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

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.

The axolotl genome and the evolution of key tissue formation regulators

“…Our data, together with data from plants and partial data from several other salamander species, show that LTR expansion is a major contributor to giant genome size across animals and plants 6,12,35 . Our assembly is sufficiently complete to reliably detect the absence of Pax3, which is present in fish and other amphibians.…”

“…1a), which is commonly used in laboratory regene ration studies owing to its compatibility with live imaging. Taking into consideration the expected challenge of assembling the complex 32-Gb genome 6 , we sequenced 110 million long reads (32× coverage, N50 read length 14.2 kb) using Pacific Biosciences (PacBio) instruments (Supplementary Information section 1) to avoid the read sampling bias that is often found when using other technologies and to span repeat-rich genomic regions that cause breaks in short-read assemblies (Fig. 1b, c).…”

A linkage map for the Newt Notophthalmus viridescens: Insights in vertebrate genome and chromosome evolution

“…To identify and genotype polymorphisms segregating within this family, we mapped RNAseq reads to the published newt transcriptome using bwa-0.7.5a (Li and Durbin, 2009), performed de-duplication using picard-tools-1.97 (http://broadinstitute.github.io/picard) and genotype calling using the HaplotypeCaller pipeline in GATK-2.7 (Looso et al, 2013; McKenna et al, 2010). Genotypes were post-filtered to include only those markers with presumptive maternal or paternal polymorphisms segregating among the 28 embryos sequenced for this study, that had variant quality scores greater equal to or greater than 100 and that were represented by a minimum of 4 reads in all individuals.…”

A time- and cost-effective strategy to sequence mammalian Y Chromosomes: an application to the de novo assembly of gorilla Y

“…This approach might be challenging to apply for very young sex chromosomes that might have not diverged enough in size and GCcontent from each other. However, individual chromosomes can also be enriched by microdissection (Zhou and Hu 2007) or laser capture dissection (Keinath et al 2015), and the computational techniques developed here also have the potential to be utilized in such situations, thus increasing the applicability of the method. Therefore, our approach provides a timely opportunity to generate data needed for the studies on sex chromosome evolution and sexbias in dispersal across populations.…”