ArticleBMC genetics2016
A high-density genetic map reveals variation in recombination rate across the genome of Daphnia magna.
Article in BMC genetics, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed, 55 citations in OpenAlex.
- Article
- Article
- The hologenome of Daphnia magna reveals possible DNA methylation and microbiome-mediated evolution of the host genome.Nucleic acids research · 2023Article
- Review
- Population-Genomic Analysis Identifies a Low Rate of Global Adaptive Fixation in the Proteins of the Cyclical Parthenogen Daphnia magna.Molecular biology and evolution · 2022Article
- Assemblies of the genomes of parasitic wasps using meta-assembly and scaffolding with genetic linkage.G3 (Bethesda, Md.) · 2022Article
- Balancing Selection for Pathogen Resistance Reveals an Intercontinental Signature of Red Queen Coevolution.Molecular biology and evolution · 2021Article
- No evidence for genetic sex determination inRoyal Society open science · 2021Article
- Anchoring a genetic map of an interspecific backcross two family to the genome builds of Elaeis.Journal of genetics · 2021Article
- High-Density Linkage Maps Based on Genotyping-by-Sequencing (GBS) Confirm a Chromosome-Level Genome Assembly and Reveal Variation in Recombination Rate for the Pacific OysterG3 (Bethesda, Md.) · 2020Article
- Identification of Mitochondrial DNA (NUMTs) in the Nuclear Genome ofInternational journal of molecular sciences · 2020Article
- Chromonomer: A Tool Set for Repairing and Enhancing Assembled Genomes Through Integration of Genetic Maps and Conserved Synteny.G3 (Bethesda, Md.) · 2020Article
- Microsporidia with Vertical Transmission Were Likely Shaped by Nonadaptive Processes.Genome biology and evolution · 2020Article
- Construction of High-Resolution RAD-Seq Based Linkage Map, Anchoring Reference Genome, and QTL Mapping of the Sex Chromosome in the Marine MedakaG3 (Bethesda, Md.) · 2019Article
- Discovery of genomic regions and candidate genes controlling shelling percentage using QTL-seq approach in cultivated peanut (Arachis hypogaea L.).Plant biotechnology journal · 2019Article
- How clonal are clones? A quest for loss of heterozygosity during asexual reproduction in Daphnia magna.Journal of evolutionary biology · 2019Article
- A genetic linkage map for the salmon louse (Lepeophtheirus salmonis): evidence for high male:female and inter-familial recombination rate differences.Molecular genetics and genomics : MGG · 2019Article
- Analysis of Genome-Wide Differentiation between Native and Introduced Populations of the Cupped Oysters Crassostrea gigas and Crassostrea angulata.Genome biology and evolution · 2018Article
- Identification of General Patterns of Sex-Biased Expression inG3 (Bethesda, Md.) · 2018Article
- Keeping Pace with the Red Queen: Identifying the Genetic Basis of Susceptibility to Infectious Disease.Genetics · 2018Article
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Authors and funding
5 authors at 3 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundRecombination rate is an essential parameter for many genetic analyses. Recombination rates are highly variable across species, populations, individuals and different genomic regions. Due to the profound influence that recombination can have on intraspecific diversity and interspecific divergence, characterization of recombination rate variation emerges as a key resource for population genomic studies and emphasises the importance of high-density genetic maps as tools for studying genome biology. Here we present such a high-density genetic map for Daphnia magna, and analyse patterns of recombination rate across the genome.
resultsA F2 intercross panel was genotyped by Restriction-site Associated DNA sequencing to construct the third-generation linkage map of D. magna. The resulting high-density map included 4037 markers covering 813 scaffolds and contigs that sum up to 77 % of the currently available genome draft sequence (v2.4) and 55 % of the estimated genome size (238 Mb). Total genetic length of the map presented here is 1614.5 cM and the genome-wide recombination rate is estimated to 6.78 cM/Mb. Merging genetic and physical information we consistently found that recombination rate estimates are high towards the peripheral parts of the chromosomes, while chromosome centres, harbouring centromeres in D. magna, show very low recombination rate estimates.
conclusionsDue to its high-density, the third-generation linkage map for D. magna can be coupled with the draft genome assembly, providing an essential tool for genome investigation in this model organism. Thus, our linkage map can be used for the on-going improvements of the genome assembly, but more importantly, it has enabled us to characterize variation in recombination rate across the genome of D. magna for the first time. These new insights can provide a valuable assistance in future studies of the genome evolution, mapping of quantitative traits and population genetic studies.
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