title: A time- and cost-effective strategy to sequence mammalian Y Chromosomes: an application to the de novo assembly of gorilla Y.
abstract: The mammalian Y Chromosome sequence, critical for studying male fertility and dispersal, is enriched in repeats and palindromes, and thus, is the most difficult component of the genome to assemble. Previously, expensive and labor-intensive BAC-based techniques were used to sequence the Y for a handful of mammalian species. Here, we present a much faster and more affordable strategy for sequencing and assembling mammalian Y Chromosomes of sufficient quality for most comparative genomics analyses and for conservation genetics applications. The strategy combines flow sorting, short- and long-read genome and transcriptome sequencing, and droplet digital PCR with novel and existing computational methods. It can be used to reconstruct sex chromosomes in a heterogametic sex of any species. We applied our strategy to produce a draft of the gorilla Y sequence. The resulting assembly allowed us to refine gene content, evaluate copy number of ampliconic gene families, locate species-specific palindromes, examine the repetitive element content, and produce sequence alignments with human and chimpanzee Y Chromosomes. Our results inform the evolution of the hominine (human, chimpanzee, and gorilla) Y Chromosomes. Surprisingly, we found the gorilla Y Chromosome to be similar to the human Y Chromosome, but not to the chimpanzee Y Chromosome. Moreover, we have utilized the assembled gorilla Y Chromosome sequence to design genetic markers for studying the male-specific dispersal of this endangered species.
authors.affiliation: Department of Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA;
authors.forename: Marta
authors.initials: M
authors.lastname: Tomaszkiewicz
authors.affiliation: Department of Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA;
authors.forename: Samarth
authors.initials: S
authors.lastname: Rangavittal
authors.affiliation: Department of Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA;
authors.forename: Monika
authors.initials: M
authors.lastname: Cechova
authors.affiliation: Genetics Program, The Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania 16802, USA;
authors.forename: Rebeca
authors.initials: R
authors.lastname: Campos Sanchez
authors.affiliation: Department of Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA;
authors.forename: Howard W
authors.initials: HW
authors.lastname: Fescemyer
authors.affiliation: Department of Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA;
authors.forename: Robert
authors.initials: R
authors.lastname: Harris
authors.affiliation: Department of Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA;
authors.forename: Danling
authors.initials: D
authors.lastname: Ye
authors.affiliation: Department of Veterinary Medicine, University of Cambridge, Cambridge CB3 0ES, United Kingdom;
authors.forename: Patricia C M
authors.initials: PC
authors.lastname: O'Brien
authors.affiliation: University of Lille 1/CNRS 59655 Villeneuve d'Ascq, France; Department of Computer Science and Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, USA; The Genome Sciences Institute of the Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania 16802, USA;
authors.forename: Rayan
authors.initials: R
authors.lastname: Chikhi
authors.affiliation: San Diego Zoo Institute for Conservation Research, Escondido, California 92027, USA;
authors.forename: Oliver A
authors.initials: OA
authors.lastname: Ryder
authors.affiliation: Department of Veterinary Medicine, University of Cambridge, Cambridge CB3 0ES, United Kingdom;
authors.forename: Malcolm A
authors.initials: MA
authors.lastname: Ferguson-Smith
authors.affiliation: Department of Computer Science and Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, USA; The Genome Sciences Institute of the Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania 16802, USA; Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA.
authors.forename: Paul
authors.initials: P
authors.lastname: Medvedev
authors.affiliation: Department of Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA;
authors.forename: Kateryna D
authors.initials: KD
authors.lastname: Makova
mesh_terms: D000818:Animals; D019295:Computational Biology / Q000379:methods; D015321:Gene Rearrangement; D016678:Genome; D023281:Genomics; D006071:Gorilla gorilla / Q000235:genetics; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D055029:Inverted Repeat Sequences; D008297:Male; D008322:Mammals / Q000235:genetics*; D018895:Microsatellite Repeats; D002679:Pan troglodytes / Q000235:genetics; D012091:Repetitive Sequences, Nucleic Acid; D017422:Sequence Analysis, DNA; D014998:Y Chromosome