Chromosome-level assembly of the common lizard (Zootoca vivipara) genome

Yurchenko, A. A., Recknagel, H. and Elmer, K. (2020) Chromosome-level assembly of the common lizard (Zootoca vivipara) genome. Genome Biology and Evolution, 12(11), pp. 1953-1960. (doi: 10.1093/gbe/evaa161) (PMID:32835354) (PMCID:PMC7643610)

Abstract

Squamate reptiles exhibit high variation in their phenotypic traits and geographical distribution and are therefore fascinating taxa for evolutionary and ecological research. However, genomic resources are very limited for this group of species, consequently inhibiting research efforts. To address this gap, we assembled a high-quality genome of the common lizard, Zootoca vivipara (Lacertidae), using a combination of high coverage Illumina (shotgun and mate-pair) and PacBio sequencing data, coupled with RNAseq data and genetic linkage map generation. The 1.46 Gbp genome assembly has a scaffold N50 of 11.52 Mbp with N50 contig size of 220.4 Kbp and only 2.96% gaps. A BUSCO analysis indicates that 97.7% of the single-copy Tetrapoda orthologs were recovered in the assembly. In total 19,829 gene models were annotated to the genome using a combination of ab initio and homology-based methods. To improve the chromosome-level assembly, we generated a high-density linkage map from wild-caught families and developed a novel analytical pipeline to accommodate multiple paternity and unknown father genotypes. We successfully anchored and oriented almost 90% of the genome on 19 linkage groups. This annotated and oriented chromosome-level reference genome represents a valuable resource to facilitate evolutionary studies in squamate reptiles.

• Item Type: Articles
• Additional Information: This research was supported by the Natural Environment Research Council [NE/N003942/1, NBAF964, NBAF1018].
• Status: Published
• Refereed: Yes
• Glasgow Author(s) Enlighten ID: Elmer, Professor Kathryn and Recknagel, Mr Hans and Yurchenko, Dr Andrey
• Authors: Yurchenko, A. A., Recknagel, H., and Elmer, K.
• College/School: College of Medical Veterinary and Life Sciences > School of Biodiversity, One Health & Veterinary Medicine
• Journal Name: Genome Biology and Evolution
• Publisher: Oxford University Press
• ISSN: 1759-6653
• ISSN (Online): 1759-6653
• Published Online: 24 August 2020
• Copyright Holders: Copyright © 2020 The Authors
• First Published: First published in Genome Biology and Evolution 12(11): 1953-1960
• Publisher Policy: Reproduced under a Creative Commons License

Project Code	Award No	Project Name	Principal Investigator	Funder's Name	Funder Ref	Lead Dept
172352		From egg-laying to live-bearing: Unravelling the genetics of a major evolutionary transition	Kathryn Elmer	Natural Environment Research Council (NERC)	NE/N003942/1	Institute of Biodiversity, Animal Health and Comparative Medicine