Journal Article

The axolotl genome and the evolution of key tissue formation regulators

Cao, Han, Roscito, Juliana G., Fei, Ji-Feng, Winkler, Sylke, Hastie, Alex R., Habermann, Bianca, Hiller, Michael, Schloissnig, Siegfried, Dahl, Andreas, Powell, Sean, Myers, Eugene W., Nowoshilow, Sergej, Cruz, Alfredo, Pippel, Martin, Knapp, Dunja, Tanaka, Elly M., Falcon, Francisco, Young, George, Pang, Andy W. C.

2018

Overview

Salamanders serve as important tetrapod models for developmental, regeneration and evolutionary studies. An extensive molecular toolkit makes the Mexican axolotl ( Ambystoma mexicanum ) a key representative salamander for molecular investigations. Here we report the sequencing and assembly of the 32-gigabase-pair axolotl genome using an approach that combined long-read sequencing, optical mapping and development of a new genome assembler (MARVEL). We observed a size expansion of introns and intergenic regions, largely attributable to multiplication of long terminal repeat retroelements. We provide evidence that intron size in developmental genes is under constraint and that species-restricted genes may contribute to limb regeneration. The axolotl genome assembly does not contain the essential developmental gene Pax3 . However, mutation of the axolotl Pax3 paralogue Pax7 resulted in an axolotl phenotype that was similar to those seen in Pax3 −/− and Pax7 −/− mutant mice. The axolotl genome provides a rich biological resource for developmental and evolutionary studies. Sequencing and assembly of the 32-Gb genome of the Mexican axolotl reveals that it lacks the developmental gene Pax3 , which is essential in other vertebrates; the genome sequence could improve our understanding of the evolution of the axolotl’s remarkable regenerative capabilities. Axolotl genome sequence Elly Tanaka, Eugene Myers and colleagues report the genome sequence of the axolotl, a model organism for developmental, regeneration and evolutionary studies. To sequence and assemble this large and complex genome, the authors used a combination of long- and short-read sequencing, optical mapping and a new genome assembly pipeline, MARVEL, optimized for long-read sequencing of complex genomes. The genome assembly shows an expansion of long terminal repeat retroelements and the presence of a large HoxA cluster, but also a reduction in the number of Pax-family genes in the genome of this popular salamander.

• Publisher: Nature Publishing Group UK,Nature Publishing Group
• Subject: 13/100 / 13/106 / 13/109 / 13/31 / 14/1 / 14/19 / 38/23 / 38/77 / 38/89 / 631/136/532/489 / 631/1647/2217/748 / 631/181/2806 / 64/114 / 64/116 / Ambystoma mexicanum / Ambystoma mexicanum - genetics / Amphibians / Animal models / Animals / Biochemistry, Molecular Biology / Bioinformatics / Biological evolution / Caudata / Computer Science / Data Structures and Algorithms / DNA, Intergenic - genetics / Evolution / Evolution, Molecular / Extracellular matrix / Gene expression / Gene mapping / Gene sequencing / Genes / Genes, Essential - genetics / Genetic aspects / Genome - genetics / Genome-wide association studies / Genomes / Genomics / Homeodomain Proteins - genetics / Humanities and Social Sciences / Introns / Introns - genetics / Life Sciences / Long terminal repeat / Male / Methods / Mexican axolotl / Mice / multidisciplinary / Mutation / Observations / Pax3 protein / PAX3 Transcription Factor - genetics / PAX7 Transcription Factor - genetics / Phenotypes / Picea - genetics / Pinus - genetics / Proteins / Regeneration / Regeneration (Biology) / Regeneration - genetics / Reptiles & amphibians / Retroelements - genetics / Science / Terminal Repeat Sequences - genetics