A high-density genetic map and molecular sex-typing assay for gerbils

Brekke, Thomas D.; Supriya, S.M.; Denver, Megan G; Thom, Angharad; Steele, Katherine A.; Mulley, John F.

doi:10.1101/567016

Cited by 5 publications

(8 citation statements)

References 33 publications

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“…However, the gerbil and murid lineages are known to have different karyotypes, so it is likely that not all subtelomeric regions in the gerbil species are subtelomeric in mouse and vice versa . To place the outlier genes onto a gerbil karyotype, we used the genetic map of M. unguiculatus produced by Brekke et al (2019) . This map includes only 1,720 out of the 8,809 (20%) sets of orthologous genes used in our analyses (and 70 out of 387 of those that were outliers in d S WS in M. unguiculatus , 18%), the remaining being located in unmapped genomic scaffolds.…”

Section: Resultsmentioning

confidence: 99%

“…We defined subtelomeric regions as those located within 5 Mb of the start and end of each M. musculus chromosome. To position genes onto the M. unguiculatus linkage groups, we used the genetic map produced by Brekke et al (2019) , which gives the average centimorgan position of each mapped scaffold in the M. unguiculatus genome assembly. We considered any scaffold mapped within 2.85 cM of linkage group starts or ends as subtelomeric, a threshold approximately equivalent to 5 Mb considering the mouse average recombination rate of 0.57 cM/Mb ( Cox et al.…”

Section: Methodsmentioning

confidence: 99%

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Runaway GC Evolution in Gerbil Genomes

Pracana

Hargreaves

Mulley

et al. 2020

Molecular Biology and Evolution

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Recombination increases the local GC-content in genomic regions through GC-biased gene conversion (gBGC). The recent discovery of a large genomic region with extreme GC-content in the fat sand rat Psammomys obesus provides a model to study the effects of gBGC on chromosome evolution. Here, we compare the GC-content and GC-to-AT substitution patterns across protein-coding genes of four gerbil species and two murine rodents (mouse and rat). We find that the known high-GC region is present in all the gerbils, and is characterized by high substitution rates for all mutational categories (AT-to-GC, GC-to-AT, and GC-conservative) both at synonymous and nonsynonymous sites. A higher AT-to-GC than GC-to-AT rate is consistent with the high GC-content. Additionally, we find more than 300 genes outside the known region with outlying values of AT-to-GC synonymous substitution rates in gerbils. Of these, over 30% are organized into at least 17 large clusters observable at the megabase-scale. The unusual GC-skewed substitution pattern suggests the evolution of genomic regions with very high recombination rates in the gerbil lineage, which can lead to a runaway increase in GC-content. Our results imply that rapid evolution of GC-content is possible in mammals, with gerbil species providing a powerful model to study the mechanisms of gBGC.

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Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Runaway GC Evolution in Gerbil Genomes

Pracana

Hargreaves

Mulley

et al. 2020

Molecular Biology and Evolution

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“…Only the Chinese hamster has not previously been annotated. We also downloaded genetic maps for house mouse (Cox et al 2009), rat (FileS4 from (Littrell et al 2018)), deer mouse (Kenney-Hunt et al 2014; Brown et al 2018), vole (‘Supplemental Table 1’ from (McGraw et al 2011)), and gerbil (Brekke et al 2019). No genetic map for Chinese hamster exists.…”

Section: Methodsmentioning

confidence: 99%

Sequence features do not drive karyotypic evolution: what are the missing correlates of genome evolution?

Brekke

Papadopulos

Swain

et al. 2022

Preprint

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Genome rearrangements are prevalent across the tree of life and even within species. After two decades of research, various suggestions have been proposed to explain which features of the genome are associated with rearrangements and the breakpoints between rearranged regions. These include: recombination rate, GC content, repetitive DNA content, gene density, and markers of chromatin conformation. Here, we use a set of six aligned rodent genomes to identify regions that have not been rearranged and characterize the breakpoint regions where rearrangements have occurred. We found no strong support for any of the expected correlations between breakpoint regions and a variety of genomic features previously identified. These results call into question the utility and repeatability of identifying chromatin characteristics associated with rearranged regions of the genome and suggest that perhaps a different explanation is in order. We analyzed rates of karyotypic evolution in each of the six lineages and found that the Mongolian gerbil genome has had the most rearrangements. That gerbils exhibit very rapid sequence evolution at a number of key DNA repair genes suggests an alternative hypothesis for patterns of genome rearrangement: karyotypic evolution may be driven by variation at a few genes that control the repair pathway used to fix double-stranded DNA breaks. Such variation may explain the heterogeneity in the rates of karyotypic evolution across species. While currently only supported by circumstantial evidence, a systematic survey of this hypothesis is now warranted.

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“…We used the coverage from each individual to identify sex-linked genomic contigs as described previously (Brekke et al, 2018, 2019) by first calculating each individuals’ sequencing effort as the sum of aligned reads for that individual. We standardised the contig-level counts by dividing by the sequencing effort of each individual and multiplying by 1,000,000.…”

Section: Methodsmentioning

confidence: 99%

Shed skin as a source of DNA for genotyping-by-sequencing (GBS) in reptiles

Brekke

Shier

Hegarty

et al. 2019

Preprint

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Association and genetic mapping studies aimed at linking genotype to phenotype are powerful tools that require large numbers of samples, complicating their use in long-lived species with low fecundity. Shed skins of snakes and other reptiles contain DNA; are a safe and ethical way of non-invasively sampling large numbers of individuals; and provide a simple mechanism by which to involve the public in scientific research. Here we test whether the DNA in dried shed skins mailed to us from citizen scientists is suitable for reduced representation sequencing approaches, specifically genotyping-by-sequencing (GBS). We find that shed skin samples provide DNA of sufficient quality and quantity for GBS, although libraries from shed skin resulted in fewer sequenced reads than libraries from snap-frozen muscle, and contained slightly fewer variants (70,685 SNPs versus 97,724). This issue is a direct result of lower read counts of the shed skin samples, and can be rectified quite simply with deeper sequencing. Skin-derived libraries also have a very slight (but significantly different) profile of transitions and transversions, suggesting that DNA damage occurs but is minimal. We conclude that shed skin-derived DNA is a good source of genomic DNA for a variety of genetic studies, and use it to identify sex-linked scaffolds in the corn snake genome.

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A high-density genetic map and molecular sex-typing assay for gerbils

Cited by 5 publications

References 33 publications

Runaway GC Evolution in Gerbil Genomes

Runaway GC Evolution in Gerbil Genomes

Sequence features do not drive karyotypic evolution: what are the missing correlates of genome evolution?

Shed skin as a source of DNA for genotyping-by-sequencing (GBS) in reptiles

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