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Automated improvement of stickleback reference genome assemblies with Lep-Anchor software
- Source :
- Molecular ecology resourcesREFERENCES. 21(6)
- Publication Year :
- 2021
-
Abstract
- SummaryWe 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 1.7 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.
- Subjects :
- 0106 biological sciences
0301 basic medicine
SELECTION
haplotype
Computer science
Contiguity
Sequence assembly
Computational biology
010603 evolutionary biology
01 natural sciences
SEQUENCE
Genome
03 medical and health sciences
Pungitius
0302 clinical medicine
Gasterosteus
Genetic variation
Genetics
DIVERGENCE
QUALITY
Animals
Ecology, Evolution, Behavior and Systematics
X chromosome
030304 developmental biology
Linkage (software)
ARCHITECTURE
0303 health sciences
CONSTRUCTION
Contig
biology
stickleback
Stickleback
Chromosome Mapping
FRAMEWORK
biology.organism_classification
EVOLUTION
Smegmamorpha
TIME
030104 developmental biology
mosaicism
genome assembly
MAP
1182 Biochemistry, cell and molecular biology
030217 neurology & neurosurgery
Software
Biotechnology
Reference genome
Subjects
Details
- ISSN :
- 17550998
- Volume :
- 21
- Issue :
- 6
- Database :
- OpenAIRE
- Journal :
- Molecular ecology resourcesREFERENCES
- Accession number :
- edsair.doi.dedup.....305ca2304deaa60eadba6fc5a409689c