ArticleScientific reports2015
Initial characterization of the large genome of the salamander Ambystoma mexicanum using shotgun and laser capture chromosome sequencing.
Article in Scientific reports, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 45 papers.
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Who cites it
45 citing papers in PubMed, 107 citations in OpenAlex.
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- Comparative analysis of amphibian genomes: An emerging resource for basic and applied research.Molecular ecology resources · 2025Article
- Key Proteins for Regeneration inScientifica · 2024Article
- Limb blastema formation: How much do we know at a genetic and epigenetic level?The Journal of biological chemistry · 2023Review
- Somatic CNV Detection by Single-Cell Whole-Genome Sequencing in Postmortem Human Brain.Methods in molecular biology (Clifton, N.J.) · 2023Article
- The salamander blastema within the broader context of metazoan regeneration.Frontiers in cell and developmental biology · 2023Review
- Metamorphosis Imposes Variable Constraints on Genome Expansion through Effects on Development.Integrative organismal biology (Oxford, England) · 2023Article
- Transposable element and host silencing activity in gigantic genomes.Frontiers in cell and developmental biology · 2023Article
- Transposable Element Diversity Remains High in Gigantic Genomes.Journal of molecular evolution · 2022Article
- The Axolotl's journey to the modern molecular era.Current topics in developmental biology · 2022Article
- Article
- Large-scale variation in single nucleotide polymorphism density within the laboratory axolotl (Ambystoma mexicanum).Developmental dynamics : an official publication of the American Association of Anatomists · 2021Article
- Gigantic Genomes Provide Empirical Tests of Transposable Element Dynamics Models.Genomics, proteomics & bioinformatics · 2021Article
- Bridging the Gap between Vertebrate Cytogenetics and Genomics with Single-Chromosome Sequencing (ChromSeq).Genes · 2021Review
- Salamanders: The molecular basis of tissue regeneration and its relevance to human disease.Current topics in developmental biology · 2021Review
- EXFI: Exon and splice graph prediction without a reference genome.Ecology and evolution · 2020Article
- Germline-Specific Repetitive Elements in Programmatically Eliminated Chromosomes of the Sea Lamprey (Genes · 2019Article
- Genomic Data Reveal Conserved Female Heterogamety in Giant Salamanders with Gigantic Nuclear Genomes.G3 (Bethesda, Md.) · 2019Article
- FGF, BMP, and RA signaling are sufficient for the induction of complete limb regeneration from non-regenerating wounds on Ambystoma mexicanum limbs.Developmental biology · 2019Article
- HDAC Regulates Transcription at the Outset of Axolotl Tail Regeneration.Scientific reports · 2019Article
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Authors and funding
6 authors at 2 institutions in 1 country.
Funding
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.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.