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)

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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:Recknagel, Mr Hans and Elmer, Professor Kathryn and Yurchenko, Dr Andrey
Authors: Yurchenko, A. A., Recknagel, H., and Elmer, K.
College/School:College of Medical Veterinary and Life Sciences > Institute of Biodiversity Animal Health and Comparative 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

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Project CodeAward NoProject NamePrincipal InvestigatorFunder's NameFunder RefLead Dept
172352From egg-laying to live-bearing: Unravelling the genetics of a major evolutionary transitionKathryn ElmerNatural Environment Research Council (NERC)NE/N003942/1Institute of Biodiversity, Animal Health and Comparative Medicine