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.

Single-molecule sequencing and chromatin conformation capture enable de novo reference assembly of the domestic goat genome

“…Mammalian genome references have generally been produced using female animals, to improve coverage of the X chromosome, relegating assembly of the Y chromosome to separate, targeted projects 53,54 . Despite using a male animal, the ARS1 assembly has better continuity of X than the short-read assemblies of a female goat, and produced some Y-associated scaffolds.…”

Sex Reversal in Reptiles: Reproductive Oddity or Powerful Driver of Evolutionary Change?

“…More sensitive cytogenetic techniques, such as comparative genomic hybridization, have revealed formerly cryptic sex chromosomes in a wide range of species [Traut et al, 1999], including sex microchromosomes and recently evolved sex chromosomes with little morphological differentiation [Traut et al, 1999;Ezaz et al, 2005;Kawai et al, 2007]. The use of sensitive molecular cytogenetics is important because the high proportion of repetitive sequences on the heteromorphic element (Y or W) renders them particularly difficult to sequence and assemble with molecular approaches [Tomaszkiewicz et al, 2016].…”

Isolating Chromosomes of the Komodo Dragon: New Tools for Comparative Mapping and Sequence Assembly

“…It can be argued that lack of chromosome-specific assemblies and the construction of chromosome maps is a weakness of many genome-sequencing efforts. However, a combination of NGS and flow sorting was used successfully for chromosomal genomics studies in wheat and barley [e.g., Šimková et al, 2008;Mayer et al, 2011;Hernandez et al, 2012;Martis et al, 2012;Cápal et al, 2015;Sánchez-Martín et al, 2016] and a few mammalian species, including the Tasmanian devil [Murchison et al, 2012], Chinese hamster [Brinkrolf et al, 2013], gorilla [Tomaszkiewicz et al, 2016], cervids , and mouse [Sudbery et al, 2009]. In reptiles, shotgun sequencing of isolated chromosomes was performed only recently by Kichigin et al [2016] to determine the sequence of A. sagrei and A. carolinensis microchromosomes and extend the work done on macrochromosomes by Alföldi et al [2011].…”