The axolotl genome and the evolution of key tissue formation regulators

Abstract

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.

A Regeneration Toolkit

“…Salamanders possess a complex genome several times the size of the human genome (Elewa et al, 2017; Nowoshilow et al, 2018). The toolkit for salamander regeneration was once dominated by methods like gene electroporation, retroviral infection, and morpholino-based knockdown (Kawakami et al, 2006; Roy et al, 2000), but additional genetic manipulations like transgenesis (Khattak et al, 2009), targeted mutations, and gene cassette knock-in technology have become available in the past few years (Fei et al, 2017; Fei et al, 2014; Flowers et al, 2017; Flowers et al, 2014).…”

“…The toolkit for salamander regeneration was once dominated by methods like gene electroporation, retroviral infection, and morpholino-based knockdown (Kawakami et al, 2006; Roy et al, 2000), but additional genetic manipulations like transgenesis (Khattak et al, 2009), targeted mutations, and gene cassette knock-in technology have become available in the past few years (Fei et al, 2017; Fei et al, 2014; Flowers et al, 2017; Flowers et al, 2014). Guided by the recent reports of the Iberian ribbed newt ( Pleurodeles waltl) and Mexican axolotl ( Ambystoma mexicanum ) genomes, the availability of these tools will increase the use of salamanders to explore understudied questions in regenerative capacity and mechanisms (Elewa et al, 2017; Nowoshilow et al, 2018). …”

TERAD: Extraction of transposable element composition from RADseq data

“…Apart from Angiosperms that have a ̴ 1000‐fold difference in genome size (Bennett & Leitch, ) (although not all of this variation is attributable to TEs), at least several animal lineages are known to vary considerably in genome size and also contain species with exceptionally large genomes. These include salamanders (14–120 Gb) (Nowoshilow et al, ), Orthoptera (1.52–16.56 Gb) and crustaceans (0.14–63.20 Gb) (Hultgren, Jeffery, Moran, & Gregory, ). However, the underlying mechanism of how these large genomes formed remains unclear because most of our knowledge about genome size change is based on lineages with small genomes (Dufresne & Jeffery, ).…”

Genome‐specific histories of divergence and introgression between an allopolyploid unisexual salamander lineage and two ancestral sexual species

“…; Nowoshilow et al. ), but the majority of these projects are in frogs that generally have smaller genomes than salamanders (Gregory ). Meanwhile, there have been successful efforts to obtain reduced representation libraries for salamanders with large genomes by either modifications of protocols to reduce off‐target reads (McCartney‐Melstad et al.…”