title: A New Reference Genome Assembly for the MicrocrustaceanDaphnia pulex.
abstract: Comparing genomes of closely related genotypes from populations with distinct demographic histories can help reveal the impact of effective population size on genome evolution. For this purpose, we present a high quality genome assembly ofDaphnia pulex(PA42), and compare this with the first sequenced genome of this species (TCO), which was derived from an isolate from a population with >90% reduction in nucleotide diversity. PA42 has numerous similarities to TCO at the gene level, with an average amino acid sequence identity of 98.8 and >60% of orthologous proteins identical. Nonetheless, there is a highly elevated number of genes in the TCO genome annotation, with ∼7000 excess genes appearing to be false positives. This view is supported by the high GC content, lack of introns, and short length of these suspicious gene annotations. Consistent with the view that reduced effective population size can facilitate the accumulation of slightly deleterious genomic features, we observe more proliferation of transposable elements (TEs) and a higher frequency of gained introns in the TCO genome.
authors.affiliation: Department of Biology, Indiana University, Bloomington, Indiana 47405 zhiqiang.yes@gmail.com.
authors.forename: Zhiqiang
authors.initials: Z
authors.lastname: Ye
authors.affiliation: Department of Biology, Indiana University, Bloomington, Indiana 47405.|Department of Biology, University of Texas at Arlington, Texas 76019.
authors.forename: Sen
authors.initials: S
authors.lastname: Xu
authors.affiliation: Department of Biology, Indiana University, Bloomington, Indiana 47405.
authors.forename: Ken
authors.initials: K
authors.lastname: Spitze
authors.affiliation: Laboratory for Environmental Toxicology, Ghent University, B-9000, Belgium.
authors.forename: Jana
authors.initials: J
authors.lastname: Asselman
authors.affiliation: Department of Biology, Indiana University, Bloomington, Indiana 47405.
authors.forename: Xiaoqian
authors.initials: X
authors.lastname: Jiang
authors.affiliation: Department of Biology, Indiana University, Bloomington, Indiana 47405.
authors.forename: Matthew S
authors.initials: MS
authors.lastname: Ackerman
authors.affiliation: Notre Dame Genomics and Bioinformatics Core Facility, University of Notre Dame, Indiana 46556.
authors.forename: Jacqueline
authors.initials: J
authors.lastname: Lopez
authors.affiliation: Notre Dame Genomics and Bioinformatics Core Facility, University of Notre Dame, Indiana 46556.
authors.forename: Brent
authors.initials: B
authors.lastname: Harker
authors.affiliation: Department of Biology, Indiana University, Bloomington, Indiana 47405.|School of Informatics and Computing, Indiana University, Bloomington, Indiana 47405.
authors.forename: R Taylor
authors.initials: RT
authors.lastname: Raborn
authors.affiliation: Hubbard Center for Genome Studies, University of New Hampshire, Durham, New Hampshire 03824.
authors.forename: W Kelley
authors.initials: WK
authors.lastname: Thomas
authors.affiliation: Hubbard Center for Genome Studies, University of New Hampshire, Durham, New Hampshire 03824.
authors.forename: Jordan
authors.initials: J
authors.lastname: Ramsdell
authors.affiliation: Department of Biological Sciences, University of Notre Dame, Indiana 46556.|Environmental Change Initiative, University of Notre Dame, Indiana 46556.
authors.forename: Michael E
authors.initials: ME
authors.lastname: Pfrender
authors.affiliation: Department of Biology, Indiana University, Bloomington, Indiana 47405.
authors.forename: Michael
authors.initials: M
authors.lastname: Lynch
mesh_terms: D000818:Animals; D004251:DNA Transposable Elements; D003621:Daphnia / Q000235:genetics*; D007438:Introns; D058977:Molecular Sequence Annotation / Q000379:methods / Q000592:standards; D012015:Reference Standards; D012680:Sensitivity and Specificity; D016415:Sequence Alignment / Q000379:methods / Q000592:standards; D000073336:Whole Genome Sequencing / Q000379:methods* / Q000592:standards
chemical_list: D004251:DNA Transposable Elements
keywords: effective population size; gene number; genome annotation; intron; mobile elements