Automated improvement of stickleback reference genome assemblies with Lep-Anchor software

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http://hdl.handle.net/10138/333019

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Kivikoski , M , Rastas , P , Löytynoja , A & Merila , J 2021 , ' Automated improvement of stickleback reference genome assemblies with Lep-Anchor software ' , Molecular Ecology Resources , vol. 21 , no. 6 , pp. 2166-2176 . https://doi.org/10.1111/1755-0998.13404

Title: Automated improvement of stickleback reference genome assemblies with Lep-Anchor software
Author: Kivikoski, Mikko; Rastas, Pasi; Löytynoja, Ari; Merila, Juha
Contributor: University of Helsinki, Ecological Genetics Research Unit
University of Helsinki, Institute of Biotechnology
University of Helsinki, Institute of Biotechnology
University of Helsinki, Organismal and Evolutionary Biology Research Programme
Date: 2021-08
Language: eng
Number of pages: 11
Belongs to series: Molecular Ecology Resources
ISSN: 1755-098X
URI: http://hdl.handle.net/10138/333019
Abstract: We describe an integrative approach to improve contiguity and haploidy of a reference genome assembly and demonstrate its impact with practical examples. With two novel features of Lep-Anchor software and a combination of dense linkage maps, overlap detection and bridging long reads, we generated an improved assembly of the nine-spined stickleback (Pungitius pungitius) reference genome. We were able to remove a significant number of haplotypic contigs, detect more genetic variation and improve the contiguity of the genome, especially that of X chromosome. However, improved scaffolding cannot correct for mosaicism of erroneously assembled contigs, demonstrated by a de novo assembly of a 1.6-Mbp inversion. Qualitatively similar gains were obtained with the genome of three-spined stickleback (Gasterosteus aculeatus). Since the utility of genome-wide sequencing data in biological research depends heavily on the quality of the reference genome, the improved and fully automated approach described here should be helpful in refining reference genome assemblies.
Subject: 1182 Biochemistry, cell and molecular biology
Gasterosteus
genome assembly
haplotype
mosaicism
Pungitius
stickleback
ARCHITECTURE
SEQUENCE
CONSTRUCTION
DIVERGENCE
EVOLUTION
FRAMEWORK
SELECTION
QUALITY
TIME
MAP
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