ArticleGenome biology and evolution2015
Construction of Ultradense Linkage Maps with Lep-MAP2: Stickleback F2 Recombinant Crosses as an Example.
Article in Genome biology and evolution, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 73 papers.
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73 citing papers in PubMed, 132 citations in OpenAlex.
- The genomic architecture of local adaptation in two connected populations of three-spined stickleback.G3 (Bethesda, Md.) · 2026Article
- Integrative linkage mapping and transcriptomic profiling uncover ozone-response modules in a peri-urban forest tree.G3 (Bethesda, Md.) · 2026Article
- First High-Density Linkage Map and Quantitative Trait Loci for Disease Resistance in Striped CatfishInternational journal of molecular sciences · 2026Article
- The fourspine stickleback (Apeltes quadracus) has an XY sex chromosome system with polymorphic inversions on both X and Y chromosomes.PLoS genetics · 2025Article
- Fine-scale contemporary recombination variation and its fitness consequences in adaptively diverging stickleback fish.Nature ecology & evolution · 2024Article
- Predicting recombination frequency from map distance.Heredity · 2023Article
- Smooth Descent: A ploidy-aware algorithm to improve linkage mapping in the presence of genotyping errors.Frontiers in genetics · 2023Article
- Chromosome-level genome sequence of the Genetically Improved Farmed Tilapia (GIFT, Oreochromis niloticus) highlights regions of introgression with O. mossambicus.BMC genomics · 2022Article
- Identification of a candidate sex determination gene in Culaea inconstans suggests convergent recruitment of an Amh duplicate in two lineages of stickleback.Journal of evolutionary biology · 2022Article
- Chromosome-level reference genome for European flat oyster (Evolutionary applications · 2022Article
- Local Adaptation and the Evolution of Genome Architecture in Threespine Stickleback.Genome biology and evolution · 2022Article
- Age-dependent genetic architecture across ontogeny of body size in sticklebacks.Proceedings. Biological sciences · 2022Article
- The evolution of huge Y chromosomes inPhilosophical transactions of the Royal Society of London. Series B, Biological sciences · 2022Article
- Chromosomal Fusions Facilitate Adaptation to Divergent Environments in Threespine Stickleback.Molecular biology and evolution · 2022Article
- A masculinizing supergene underlies an exaggerated male reproductive morph in a spider.Nature ecology & evolution · 2022Article
- Fine dissection of limber pine resistance to Cronartium ribicola using targeted sequencing of the NLR family.BMC genomics · 2021Article
- Whole-genome sequencing reveals sex determination and liver high-fat storage mechanisms of yellowstripe goby (Mugilogobius chulae).Communications biology · 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
- Assembly of whole-chromosome pseudomolecules for polyploid plant genomes using outbred mapping populations.Nature genetics · 2020Article
- From molecules to populations: appreciating and estimating recombination rate variation.Nature reviews. Genetics · 2020Review
13 more citing papers are in PubMed but not listed here.
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Authors and funding
5 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
High-density linkage maps are important tools for genome biology and evolutionary genetics by quantifying the extent of recombination, linkage disequilibrium, and chromosomal rearrangements across chromosomes, sexes, and populations. They provide one of the best ways to validate and refine de novo genome assemblies, with the power to identify errors in assemblies increasing with marker density. However, assembly of high-density linkage maps is still challenging due to software limitations. We describe Lep-MAP2, a software for ultradense genome-wide linkage map construction. Lep-MAP2 can handle various family structures and can account for achiasmatic meiosis to gain linkage map accuracy. Simulations show that Lep-MAP2 outperforms other available mapping software both in computational efficiency and accuracy. When applied to two large F2-generation recombinant crosses between two nine-spined stickleback (Pungitius pungitius) populations, it produced two high-density (∼6 markers/cM) linkage maps containing 18,691 and 20,054 single nucleotide polymorphisms. The two maps showed a high degree of synteny, but female maps were 1.5-2 times longer than male maps in all linkage groups, suggesting genome-wide recombination suppression in males. Comparison with the genome sequence of the three-spined stickleback (Gasterosteus aculeatus) revealed a high degree of interspecific synteny with a low frequency (<5%) of interchromosomal rearrangements. However, a fairly large (ca. 10 Mb) translocation from autosome to sex chromosome was detected in both maps. These results illustrate the utility and novel features of Lep-MAP2 in assembling high-density linkage maps, and their usefulness in revealing evolutionarily interesting properties of genomes, such as strong genome-wide sex bias in recombination rates.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.