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

Juliana G Roscito,Andreas Dahl,Kees-Jan Francoijs,Katrin Sameith,Michael Hiller,Georg Papoutsoglou,Gene Myers,Martin Pippel,Sylke Winkler

doi:10.1093/gigascience/giy141

Abstract

BackgroundReptiles are a species-rich group with great phenotypic and life history diversity but are highly underrepresented among the vertebrate species with sequenced genomes.ResultsHere, we report a high-quality genome assembly of the tegu lizard, Salvator merianae, the first lacertoid with a sequenced genome. We combined 74X Illumina short-read, 29.8X Pacific Biosciences 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. As in other reptiles, long interspersed nuclear elements comprise the most abundant transposon class. We used transcriptomic data, homology- and de novo gene predictions to annotate 22,413 coding genes, of which 16,995 (76%) likely have human orthologs as inferred by CESAR-derived gene mappings. Finally, we generated a multiple genome alignment comprising 10 squamates and 7 other amniote species and identified conserved regions that are under evolutionary constraint. CNEs cover 38 Mb (1.8%) of the tegu genome, with 3.3 Mb in these elements being squamate specific. In contrast to placental mammal-specific CNEs, very few of these squamate-specific CNEs (<20 Kb) overlap transposons, highlighting a difference in how lineage-specific CNEs originated in these two clades.ConclusionsThe tegu lizard genome together with the multiple genome alignment and comprehensive conserved element datasets provide a valuable resource for comparative genomic studies of reptiles and other amniotes.

Highlights

Comparative whole-genome analyses are of great importance to understanding the evolutionary trajectory of different species
Since GMcloser extends scaffold ends with the Pacific Biosciences (PacBio) reads, which could provide new anchor points for Illumina mate-pair reads, we subsequently applied another round of scaffolding using our Illumina data and SSPACE [25]
We combined Illumina short-read with PacBio long-read sequencing and Bionano optical mapping technologies to obtain an assembly with fewer gaps

Summary

Introduction

Comparative whole-genome analyses are of great importance to understanding the evolutionary trajectory of different species. Squamate reptiles comprise a species-rich group of approximately 6,500 lizards, 3,700 snakes, and 200 amphisbaenian species [1] This group is heavily under-represented among the vertebrate species with sequenced genomes, especially considering the great morphological, behavioral, and life history diversity in this group. Squamates have been gaining attention for their relevance in understanding vertebrate evolution, as well as for reptile-specific features that are of human interest, such as venom with medical implications and adhesive features of gecko feet. This interest resulted in the sequencing and assembly of additional squamate genomes. Conclusions: The tegu lizard genome together with the multiple genome alignment and comprehensive conserved element datasets provide a valuable resource for comparative genomic studies of reptiles and other amniotes

Methods

Results

Conclusion