date de publication:
Oct 2021
Oct 2021
Historique:
revised:
06
05
2021
received:
03
02
2021
accepted:
26
05
2021
pubmed:
8
6
2021
medline:
18
9
2021
entrez:
7
6
2021
Statut:
ppublish
Résumé
With the advent of chromatin-interaction maps, chromosome-level genome assemblies have become a reality for a wide range of organisms. Scaffolding quality is, however, difficult to judge. To explore this gap, we generated multiple chromosome-scale genome assemblies of an emerging wild animal model for carcinogenesis, the California sea lion (Zalophus californianus). Short-read assemblies were scaffolded with two independent chromatin interaction mapping data sets (Hi-C and Chicago), and long-read assemblies with three data types (Hi-C, optical maps and 10X linked reads) following the "Vertebrate Genomes Project (VGP)" pipeline. In both approaches, 18 major scaffolds recovered the karyotype (2n = 36), with scaffold N50s of 138 and 147 Mb, respectively. Synteny relationships at the chromosome level with other pinniped genomes (2n = 32-36), ferret (2n = 34), red panda (2n = 36) and domestic dog (2n = 78) were consistent across approaches and recovered known fissions and fusions. Comparative chromosome painting and multicolour chromosome tiling with a panel of 264 genome-integrated single-locus canine bacterial artificial chromosome probes provided independent evaluation of genome organization. Broad-scale discrepancies between the approaches were observed within chromosomes, most commonly in translocations centred around centromeres and telomeres, which were better resolved in the VGP assembly. Genomic and cytological approaches agreed on near-perfect synteny of the X chromosome, and in combination allowed detailed investigation of autosomal rearrangements between dog and sea lion. This study presents high-quality genomes of an emerging cancer model and highlights that even highly fragmented short-read assemblies scaffolded with Hi-C can yield reliable chromosome-level scaffolds suitable for comparative genomic analyses.
Identifiants
pubmed: 34097816
doi: 10.1111/1755-0998.13443
pmc: PMC9732816
mid: NIHMS1849478
doi:
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
2455-2470Subventions
Organisme : LUDWIG-MAXIMILIANS-UNIVERSITAET MUNCHEN
Organisme : Deutsche Forschungsgemeinschaft
ID : 424119118
Organisme : Intramural NIST DOC
ID : 9999-NIST
Pays : United States
Organisme : Morris Animal Foundation
ID : D10ZO-003
Organisme : Deutsche Forschungsgemeinschaft
ID : HO 5122/4-1
Organisme : NCSU Cancer Genomics Funds
Informations de copyright
© 2021 The Authors. Molecular Ecology Resources published by John Wiley & Sons Ltd.
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