title: A Male-Specific Genetic Map of the Microcrustacean Daphnia pulex Based on Single-Sperm Whole-Genome Sequencing.
abstract: Genetic linkage maps are critical for assembling draft genomes to a meaningful chromosome level and for deciphering the genomic underpinnings of biological traits. The estimates of recombination rates derived from genetic maps also play an important role in understanding multiple aspects of genomic evolution such as nucleotide substitution patterns and accumulation of deleterious mutations. In this study, we developed a high-throughput experimental approach that combines fluorescence-activated cell sorting, whole-genome amplification, and short-read sequencing to construct a genetic map using single-sperm cells. Furthermore, a computational algorithm was developed to analyze single-sperm whole-genome sequencing data for map construction. These methods allowed us to rapidly build a male-specific genetic map for the freshwater microcrustacean Daphnia pulex, which shows significant improvements compared to a previous map. With a total of mapped 1672 haplotype blocks and an average intermarker distance of 0.87 cM, this map spans a total genetic distance of 1451 Kosambi cM and comprises 90% of the resolved regions in the current Daphnia reference assembly. The map also reveals the mistaken mapping of seven scaffolds in the reference assembly onto chromosome II by a previous microsatellite map based on F2 crosses. Our approach can be easily applied to many other organisms and holds great promise for unveiling the intragenomic and intraspecific variation in the recombination rates.
authors.affiliation: Department of Biology, Indiana University, Bloomington, Indiana 47405 senxu@indiana.edu.
authors.forename: Sen
authors.initials: S
authors.lastname: Xu
authors.affiliation: Department of Biology, Indiana University, Bloomington, Indiana 47405.
authors.forename: Matthew S
authors.initials: MS
authors.lastname: Ackerman
authors.affiliation: Department of Biology, Indiana University, Bloomington, Indiana 47405.
authors.forename: Hongan
authors.initials: H
authors.lastname: Long
authors.affiliation: Department of Biology, Indiana University, Bloomington, Indiana 47405.
authors.forename: Lydia
authors.initials: L
authors.lastname: Bright
authors.affiliation: Department of Biology, Indiana University, Bloomington, Indiana 47405.
authors.forename: Ken
authors.initials: K
authors.lastname: Spitze
authors.affiliation: Hubbard Center for Genome Studies and Department of Molecular Cellular and Biomedical Sciences, University of New Hampshire, Durham, New Hampshire 03824.
authors.forename: Jordan S
authors.initials: JS
authors.lastname: Ramsdell
authors.affiliation: Hubbard Center for Genome Studies and Department of Molecular Cellular and Biomedical Sciences, University of New Hampshire, Durham, New Hampshire 03824.
authors.forename: W Kelley
authors.initials: WK
authors.lastname: Thomas
authors.affiliation: Department of Biology, Indiana University, Bloomington, Indiana 47405.
authors.forename: Michael
authors.initials: M
authors.lastname: Lynch
mesh_terms: D000465:Algorithms; D000818:Animals; D002874:Chromosome Mapping / Q000379:methods*; D003621:Daphnia / Q000235:genetics*; D005434:Flow Cytometry; D016678:Genome; D008297:Male; D020641:Polymorphism, Single Nucleotide; D017422:Sequence Analysis, DNA / Q000379:methods*; D059010:Single-Cell Analysis / Q000379:methods*; D013094:Spermatozoa / Q000166:cytology*
keywords: fluorescence-activated cell sorting; meiosis; single cell; whole-genome amplification