Chromosomal rearrangements are associated with higher rates of molecular evolution in mammals

Marquès‐Bonet, Tomàs; Navarro, Arcadi

doi:10.1016/j.gene.2005.05.007

Cited by 22 publications

(25 citation statements)

References 63 publications

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“…We also observed a significant increase in divergence and GþC content in interstitial regions that are sites of syntenic breakpoints 54,56 ( Supplementary Fig. S7).…”

Section: Generating a Draft Genome Sequencementioning

confidence: 69%

Genome sequence, comparative analysis and haplotype structure of the domestic dog

Lindblad‐Toh¹,

Wade²,

Mikkelsen³

et al. 2005

Nature

2,236

2,079

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Here we report a high-quality draft genome sequence of the domestic dog (Canis familiaris), together with a dense map of single nucleotide polymorphisms (SNPs) across breeds. The dog is of particular interest because it provides important evolutionary information and because existing breeds show great phenotypic diversity for morphological, physiological and behavioural traits. We use sequence comparison with the primate and rodent lineages to shed light on the structure and evolution of genomes and genes. Notably, the majority of the most highly conserved non-coding sequences in mammalian genomes are clustered near a small subset of genes with important roles in development. Analysis of SNPs reveals long-range haplotypes across the entire dog genome, and defines the nature of genetic diversity within and across breeds. The current SNP map now makes it possible for genome-wide association studies to identify genes responsible for diseases and traits, with important consequences for human and companion animal health.

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“…We also observed a significant increase in divergence and GþC content in interstitial regions that are sites of syntenic breakpoints 54,56 ( Supplementary Fig. S7).…”

Section: Generating a Draft Genome Sequencementioning

confidence: 69%

Genome sequence, comparative analysis and haplotype structure of the domestic dog

Lindblad‐Toh¹,

Wade²,

Mikkelsen³

et al. 2005

Nature

2,236

2,079

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“…Previous studies found that EBRs tend to show higher divergence rates than other regions in the genome (Navarro et al 1997; Marques-Bonet and Navarro 2005) and lower recombination rates (Farré et al 2013). Mirroring these results, we detected a significant reduction on recombination rates within EBRs when compared with the rest of the mouse genome.…”

Section: Discussionmentioning

confidence: 94%

Mammalian comparative genomics reveals genetic and epigenetic features associated with genome reshuffling in Rodentia

et al. 2016

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Understanding how mammalian genomes have been reshuffled through structural changes is fundamental to the dynamics of its composition, evolutionary relationships between species and, in the long run, speciation. In this work, we reveal the evolutionary genomic landscape in Rodentia, the most diverse and speciose mammalian order, by whole-genome comparisons of six rodent species and six representative outgroup mammalian species. The reconstruction of the evolutionary breakpoint regions across rodent phylogeny shows an increased rate of genome reshuffling that is approximately two orders of magnitude greater than in other mammalian species here considered. We identified novel lineage and clade-specific breakpoint regions within Rodentia and analyzed their gene content, recombination rates and their relationship with constitutive lamina genomic associated domains, DNase I hypersensitivity sites and chromatin modifications. We detected an accumulation of protein-coding genes in evolutionary breakpoint regions, especially genes implicated in reproduction and pheromone detection and mating. Moreover, we found an association of the evolutionary breakpoint regions with active chromatin state landscapes, most probably related to gene enrichment. Our results have two important implications for understanding the mechanisms that govern and constrain mammalian genome evolution. The first is that the presence of genes related to species-specific phenotypes in evolutionary breakpoint regions reinforces the adaptive value of genome reshuffling. Second, that chromatin conformation, an aspect that has been often overlooked in comparative genomic studies, might play a role in modeling the genomic distribution of evolutionary breakpoints.

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“…This theory, building upon our own work (Webber and Ponting 2005) and that of others (Duret et al , 2006Marques-Bonet and Navarro 2005), assumes that high recombination rates maintain high G+C levels, and that chromosomal regions of high G+C are unusually susceptible to breakage and consequent rearrangement. It provides five testable predictions.…”

Section: Chromosomal Rearrangementsmentioning

confidence: 98%

“…This is because synteny break regions, at least in eutheria, are enriched within regions exhibiting high G+C levels and d S rates (Marques-Bonet and Navarro 2005;Webber and Ponting 2005). Thus, we might expect rearrangements to have occurred preferentially in the Monodelphis X chromosome and near the autosomal telomeres.…”

Section: Chromosomal Rearrangementsmentioning

confidence: 99%

An analysis of the gene complement of a marsupial,Monodelphis domestica: Evolution of lineage-specific genes and giant chromosomes

Goodstadt¹,

Heger²,

Webber³

et al. 2007

Genome Res.

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The newly sequenced genome of Monodelphis domestica not only provides the out-group necessary to better understand our own eutherian lineage, but it enables insights into the innovative biology of metatherians. Here, we compare Monodelphis with Homo sequences from alignments of single nucleotides, genes, and whole chromosomes. Using PhyOP, we have established orthologs in Homo for 82% (15,250) of Monodelphis gene predictions. Those with single orthologs in each species exhibited a high median synonymous substitution rate (d S = 1.02), thereby explaining the relative paucity of aligned regions outside of coding sequences. Orthology assignments were used to construct a synteny map that illustrates the considerable fragmentation of Monodelphis and Homo karyotypes since their therian last common ancestor. Fifteen percent of Monodelphis genes are predicted, from their low divergence at synonymous sites, to have been duplicated in the metatherian lineage. The majority of Monodelphis-specific genes possess predicted roles in chemosensation, reproduction, adaptation to specific diets, and immunity. Using alignments of Monodelphis genes to sequences from either Homo or Trichosurus vulpecula (an Australian marsupial), we show that metatherian X chromosomes have elevated silent substitution rates and high G+C contents in comparison with both metatherian autosomes and eutherian chromosomes. Each of these elevations is also a feature of subtelomeric chromosomal regions. We attribute these observations to high rates of female-specific recombination near the chromosomal ends and within the X chromosome, which act to sustain or increase G+C levels by biased gene conversion. In particular, we propose that the higher G+C content of the Monodelphis X chromosome is a direct consequence of its small size relative to the giant autosomes.

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Chromosomal rearrangements are associated with higher rates of molecular evolution in mammals

Cited by 22 publications

References 63 publications

Genome sequence, comparative analysis and haplotype structure of the domestic dog

Genome sequence, comparative analysis and haplotype structure of the domestic dog

Mammalian comparative genomics reveals genetic and epigenetic features associated with genome reshuffling in Rodentia

An analysis of the gene complement of a marsupial,Monodelphis domestica: Evolution of lineage-specific genes and giant chromosomes

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