Dissecting functional elements in giant genomes using the first generation of high quality salamander assemblies

A high-quality single-haplotype assembly of the 32 Gb Ambystoma mexicanum genome enabled identification of >523,000 highly conserved non-coding elements, mostly lineage-unique.

• Why it matters: Giant salamander genomes have expanded introns and intergenic DNA, making it hard to pinpoint functional regulatory sequences tied to traits like regeneration.
• What they did: The team built an F1 hybrid-based assembly and used multi-genome alignments to salamanders meeting VGP metrics, then validated conserved elements with chromatin-state and enhancer-activity measures.
• The result: Orthogonal assays linked many conserved elements to cis-regulatory sequences and found several thousand used during regeneration, enabling functional genomic studies in salamander models.

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