The Red Fox Y-Chromosome in Comparative Context

While the number of mammalian genome assemblies has proliferated, Y-chromosome assemblies have lagged behind. This discrepancy is caused by biological features of the Y-chromosome, such as its high repeat content, that present challenges to assembly with short-read, next-generation sequencing technologies. Partial Y-chromosome assemblies have been developed for the cat (Felis catus), dog (Canis lupus familiaris), and grey wolf (Canis lupus lupus), providing the opportunity to examine the red fox (Vulpes vulpes) Y-chromosome in the context of closely related species. Here we present a data-driven approach to identifying Y-chromosome sequence among the scaffolds that comprise the short-read assembled red fox genome. First, scaffolds containing genes found on the Y-chromosomes of cats, dogs, and wolves were identified. Next, analysis of the resequenced genomes of 15 male and 15 female foxes revealed scaffolds containing male-specific k-mers and patterns of inter-sex copy number variation consistent with the heterogametic chromosome. Analyzing variation across these two metrics revealed 171 scaffolds containing 3.37 Mbp of putative Y-chromosome sequence. The gene content of these scaffolds is consistent overall with that of the Y-chromosome in other carnivore species, though the red fox Y-chromosome carries more copies of BCORY2 and UBE1Y than has been reported in related species and fewer copies of SRY than in other canids. The assignment of these scaffolds to the Y-chromosome serves to further characterize the content of the red fox draft genome while providing resources for future analyses of canid Y-chromosome evolution

Characterization of the sex chromosomes in spinach

Plant sex chromosomes have evolved from the autosomes of hermaphroditic species to maintain dioecy. The major barriers to sex chromosome characterization have been the inherent difficulties of working with a non-recombining sex determining region that make sequencing and mapping the Male-Specific region of the Y chromosome (MSY) painstaking. Here we use YY spinach (Spinacia oleracea L.) to characterize the MSY and the X-specific region of the X chromosome. A screen of 395 accessions in the USDA germplasm collection found a single accession that segregates YY progeny. The YY genotype was verified by a genetic cross and a novel X-specific marker. Potential novel X-specific sequences were found by depth of coverage analysis comparing alignments of male and female sequences to an XX reference. Of the 19 candidates found by depth of coverage, only one was verified as X-specific. The marker SpoX amplifies products from XX and XY but not YY templates. Pooled genomic DNA of 16 YY individuals selected by SpoX was sequenced at 63X using PacBio. Sequence data was assembled into an 823 Mbp assembly using CANU so the YY assembly could be compared to a 911 Mbp XX assembly. Seven genes that were non-repetitive sequences were found on a 1.14 X-specific contig from the XX assembly, and were queried by BLAST to the YY assembly to find their MSY homologs, which totaled 427 kb of novel Y chromosome sequence. On the Y contigs, the percentage uncovered by female k-mers decreased from 9.5% to 0.6% between positions 65.8 Mbp and 66.7 Mbp on the X chromosome, indicating that it is the location of one of the boundaries of the non-recombining region. The discovery of an accession which reliably segregates YY plants makes for unprecedented opportunity to study X and Y chromosomes in spinach. By comparing YY and XX genomes, the genomic basis of X and Y chromosome differentiation and evolution that gave rise to dioecy can be elucidated