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Genome Res. 2019 Feb;29(2):317-324. doi: 10.1101/gr.241901.118. Epub 2019 Jan 24.

A chromosome-scale assembly of the axolotl genome.

Author information

1
Department of Biology, University of Kentucky, Lexington, Kentucky 40506, USA.
2
Department of Embryology, Carnegie Institution for Science, Baltimore, Maryland 21218, USA.
3
Department of Neuroscience, University of Kentucky, Lexington, Kentucky 40506, USA.
4
Ambystoma Genetic Stock Center, University of Kentucky, Lexington, Kentucky 40506, USA.
5
Spinal Cord and Brain Injury Research Center, University of Kentucky, Lexington, Kentucky 40506, USA.

Abstract

The axolotl (Ambystoma mexicanum) provides critical models for studying regeneration, evolution, and development. However, its large genome (∼32 Gb) presents a formidable barrier to genetic analyses. Recent efforts have yielded genome assemblies consisting of thousands of unordered scaffolds that resolve gene structures, but do not yet permit large-scale analyses of genome structure and function. We adapted an established mapping approach to leverage dense SNP typing information and for the first time assemble the axolotl genome into 14 chromosomes. Moreover, we used fluorescence in situ hybridization to verify the structure of these 14 scaffolds and assign each to its corresponding physical chromosome. This new assembly covers 27.3 Gb and encompasses 94% of annotated gene models on chromosomal scaffolds. We show the assembly's utility by resolving genome-wide orthologies between the axolotl and other vertebrates, identifying the footprints of historical introgression events that occurred during the development of axolotl genetic stocks, and precisely mapping several phenotypes including a large deletion underlying the cardiac mutant. This chromosome-scale assembly will greatly facilitate studies of the axolotl in biological research.

PMID:
30679309
PMCID:
PMC6360810
DOI:
10.1101/gr.241901.118
[Indexed for MEDLINE]
Free PMC Article

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