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.

Document Type


Publication Date


Notes/Citation Information

Published in Genome Research, v. 29, no. 2, p. 317-324.

© 2019 Smith et al.

This article is distributed exclusively by Cold Spring Harbor Laboratory Press for the first six months after the full-issue publication date (see http://genome.cshlp.org/site/misc/terms.xhtml). After six months, it is available under a Creative Commons License (Attribution-NonCommercial 4.0 International), as described at http://creativecommons.org/licenses/by-nc/4.0/.

Digital Object Identifier (DOI)


Funding Information

This work was funded by grants from the National Institutes of Health (NIH) (R24OD010435) and Department of Defense (DOD) (W911NF1110475) to S.R.V. Animals used in this study were provided by the Ambystoma Genetic Stock Center, which is currently funded by the NIH (P40OD019794) and previously by the National Science Foundation (NSF) (DBI-0951484) to S.R.V.

Related Content

Supplemental material is available as the additional files listed at the end of this record.

Sequence data for this study have been submitted to the NCBI BioProject (https://www.ncbi.nlm.nih.gov/bioproject) under accession numbers PRJNA477812 (hybrid cross) and PRJNA509654 (Ambystoma tigrinum). Polymorphism data have been submitted to the European Variation Archive (EVA, https://www.ebi.ac.uk/eva/) under accession number PRJEB30506. The Genome assembly is deposited to the GenBank assembly (https://www.ncbi.nlm.nih.gov/assembly) under accession number GCA_002915635.2 and as an assembly hub accessible through the UCSC Genome Browser (http://genome.ucsc.edu/cgi-bin/ hgGateway?genome=Amex_PQ.v4&hubUrl=http://salamander.uky. edu/hubExamples/hubAssembly/Amex_PQ.v4.HUB/hub.txt). The source code of the SparseGenotyping software can be found as Supplemental Code and is available on GitHub, https://github.com/timnat/SparseGenotyping.

Supplemental_Code.txt (9 kB)
Supplemental file 1

Supplemental_Figures.pdf (9490 kB)
Supplemental file 2

Supplemental_Table_1.xlsx (12 kB)
Supplemental file 3

Supplemental_Table_2.xlsx (950 kB)
Supplemental file 4

Supplemental_Table_3.xlsx (9 kB)
Supplemental file 5

Supplemental_Table_4.xlsx (420 kB)
Supplemental file 6

Supplemental_Table_5.xlsx (392 kB)
Supplemental file 7

Supplemental_Table_6.xlsx (489 kB)
Supplemental file 8

Supplemental_Table_7.xlsx (13 kB)
Supplemental file 9

Available for download on Thursday, August 01, 2019