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, driven primarily by expansion of repeat elements and slow rates of DNA loss. However, species in the lungless genus Desmognathus (Plethodontidae) have some of the smallest genomes at ∼13 to 15 GB, though previous sequencing attempts with short-read assemblies were still fragmentary. Here, we assemble an annotated draft genome of Desmognathus fuscus using PacBio HiFi reads and transcriptomic data from 2 specimens from the same population. The combined dataset resulted in a 16.1 GB assembly in 19,632 contigs and an L/N50 of 2,459/1.74 MB, with the longest contig at 27.9 MB. This may still be slightly larger than the true size due to incomplete resolution of repeat regions. The assembly is highly complete with 93% of the 5,310 Tetrapoda BUSCO orthologs. Only 25% of the genome is single copy with 75% corresponding to transposable elements, mostly LTRs (36% of the genome) and LINEs (15%). We estimate an early expansion and slow contraction of LINEs followed by a quick recent expansion of both LTRs and DNA transposons. We identified 12,408 protein-coding genes with a common name in 1 or more reference databases. Finally, we used mother-offspring RNAseq data from an unrelated D. fuscus clutch to create a high-density linkage map, yielding 14 primary linkage groups and 2 smaller scaffolds covering 7.5 Gb and incorporating 46.5% of the genome and 60% of the mRNAs. This chromosome-scale assembly represents a new benchmark for plethodontid salamander genomics.