Initial characterization of the large genome of the salamander Ambystoma mexicanum using shotgun and laser capture chromosome sequencing.

Melissa C Keinath,Vladimir A Timoshevskiy,Nataliya Y Timoshevskaya,S Randal Voss,Jeramiah J Smith,Panagiotis A Tsonis

doi:10.1038/srep16413

Melissa C Keinath, Vladimir A Timoshevskiy + Show 4 more

Open Access

https://doi.org/10.1038/srep16413

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Journal: Scientific Reports	Publication Date: Nov 10, 2015
Citations: 96	License type: CC BY 4.0

Affiliation: University of Kentucky, University of Dayton

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.

Highlights

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
Large genome size and repetitive DNA content are often cited as challenges for genome assembly, and the impact of these factors is dependent on the genomic distribution of repetitive and single copy sequences
A total of 16 lanes of Illumina shotgun sequence data (2 × 100 bp) were generated for a single female A. mexicanum, obtained from the standard laboratory strain maintained by the Ambystoma Genetic Stock Center (Animal #13003.1), yielding > 0.6 Tb of raw sequence data

Summary

Introduction

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. 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 lasercaptured 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. Considerable progress has been made in recent years to enhance genomic and molecular resources for a species with a genome size that falls toward the upper end of the vertebrate range, the primary salamander model Ambystoma mexicanum (Mexican axolotl). No salamander genome has been sampled sufficiently to establish the overall size and sequence composition of repetitive (and single copy) regions, and the inherent complexity of the genome assembly problem

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