DiscoverY: a classifier for identifying Y chromosome sequences in male assemblies

Abstract

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.

Dynamic evolution of great ape Y chromosomes

“…For bonobo and Sumatran orangutan, we generated and assembled ( 53 ) deep-coverage short sequencing reads from male individuals and identified putative Y contigs by mapping them against the corresponding female reference assemblies ( 54 ). These contigs were then scaffolded with mate-pair reads ( 55 ).…”

Representation ofk-Mer Sets Using Spectrum-Preserving String Sets

“…This approach is unsatisfactory because (1) as shown in this article, it takes substantially more space than direct k-mer compression, (2) k-mer counting on the fly adds significant time and memory to the decompression process, and (3) there are applications where the k-mer set cannot be reproduced by simply counting k-mers in a FASTA file, for example, when it is a product of a multi-sample error correction algorithm (Yang et al, 2012). Further, there are applications where the k-mer set is not related to sequence read data at all, for example, a universal hitting set (Orenstein et al, 2017), a chromosome-specific reference dictionary (Rangavittal et al, 2019), or a winnowed min-hash sketch [e.g., as in Sahlin and , or see Marçais et al (2019) and Rowe (2019) for a survey].…”

A Phased Canis lupus familiaris Labrador Retriever Reference Genome Utilizing High Molecular Weight DNA Extraction Methods and High Resolution Sequencing Technologies

“…Yella is a male Labrador Retriever, and while reads from the Y-chromosome could be detected via alignment to an existing partial Y chromosome reference sequence, the Y-chromosome for Yella was not able to be resolved beyond an acceptable threshold for a published reference genome. This is similar to issues experienced across mammalian genomics, in which the short and highly repetitive nature of the Y-chromosome, along with its homology to the Xchromosome can make it difficult to detect and assemble (G. Li et al 2013;Oetjens et al 2018;Carvalho and Clark 2013;Rangavittal et al 2019).…”