Supporting data for "The genome of the tegu lizard Salvator merianae: combining Illumina, PacBio, and optical mapping data to generate a highly contiguous assembly"

Reptiles are a species-rich group with a great phenotypic and life history diversity, but are highly underrepresented among the vertebrate species with sequenced genomes. Here, we report the genome assembly of the tegu lizard Salvator merianae, the first lacertid with a sequenced genome. We combined Illumina short read, PacBio long read and optical mapping data to generate a high-quality assembly with a scaffold N50 value of 55.4 Mb. The contig N50 value of this assembly is 521 Kb, making it the most contiguous reptile assembly so far. We show that the tegu assembly has the highest completeness of coding genes and conserved non-exonic elements (CNEs) compared to other reptiles. Furthermore, the tegu assembly has the highest number of evolutionarily conserved CNE pairs, corroborating a high assembly contiguity in intergenic regions. Like in other reptiles, Long Interspersed Nuclear Elements (LINEs) comprise the largest transposon class. We used transcriptomics data, homology- and de novo gene predictions to annotate 19,101 coding genes, of which 14,636 (77%) likely have human orthologs as inferred by CESAR-derived gene mappings. Finally, we generated a reptile-focused multiple genome alignment comprising 10 squamates and 7 other amniote species and identified conserved regions that are under evolutionary constraint. Conserved non-exonic elements cover 38 Mb (1.8%) of the tegu genome, with 3.3 Mb in these elements being reptile-specific. Some of these reptile-specific CNEs, totalling 20 Kb, originated from inserted transposons; however, overall this evolutionary mechanism is rare. The tegu lizard genome together with the multiple genome alignment and comprehensive conserved element datasets provides a valuable resource for comparative genomic studies of reptiles and other amniotes.