Supporting data for: The genome of the relict earless monitor lizard, <em>Lanthanotus borneensis</em>, and the Toxicofera hypothesis

The Earless Monitor Lizard, Lanthanotus borneensis, is a unique living fossil restricted to the island of Borneo and a possible key to understanding the evolution of the venom delivery system and secondary adaptation to water in reptiles and snakes (Squamata). We have sequenced and de novo assembled the genome of L. borneensis to a total size of 1.5 Gbp, 975 contigs with an N50 of 52 Mbp and an L50 of 9. The genome completeness is estimated to be 93% based on the Sauropsida OrthoDB core gene set. A genome-wide set of Lepidosauria orthologs was compiled to reconstruct and date their phylogeny, resulting in 966 protein-coding sequences amounting to a concatenated alignment of 356 kbp with 188 kbp parsimony-informative sites. Based on this phylogenomic analysis, one of the largest of its kind yet conducted for Squamata, we identified that a Toxicofera clade (comprising Serpentes, Anguimorpha, and Iguania) is supported by a plurality of gene trees, but critically, support for relationships ..., Genome construction A de novo assembly was constructed using the PacBio CLR long reads and Illumina paired-end short reads. Initial assembly was conducted with Miniasm v0.3_r179 (Li, 2016), following read overlap detection using Minimap2 v2.14 (Li, 2018) with the “map-pb” preset. The resulting assembly was polished with two rounds of Racon v1.3.1 (Vaser et al., 2017), each preceded by realignment of the PacBio reads to the intermediate assembly with Minimap2. Subsequently, two rounds of polishing were performed with Pilon v1.23 (Walker et al., 2014), using the Illumina paired-end reads. Reads were aligned to the intermediate assembly using BWA-MEM v0.7.17 (Li, 2013), and alignments were sorted and indexed using Samtools v1.9 (Li et al., 2009). Pilon v1.23 (Walker et al., 2014) was run with default parameters using the “--frags” option. To annotate repetitive elements, the assembly was first soft-masked using RepeatMasker v4.1.5 (http://www.repeatmasker.org) with the built-in Anopheles r..., # Supporting data for: The genome of the relict earless monitor lizard, *Lanthanotus borneensis*, and the Toxicofera hypothesis Dataset DOI: [10.5061/dryad.stqjq2cg9](10.5061/dryad.stqjq2cg9) ## Description of the data and file structure `Summary:` This dataset contains a de novo genome assembly as well as a detailed annotation of the Earless Monitor Lizard (*Lanthanotus borneensis*). The genome was assembled using PacBio CLR reads using the software Miniasm. The annotation was done on a genome with soft-masks for repetitive regions using the MAKER pipeline Furthermore, this dataset includes a collection of high-quality orthologous sequences collected between Lepidosauria genomes using the GEMOMA-to-Phylogeny pipeline and publicly available homology data. These orthologs are provided as amino acid fasta sequences as well as a collection of gene trees constructed using IQTree and a maximum likelihood (ML) approach with 1000 bootstrap replications. Final species trees were construct..., ,