The Red Fox Y-Chromosome in Comparative Context

Rando, Halie M.; Wadlington, William H.; Johnson, Jennifer L.; Stutchman, Jeremy; Trut, Lyudmila N.; Farré, Marta; Kukekova, Anna V.

doi:10.3390/genes10060409

Cited by 6 publications

(6 citation statements)

References 66 publications

(177 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The evolutionary dynamics of the Y chromosome involves acquisition, loss, and amplification of genes and genomic regions, resulting in structural complexity and broad variation across mammalian species [ 4 , 10 , 14 , 16 , 18 , 32 , 33 ]. These features complicate MSY sequence assembly and to date, only three primate [ 16 , 33 , 34 ] and the mouse [ 17 ] MSYs are complete, with high-quality MSY draft assemblies available for another handful of mammalian species (gorilla [ 35 ], marmoset [ 19 ], rat [ 19 ], dog [ 32 ], cat [ 32 ], pig [ 16 ], bull [ 19 , 36 , 37 ], horse [ 18 ], and opossum [ 19 ]), and partial MSY sequences have been obtained for a few more domestic and wild species (goat [ 38 ], sheep [ 27 , 29 ], red fox [ 39 ], brown and polar bears [ 40 , 41 ], and whales [ 42 ]).…”

Section: Introductionmentioning

confidence: 99%

An 8.22 Mb Assembly and Annotation of the Alpaca (Vicugna pacos) Y Chromosome

Jevit

Davis

Castaneda

et al. 2021

Genes

View full text Add to dashboard Cite

The unique evolutionary dynamics and complex structure make the Y chromosome the most diverse and least understood region in the mammalian genome, despite its undisputable role in sex determination, development, and male fertility. Here we present the first contig-level annotated draft assembly for the alpaca (Vicugna pacos) Y chromosome based on hybrid assembly of short- and long-read sequence data of flow-sorted Y. The latter was also used for cDNA selection providing Y-enriched testis transcriptome for annotation. The final assembly of 8.22 Mb comprised 4.5 Mb of male specific Y (MSY) and 3.7 Mb of the pseudoautosomal region. In MSY, we annotated 15 X-degenerate genes and two novel transcripts, but no transposed sequences. Two MSY genes, HSFY and RBMY, are multicopy. The pseudoautosomal boundary is located between SHROOM2 and HSFY. Comparative analysis shows that the small and cytogenetically distinct alpaca Y shares most of MSY sequences with the larger dromedary and Bactrian camel Y chromosomes. Most of alpaca X-degenerate genes are also shared with other mammalian MSYs, though WWC3Y is Y-specific only in alpaca/camels and the horse. The partial alpaca Y assembly is a starting point for further expansion and will have applications in the study of camelid populations and male biology.

show abstract

Section: Introductionmentioning

confidence: 99%

An 8.22 Mb Assembly and Annotation of the Alpaca (Vicugna pacos) Y Chromosome

Jevit

Davis

Castaneda

et al. 2021

Genes

View full text Add to dashboard Cite

show abstract

“…We then sequenced the pooled enriched library on an Illumina MiSeq lane SR300 at the UC Davis Genome Center. Additionally, we included HiSeq2500 reads (PE 150) from 2 male red fox whole-genome shotgun libraries sequenced for a different project [ 18 ].…”

Section: Methodsmentioning

confidence: 99%

Sequencing Red Fox Y Chromosome Fragments to Develop Phylogenetically Informative SNP Markers and Glimpse Male-Specific Trans-Pacific Phylogeography

