Extensive Conservation of Sex Chromosome Organization Between Cat and Human Revealed by Parallel Radiation Hybrid Mapping

Murphy, William J.; Sun, Shan; Chen, Zhang-qun; Pecon-Slattery, Jill; O’Brien, Stephen J.

doi:10.1101/gr.9.12.1223

Cited by 105 publications

(85 citation statements)

References 44 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Of note, FCA053 could not be placed on the cat, dog, or human assemblies. For other cat X markers the colinearity between the domestic cat, dog, and human X chromosome coordinates is shown in supplemental Figure 1 and confirms the conserved synteny of the mammalian X chromosome between dog, human, and cat, as previously reported by Murphy et al (1999).…”

Section: Resultssupporting

confidence: 66%

A Domestic cat X Chromosome Linkage Map and the Sex-LinkedorangeLocus: Mapping oforange, Multiple Origins and Epistasis Overnonagouti

et al. 2009

View full text Add to dashboard Cite

A comprehensive genetic linkage map of the domestic cat X chromosome was generated with the goal of localizing the genomic position of the classic X-linked orange (O) locus. Microsatellite markers with an average spacing of 3 Mb were selected from sequence traces of the cat 1.93 whole genome sequence (WGS), including the pseudoautosomal region 1 (PAR1). Extreme variation in recombination rates (centimorgans per megabase) was observed along the X chromosome, ranging from a virtual absence of recombination events in a region estimated to be .30 Mb to recombination frequencies of 15.7 cM/Mb in a segment estimated to be ,0.3 Mb. This detailed linkage map was applied to position the X-linked orange gene, placing this locus on the q arm of the X chromosome, as opposed to a previously reported location on the p arm. Fine mapping placed the locus between markers at positions 106 and 116.8 Mb in the current 1.93-coverage sequence assembly of the cat genome. Haplotype analysis revealed potential recombination events that could reduce the size of the candidate region to 3.5 Mb and suggested multiple origins for the orange phenotype in the domestic cat. Furthermore, epistasis of orange over nonagouti was demonstrated at the genetic level.

show abstract

Section: Resultssupporting

confidence: 66%

A Domestic cat X Chromosome Linkage Map and the Sex-LinkedorangeLocus: Mapping oforange, Multiple Origins and Epistasis Overnonagouti

et al. 2009

View full text Add to dashboard Cite

show abstract

“…Moreover, by focusing on the organization of the Z chromosome, we can address the degree of sex chromosome conservation in a system of female heterogamety. The latter is motivated by the fact that while there have been numerous interchromosomal rearrangements among autosomes during mammalian evolution (Murphy et al 2005), the gene content of the X chromosome is largely conserved across all eutherian lineages (Murphy et al 1999;Raudsepp et al 2004). Is this a consequence of the mode of dosage compensation in mammals or is it a general feature of sex chromosome evolution?…”

Section: Discussionmentioning

confidence: 99%

Genetic Mapping in a Natural Population of Collared Flycatchers (Ficedula albicollis): Conserved Synteny but Gene Order Rearrangements on the Avian Z Chromosome

Backström¹,

Brandström²,

Gustafsson

et al. 2006

Genetics

100

View full text Add to dashboard Cite

Data from completely sequenced genomes are likely to open the way for novel studies of the genetics of nonmodel organisms, in particular when it comes to the identification and analysis of genes responsible for traits that are under selection in natural populations. Here we use the draft sequence of the chicken genome as a starting point for linkage mapping in a wild bird species, the collared flycatcher-one of the most well-studied avian species in ecological and evolutionary research. A pedigree of 365 flycatchers was established and genotyped for single nucleotide polymorphisms in 23 genes selected from (and spread over most of ) the chicken Z chromosome. All genes were also found to be located on the Z chromosome in the collared flycatcher, confirming conserved synteny at the level of gene content across distantly related avian lineages. This high degree of conservation mimics the situation seen for the mammalian X chromosome and may thus be a general feature in sex chromosome evolution, irrespective of whether there is male or female heterogamety. Alternatively, such unprecedented chromosomal conservation may be characteristic of most chromosomes in avian genome evolution. However, several internal rearrangements were observed, meaning that the transfer of map information from chicken to nonmodel bird species cannot always assume conserved gene orders. Interestingly, the rate of recombination on the Z chromosome of collared flycatchers was only 50% that of chicken, challenging the widely held view that birds generally have high recombination rates.

show abstract

“…Cold Spring Harbor Laboratory Press on May 11, 2018 -Published by genome.cshlp.org Downloaded from chromosome (Murphy et al 1999;Davis et al 2009;Ma et al 2010), which would preclude an inversion-based mechanism to explain this extremely large nonrecombining region that is shared across divergent mammalian orders.…”

Section: Wwwgenomeorgmentioning

confidence: 99%

Phylogenomic evidence for ancient hybridization in the genomes of living cats (Felidae)

et al. 2015

Self Cite

View full text Add to dashboard Cite

Inter-species hybridization has been recently recognized as potentially common in wild animals, but the extent to which it shapes modern genomes is still poorly understood. Distinguishing historical hybridization events from other processes leading to phylogenetic discordance among different markers requires a well-resolved species tree that considers all modes of inheritance and overcomes systematic problems due to rapid lineage diversification by sampling large genomic character sets. Here, we assessed genome-wide phylogenetic variation across a diverse mammalian family, Felidae (cats). We combined genotypes from a genome-wide SNP array with additional autosomal, X-and Y-linked variants to sample ∼150 kb of nuclear sequence, in addition to complete mitochondrial genomes generated using light-coverage Illumina sequencing. We present the first robust felid time tree that accounts for unique maternal, paternal, and biparental evolutionary histories. Signatures of phylogenetic discordance were abundant in the genomes of modern cats, in many cases indicating hybridization as the most likely cause. Comparison of big cat whole-genome sequences revealed a substantial reduction of X-linked divergence times across several large recombination cold spots, which were highly enriched for signatures of selection-driven postdivergence hybridization between the ancestors of the snow leopard and lion lineages. These results highlight the mosaic origin of modern felid genomes and the influence of sex chromosomes and sex-biased dispersal in post-speciation gene flow. A complete resolution of the tree of life will require comprehensive genomic sampling of biparental and sex-limited genetic variation to identify and control for phylogenetic conflict caused by ancient admixture and sex-biased differences in genomic transmission.

show abstract

Extensive Conservation of Sex Chromosome Organization Between Cat and Human Revealed by Parallel Radiation Hybrid Mapping

Cited by 105 publications

References 44 publications

A Domestic cat X Chromosome Linkage Map and the Sex-LinkedorangeLocus: Mapping oforange, Multiple Origins and Epistasis Overnonagouti

A Domestic cat X Chromosome Linkage Map and the Sex-LinkedorangeLocus: Mapping oforange, Multiple Origins and Epistasis Overnonagouti

Genetic Mapping in a Natural Population of Collared Flycatchers (Ficedula albicollis): Conserved Synteny but Gene Order Rearrangements on the Avian Z Chromosome

Phylogenomic evidence for ancient hybridization in the genomes of living cats (Felidae)

Contact Info

Product

Resources

About