Abstract

Vertebrates exhibit substantial diversity in genome size, and some of the largest genomes exist in species that uniquely inform diverse areas of basic and biomedical research. For example, the salamander Ambystoma mexicanum (the Mexican axolotl) is a model organism for studies of regeneration, development and genome evolution, yet its genome is ~10× larger than the human genome. As part of a hierarchical approach toward improving genome resources for the species, we generated 600 Gb of shotgun sequence data and developed methods for sequencing individual laser-captured chromosomes. Based on these data, we estimate that the A. mexicanum genome is ~32 Gb. Notably, as much as 19 Gb of the A. mexicanum genome can potentially be considered single copy, which presumably reflects the evolutionary diversification of mobile elements that accumulated during an ancient episode of genome expansion. Chromosome-targeted sequencing permitted the development of assemblies within the constraints of modern computational platforms, allowed us to place 2062 genes on the two smallest A. mexicanum chromosomes and resolves key events in the history of vertebrate genome evolution. Our analyses show that the capture and sequencing of individual chromosomes is likely to provide valuable information for the systematic sequencing, assembly and scaffolding of large genomes.

Document Type

Article

Publication Date

11-10-2015

Notes/Citation Information

Published in Scientific Reports, v. 5, article 16413, p. 1-13.

This work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/

Digital Object Identifier (DOI)

http://dx.doi.org/10.1038/srep16413

Funding Information

This work was funded by grants from the National Institutes of Health (NIH) (R24OD010435 and EY10540) and Department of Defence (DOD) (W911NF1110475). The axolotl for this study was 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).

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Supplementary Information

srep16413-s2.xlsx (247 kB)
Supplementary Table 1

srep16413-s3.xlsx (47 kB)
Supplementary Table 2

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