Sacks

Lounsberry

Rando

et al. 2021

Genes

Self Cite

View full text Add to dashboard Cite

The red fox (Vulpes vulpes) has a wide global distribution with many ecotypes and has been bred in captivity for various traits, making it a useful evolutionary model system. The Y chromosome represents one of the most informative markers of phylogeography, yet it has not been well-studied in the red fox due to a lack of the necessary genomic resources. We used a target capture approach to sequence a portion of the red fox Y chromosome in a geographically diverse red fox sample, along with other canid species, to develop single nucleotide polymorphism (SNP) markers, 13 of which we validated for use in subsequent studies. Phylogenetic analyses of the Y chromosome sequences, including calibration to outgroups, confirmed previous estimates of the timing of two intercontinental exchanges of red foxes, the initial colonization of North America from Eurasia approximately half a million years ago and a subsequent continental exchange before the last Pleistocene glaciation (~100,000 years ago). However, in contrast to mtDNA, which showed unidirectional transfer from Eurasia to North America prior to the last glaciation, the Y chromosome appears to have been transferred from North America to Eurasia during this period. Additional sampling is needed to confirm this pattern and to further clarify red fox Y chromosome phylogeography.

show abstract

“…2013; Rando et al . 2019); the Chinese raccoon dogs were examined by us for the first time. We further analyzed the copy number of the 5′‐flanking region of the SRY and found that, in each animal, the number of the CDS and 5′‐flanking sequences were concordant.…”

Section: Species/dog Breed Copy Number In Dsd Dogs (N; %) Copy Number In Controls (N; %)mentioning

confidence: 99%

“…The modal number of SRY copies in dogs, wolves, Chinese raccoon dogs, and red foxes was 3, 3, 3, and 1 respectively; however, variability of the copy number was only observed in Yorkshire Terriers and red foxes (Table 1). In earlier studies, the SRY copy number was found to be 7, 3, and 1, in dogs, wolves, and red foxes respectively (Li et al 2013;Rando et al 2019); the Chinese raccoon dogs were examined by us for the first time. We further analyzed the copy number of the 5 0 -flanking region of the SRY and found that, in each animal, the number of the CDS and 5 0 -flanking sequences were concordant.…”

mentioning

confidence: 96%

See 1 more Smart Citation

Copy number variation of the SRY gene showed an association with disorders of sex development in Yorkshire Terrier dogs

2021

View full text Add to dashboard Cite

The molecular background of disorders of sex development (DSD) in dogs is poorly understood. Several copies of the SRY genes have been reported in the dog genome. We used droplet digital PCR with the aim of determining variability in SRY copy number and its association with DSD in dogs. Altogether 19 DSD male dogs (XY DSD) of 10 breeds and 87 control dogs of eight breeds were analyzed. Moreover, we performed a comparative analysis of SRY copy number in other canids: wolves (3), red foxes ( 16), and Chinese raccoon dogs (10). We found that the modal number of SRY copies in dogs, wolves, red foxes, and Chinese raccoon dogs was 3, 3, 1, and 3 respectively. Variability of copy number was only observed in Yorkshire Terriers (two or three copies) and red foxes (one or two copies). An analysis of six DSD Yorkshire Terriers and 38 control males of this breed showed that 50% of the DSD dogs had two copies, while the incidence of this variant was significantly lower in the control dogs (10.5%). Searching for the copy number of the coding and 5 0 -flanking fragments revealed full concordance with the copy number. These fragments were also sequenced in DSD ( 19) and control (24) dogs, and no DNA variants were found. We conclude that, in the dog, two or three functional copies of the SRY gene are present, and a smaller number of copies showed an association with the risk of DSD phenotype in Yorkshire Terriers.

show abstract

The Red Fox Y-Chromosome in Comparative Context

Cited by 6 publications

References 66 publications

An 8.22 Mb Assembly and Annotation of the Alpaca (Vicugna pacos) Y Chromosome

An 8.22 Mb Assembly and Annotation of the Alpaca (Vicugna pacos) Y Chromosome

Sequencing Red Fox Y Chromosome Fragments to Develop Phylogenetically Informative SNP Markers and Glimpse Male-Specific Trans-Pacific Phylogeography

Copy number variation of the SRY gene showed an association with disorders of sex development in Yorkshire Terrier dogs

Contact Info

Product

Resources

About