Show simple item record

dc.contributor.authorTomaszkiewicz, Marta
dc.contributor.authorRangavittal, Samarth
dc.contributor.authorCechova, Monika
dc.contributor.authorSanchez, Rebeca Campos
dc.contributor.authorFescemyer, Howard W.
dc.contributor.authorHarris, Robert
dc.contributor.authorYe, Danling
dc.contributor.authorO'Brien, Patricia C. M.
dc.contributor.authorChikhi, Rayan
dc.contributor.authorRyder, Oliver A.
dc.contributor.authorFerguson-Smith, Malcolm A.
dc.contributor.authorMedvedev, Paul
dc.contributor.authorMakova, Kateryna D.
dc.date.accessioned2020-06-12T01:40:24Z
dc.date.available2020-06-12T01:40:24Z
dc.date.issued2016
dc.identifier.issn1088-9051, 1549-5469
dc.identifier.doi10.1101/gr.199448.115
dc.identifier.urihttp://hdl.handle.net/20.500.12634/379
dc.description.abstractThe 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.
dc.language.isoen
dc.relation.urlhttp://genome.cshlp.org/content/26/4/530
dc.rights© 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/.
dc.rights.urihttp://creativecommons.org/licenses/by-nc/4.0/
dc.subjectGORILLAS
dc.subjectCHROMOSOMES
dc.subjectGENOMICS
dc.subjectEXPERIMENTAL METHODS
dc.subjectTECHNOLOGICAL INNOVATIONS
dc.titleA time- and cost-effective strategy to sequence mammalian Y Chromosomes: an application to the de novo assembly of gorilla Y
dc.typeArticle
dc.source.journaltitleGenome Research
dc.source.volume26
dc.source.issue4
dc.source.beginpage530
dc.source.endpage540
dcterms.dateAccepted
refterms.dateFOA2020-06-17T02:07:49Z
html.description.abstractThe 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.


Files in this item

Thumbnail
Name:
Tomaszkiewicz_2016_GenomeResea ...
Size:
712.1Kb
Format:
PDF

This item appears in the following Collection(s)

  • Conservation Science Publications
    Works by SDZWA's Conservation Scientists and co-authors. Includes books, book sections, articles and conference publications and presentations.

Show simple item record

© 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/.
Except where otherwise noted, this item's license is described as © 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/.