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.

The mammalian male-specific Y chromosome plays a critical role in sex determination and male fertility. However, because of its repetitive and haploid nature, it is frequently absent from genome assemblies and remains enigmatic. The Y chromosomes of great apes represent a particular puzzle: their gene content is more similar between human and gorilla than between human and chimpanzee, even though human and chimpanzee share a more recent common ancestor. To solve this puzzle, here we constructed a dataset including Ys from all extant great ape genera. We generated assemblies of bonobo and orangutan Ys from short and long sequencing reads and aligned them with the publicly available human, chimpanzee, and gorilla Y assemblies. Analyzing this dataset, we found that the genus Pan, which includes chimpanzee and bonobo, experienced accelerated substitution rates. Pan also exhibited elevated gene death rates. These observations are consistent with high levels of sperm competition in Pan. Furthermore, we inferred that the great ape common ancestor already possessed multicopy sequences homologous to most human and chimpanzee palindromes. Nonetheless, each species also acquired distinct ampliconic sequences. We also detected increased chromatin contacts between and within palindromes (from Hi-C data), likely facilitating gene conversion and structural rearrangements. Our results highlight the dynamic mode of Y chromosome evolution and open avenues for studies of male-specific dispersal in endangered great ape species.

Background Although the Y chromosome plays an important role in male sex determination and fertility, it is currently understudied due to its haploid and repetitive nature. Methods to isolate Y-specific contigs from a whole-genome assembly broadly fall into two categories. The first involves retrieving Y-contigs using proportion sharing with a female, but such a strategy is prone to false positives in the absence of a high-quality, complete female reference. A second strategy uses the ratio of depth of coverage from male and female reads to select Y-contigs, but such a method requires high-depth sequencing of a female and cannot utilize existing female references. Results We develop a k -mer based method called DiscoverY, which combines proportion sharing with female with depth of coverage from male reads to classify contigs as Y-chromosomal. We evaluate the performance of DiscoverY on human and gorilla genomes, across different sequencing platforms including Illumina, 10X, and PacBio. In the cases where the male and female data are of high quality, DiscoverY has a high precision and recall and outperforms existing methods. For cases when a high quality female reference is not available, we quantify the effect of using draft reference or even just raw sequencing reads from a female. Conclusion DiscoverY is an effective method to isolate Y-specific contigs from a whole-genome assembly. However, regions homologous to the X chromosome remain difficult to detect. Electronic supplementary material The online version of this article (10.1186/s12864-019-5996-3) contains supplementary material, which is available to authorized users.

Supplementary data are available at Bioinformatics online.

The mammalian male-specific Y chromosome plays a critical role in sex determination and male fertility. However, because of its repetitive and haploid nature, it is frequently absent from genome assemblies and remains enigmatic. The Y chromosomes of great apes represent a particular puzzle: their gene content is more similar between human and gorilla than between human and chimpanzee, even though human and chimpanzee shared a more recent common ancestor. To solve this puzzle, here we constructed a dataset including Ys from all extant great ape genera. We generated assemblies of bonobo and orangutan Ys, from short and long sequencing reads, and aligned them with the publicly available human, chimpanzee and gorilla Y assemblies. Analyzing this dataset, we found that the genus Pan , including chimpanzee and bonobo, experienced accelerated substitution rates. Additionally, Pan also exhibited elevated gene death rates. These observations are consistent with high levels of sperm competition in Pan . Furthermore, we inferred that the great ape common ancestor already possessed multi-copy sequences homologous to most human and chimpanzee palindromes. Nonetheless, each species also acquired distinct ampliconic sequences. We also detected increased chromatin contacts between and within palindromes (from Hi-C data), likely facilitating gene conversion and structural rearrangements. Moreover, our ENCODE data analysis suggested that Y palindromes exist to promote gene conversion preventing degradation of not only genes, as is commonly believed, but also gene regulatory sites. Our results highlight the dynamic mode of Y chromosome evolution, and open avenues for studies of male-specific dispersal in endangered great ape species.