The giant axolotl genome uncovers the evolution, scaling, and transcriptional control of complex gene loci

Proc Natl Acad Sci U S A. 2021 Apr 13;118(15):e2017176118. doi: 10.1073/pnas.2017176118.

Abstract

Vertebrates harbor recognizably orthologous gene complements but vary 100-fold in genome size. How chromosomal organization scales with genome expansion is unclear, and how acute changes in gene regulation, as during axolotl limb regeneration, occur in the context of a vast genome has remained a riddle. Here, we describe the chromosome-scale assembly of the giant, 32 Gb axolotl genome. Hi-C contact data revealed the scaling properties of interphase and mitotic chromosome organization. Analysis of the assembly yielded understanding of the evolution of large, syntenic multigene clusters, including the Major Histocompatibility Complex (MHC) and the functional regulatory landscape of the Fibroblast Growth Factor 8 (Axfgf8) region. The axolotl serves as a primary model for studying successful regeneration.

Keywords: Topological Associating Domains; axolotl; genome assembly; regeneration.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Ambystoma mexicanum / genetics*
  • Animals
  • Chromosomes / genetics
  • Evolution, Molecular*
  • Genetic Loci
  • Genome*
  • Transcriptome