A time- and cost-effective strategy to sequence mammalian Y Chromosomes: an application to the de novo assembly of gorilla Y
Marta Tomaszkiewicz 1,9, Samarth Rangavittal 1,9, Monika Cechova 1,9, Rebeca Campos Sanchez 2, Howard W. Fescemyer 1, Robert Harris 1, Danling Ye 1, Patricia C.M. O'Brien 3, Rayan Chikhi 4,5,6, Oliver A. Ryder 7, Malcolm A. Ferguson-Smith 3, Paul Medvedev 5,6,8 and Kateryna D. Makova 1
+ Author Affiliations
1Department of Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA;
2Genetics Program, The Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania 16802, USA;
3Department of Veterinary Medicine, University of Cambridge, Cambridge CB3 0ES, United Kingdom;
4University of Lille 1/CNRS 59655 Villeneuve d'Ascq, France;
5Department of Computer Science and Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, USA;
6The Genome Sciences Institute of the Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania 16802, USA;
7San Diego Zoo Institute for Conservation Research, Escondido, California 92027, USA;
8Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA
Corresponding authors: kdm16@psu.edu, pashadag@cse.psu.edu
↵9 These authors contributed equally to this work.
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.
Footnotes
[Supplemental material is available for this article.]
Article published online before print. Article, supplemental material, and publication date are at http://www.genome.org/cgi/doi/10.1101/gr.199448.115.
Freely available online through the Genome Research Open Access option.
Received September 11, 2015. Accepted January 21, 2016.
© 2016 Tomaszkiewicz et al.; Published by Cold Spring Harbor Laboratory Press
This article, published in Genome Research, is available under a Creative Commons License (Attribution-NonCommercial 4.0 International), as described at http://creativecommons.org/licenses/by-nc/4.0/.
