Mapping DNA structural variation in dogs

Chen, Weikang; Swartz, Joshua D.; Rush, Laura J.; Álvarez, Carlos E.

doi:10.1101/gr.083741.108

Cited by 128 publications

(152 citation statements)

References 64 publications

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“…It is tempting to speculate that the development of formations where sulci can not be unambiguously identified (Figs 1c,6) are the result of perturbations in the early cortical environment (Goldman and Galkin 1978;Hilgetag and Barbas 2006). Such speculations could be tested in an animal model with cortical convolutions-such as the ferret (Smart and McSherry 1986) or the dog, where the recent sequencing of the genome raises the possibility of experiments on the association between genetic polymorphisms in transcription factors or other molecular signals and the interactive development of cortical folding, cytoarchitecture, and fiber connections (Parker et al 2004;Karlsson and LindbladToh 2008;Sutter et al 2008;Chen et al 2009). …”

Section: Future Researchmentioning

confidence: 99%

Paracingulate asymmetry in anterior and midcingulate cortex: sex differences and the effect of measurement technique

et al. 2009

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Many structural brain asymmetries accompany left hemisphere language dominance. For example, the cingulate sulcus is larger in the medial cortex of the right hemisphere, while the more dorsal paracingulate sulcus is larger on the left. The functional significance of these asymmetries is unknown because fMRI studies rarely attempt to localize activation to specific sulci, possibly due to difficulties in consistent sulcal identification. In medial cortex, for example, there are many regions of partial sulcal overlap where MRI images do not provide sufficient information to unambiguously distinguish a paracingulate sulcus from a displaced anterior cingulate segment. As large samples of postmortem material are rarely available for cytoarchitectural studies of sulcal variation, we have investigated the effect of variation in boundary and sulcal definition on paracingulate asymmetry in the MRI scans of 200 healthy adults (100 men, 100 women). Although women displayed a reliable asymmetry in the size of the paracingulate sulcus, regardless of boundary definition or technique, asymmetry was greatest when (1) the measurement was limited to the midcingulate region between the genu and the anterior commissure; and (2) the more dorsal of two overlapping sulci was always classified as a paracingulate sulcus (rather than as a displaced cingulate segment). The fact that paracingulate asymmetry is maximal in the midcingulate region suggests that this region may play a particular role in hemispheric specialization for language. Future work should investigate the structural and functional correlates of sulcal variation in this region.

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Section: Future Researchmentioning

confidence: 99%

Paracingulate asymmetry in anterior and midcingulate cortex: sex differences and the effect of measurement technique

et al. 2009

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“…Indeed, copy-number variants (CNVs; sometimes also called 'copy-number polymorphisms' or CNPs) have been shown to be widespread in a variety of organisms, including humans (Sebat et al 2004;Conrad et al 2006;McCarroll et al 2006;Redon et al 2006), mice (Graubert et al 2007;She et al 2008), chimpanzees (Perry et al 2006, rhesus macaques (Lee et al 2008), cows (Liu et al 2010), dogs (Chen et al 2009;Nicholas et al 2009), chickens (Griffin et al 2008), maize (Springer et al 2009), Arabidopsis thaliana (Ossowski et al 2008), fruitflies (Dopman & Hartl 2007;Emerson et al 2008), Caenorhabditis elegans (Maydan et al 2010) and Saccharomyces cerevisiae (Carreto et al 2008). Though it is often harder to experimentally identify and genotype CNVs relative to SNPs and indels, many are big enough to encompass whole genes and are therefore more likely to affect organismal fitness.…”

Section: Introductionmentioning

confidence: 99%

Gene copy-number polymorphism in nature

2010

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Differences between individuals in the copy-number of whole genes have been found in every multicellular species examined thus far. Such differences result in unique complements of protein-coding genes in all individuals, and have been shown to underlie adaptive phenotypic differences. Here, we review the evidence for copy-number variants (CNVs), focusing on the methods used to detect them and the molecular mechanisms responsible for generating this type of variation. Although there are multiple technical and computational challenges inherent to these experimental methods, next-generation sequencing technologies are making such experiments accessible in any system with a sequenced genome. We further discuss the connection between copy-number variation within species and copynumber divergence between species, showing that these values are exactly what one would expect from similar comparisons of nucleotide polymorphism and divergence. We conclude by reviewing the growing body of evidence for natural selection on copy-number variants. While it appears that most genic CNVsespecially deletions-are quickly eliminated by selection, there are now multiple studies demonstrating a strong link between copy-number differences at specific genes and phenotypic differences in adaptive traits. We argue that a complete understanding of the molecular basis for adaptive natural selection necessarily includes the study of copy-number variation.

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“…It is clear that copy number variability is a common feature of a wide range of species, from flies (Dopman and Hartl 2007) to maize (Schnable et al 2009), and including mice (Egan et al 2007;Graubert et al 2007;Cahan et al 2009), rats (Guryev et al 2008), dogs (Chen et al 2009), pigs (Ramayo Caldas et al 2010), goats (Fontanesi et al 2010), macaques , and chimpanzees . CNVs have been associated with traits of evolutionary interest, especially human disease-related traits (see, e.g., Craddock et al 2010, and references therein), but also traits in other species such as breed-specific features in dogs (Chen et al 2009), metabolic traits in mice (Orozco et al 2009), and, possibly, phenotypic differences in inbred lines of maize (Schnable et al 2009). In addition, in humans and other mammals, CNVs are linked to segmental duplications (SDs) (Eichler 2006), which adds interest to their study in our lineage, especially in light of the outburst of segmental duplication activity that occurred in our common ancestor with the African great apes (Marques-Bonet et al 2009).…”

mentioning

confidence: 99%

Copy number variation analysis in the great apes reveals species-specific patterns of structural variation

Gazave¹,

Darré²,

Morcillo-Suárez³

et al. 2011

Genome Res.

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Copy number variants (CNVs) are increasingly acknowledged as an important source of evolutionary novelties in the human lineage. However, our understanding of their significance is still hindered by the lack of primate CNV data. We performed intraspecific comparative genomic hybridizations to identify loci harboring copy number variants in each of the four great apes: bonobos, chimpanzees, gorillas, and orangutans. For the first time, we could analyze differences in CNV location and frequency in these four species, and compare them with human CNVs and primate segmental duplication (SD) maps. In addition, for bonobo and gorilla, patterns of CNV and nucleotide diversity were studied in the same individuals. We show that CNVs have been subject to different selective pressures in different lineages. Evidence for purifying selection is stronger in gorilla CNVs overlapping genes, while positive selection appears to have driven the fixation of structural variants in the orangutan lineage. In contrast, chimpanzees and bonobos present high levels of common structural polymorphism, which is indicative of relaxed purifying selection together with the higher mutation rates induced by the known burst of segmental duplication in the ancestor of the African apes. Indeed, the impact of the duplication burst is noticeable by the fact that bonobo and chimpanzee share more CNVs with gorilla than expected. Finally, we identified a number of interesting genomic regions that present high-frequency CNVs in all great apes, while containing only very rare or even pathogenic structural variants in humans.

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Mapping DNA structural variation in dogs

Cited by 128 publications

References 64 publications

Paracingulate asymmetry in anterior and midcingulate cortex: sex differences and the effect of measurement technique

Paracingulate asymmetry in anterior and midcingulate cortex: sex differences and the effect of measurement technique

Gene copy-number polymorphism in nature

Copy number variation analysis in the great apes reveals species-specific patterns of structural variation

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