A time- and cost-effective strategy to sequence mammalian Y chromosomes: An application to the de novo assembly of gorilla Y

Marta Tomaszkiewicz, Samarth Rangavittal, Monika Cechova, Rebeca Campos Sanchez, Howard W. Fescemyer, Robert Harris, Danling Ye, Patricia C.M. O'Brien, Rayan Chikhi, Oliver A. Ryder, Malcolm A. Ferguson-Smith, Paul Medvedev, Kateryna D. Makova

Research output: Contribution to journalArticle

37 Scopus citations


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.

Original languageEnglish (US)
Pages (from-to)530-540
Number of pages11
JournalGenome research
Issue number4
StatePublished - Apr 2016


All Science Journal Classification (ASJC) codes

  • Genetics
  • Genetics(clinical)

Cite this

Tomaszkiewicz, M., Rangavittal, S., Cechova, M., Sanchez, R. C., Fescemyer, H. W., Harris, R., Ye, D., O'Brien, P. C. M., Chikhi, R., Ryder, O. A., Ferguson-Smith, M. A., Medvedev, P., & Makova, K. D. (2016). A time- and cost-effective strategy to sequence mammalian Y chromosomes: An application to the de novo assembly of gorilla Y. Genome research, 26(4), 530-540. https://doi.org/10.1101/gr.199448.115