Y chromosome conserved anchored tagged sequences (YCATS) for the analysis of mammalian male‐specific DNA

TLDR

Y‑chromosome haplotyping using microsatellites or SNPs is a powerful tool for evolutionary studies of humans and wild species, but its application is limited by the scarcity of Y‑chromosome markers and sequence data in natural populations. The study aims to develop a large‑scale set of Y‑chromosome conserved anchor tagged sequence (YCATS) markers across mammals using PCR screening. The authors designed exonic primers flanking 48 Y‑linked introns from human and mouse, screened them across 20 mammalian species, and analyzed factors such as rapid Y‑chromosome evolution, male‑biased mutation, adaptive pressures, non‑recombination dynamics, and X‑chromosome homology that influence marker development. On average, 10 introns per species were amplified, yielding 100 kb of Y‑chromosome sequence, and human intron size moderately predicts intron size in other mammals (r² = 0.45) while larger human fragments are less likely to amplify.

Abstract

Abstract Y chromosome haplotyping based on microsatellites or single nucleotide polymorphisms has recently proven to be a powerful approach for evolutionary studies of human populations, and also holds great promise for the studies of wild species. However, the use of the approach is hampered in most natural populations by the lack of Y chromosome markers and sequence information. Here, we report the large‐scale development of Y chromosome conserved anchor tagged sequence (YCATS) markers in mammals by a polymerase chain reaction screening approach. Exonic primers flanking 48 different introns of Y‐linked genes were developed based on human and mouse sequences, and screened on a set of 20 different mammals. On average about 10 introns were amplified for each species and a total of 100 kb of Y chromosome sequence were obtained. Intron size in humans was a reasonable predictor of intron size in other mammals ( r 2 = 0.45) and there was a negative correlation between human fragment size and amplification success. We discuss a number of factors affecting the possibility of developing conserved Y chromosome markers, including fast evolution of Y chromosome sequences due to male‐biased mutation and adaptive evolution of male‐specific genes, dynamic evolution of the Y chromosome due to being a nonrecombining unit, and homology with X chromosome sequences.