The first complete assembly for a lungless urodelan with a "miniaturized" genome, the Northern Dusky Salamander (Plethodontidae: Desmognathus fuscus)

Salamanders have some of the largest genomes among animals. However, there is a great disparity in total size, ranging from ~8-120GB depending on the lineage. Species in the lungless genus Desmognathus (Plethodontidae) are among the smallest, with estimated genome sizes of 13-15GB. Salamander genomes have exceptional interest in numerous topics ranging from genome-size evolution, the genetic basis of evolutionary differences in life history, and the physiological basis of regeneration, vision, and immunity. However, their large genomes have limited previous attempts at sequencing and assembly, particularly given the difficulties of mapping extensive repeat regions with short-read data. Here we assemble a draft genome of Desmognathus fuscus using PacBio HiFi reads and generate transcriptomic data from two specimens. The combined assembly resulted in a 16.1GB genome in 19,640 contigs and an N/L50 of 2,455/1.75MB, with the longest contig at 27.9MB. The assembly and transcriptome are nearly complete with 93% of the 5,310 BUSCO tetrapod orthologs identified. Attempts to scaffold these data to the existing Ambystoma genome resulted in only 5.8GB of the D. fuscus genome mapping to this reference. This low success suggests substantial syntenic and sequence divergence across salamanders, which may be the result of significant miniaturization in the Desmognathus genome. Identification and annotation of transposable elements reveals that only 26% of the genome is single copy with 74% corresponding to TEs. The most common class of TE in the genome are LTRs (35% of the total genome) and LINEs (~15% of the genome). The relative divergence landscape of these TEs shows an early expansion and slow contraction of LINEs, followed by a quick recent expansion of both LTRs and DNA transposons. This assembly will serve as an important reference for amphibian genomics.