Human, Mouse, and Rat Genome Large-Scale Rearrangements: Stability Versus Speciation

Zhao, Shaying; Shetty, Jyoti; Hou, Lihua; Delcher, Arthur L.; Zhu, Baoli; Osoegawa, Kazutoyo; Jong, Pieter J. de; Nierman, William C.; Strausberg, Robert L.; Fraser, Claire M.

doi:10.1101/gr.2663304

Cited by 134 publications

(115 citation statements)

References 61 publications

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“…Karyotypic methods for detecting inversions are reasonably powerful in flies because of the high resolution provided by salivary chromosomes, but are much less effective in almost all other groups of organisms. Sequence-based comparisons of fixed inversion differences between species are just now becoming possible, and early results do indeed suggest that there have been more inversions fixed than had been previously thought (Bourque et al 2004;Zhao et al 2004;Mikkelsen et al 2005). Several biological factors may limit how often the local adaptation mechanism can come into play.…”

Section: Discussionmentioning

confidence: 97%

Chromosome Inversions, Local Adaptation and Speciation

2006

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We study the evolution of inversions that capture locally adapted alleles when two populations are exchanging migrants or hybridizing. By suppressing recombination between the loci, a new inversion can spread. Neither drift nor coadaptation between the alleles (epistasis) is needed, so this local adaptation mechanism may apply to a broader range of genetic and demographic situations than alternative hypotheses that have been widely discussed. The mechanism can explain many features observed in inversion systems. It will drive an inversion to high frequency if there is no countervailing force, which could explain fixed differences observed between populations and species. An inversion can be stabilized at an intermediate frequency if it also happens to capture one or more deleterious recessive mutations, which could explain polymorphisms that are common in some species. This polymorphism can cycle in frequency with the changing selective advantage of the locally favored alleles. The mechanism can establish underdominant inversions that decrease heterokaryotype fitness by several percent if the cause of fitness loss is structural, while if the cause is genic there is no limit to the strength of underdominance that can result. The mechanism is expected to cause loci responsible for adaptive species-specific differences to map to inversions, as seen in recent QTL studies. We discuss data that support the hypothesis, review other mechanisms for inversion evolution, and suggest possible tests.

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Section: Discussionmentioning

confidence: 97%

Chromosome Inversions, Local Adaptation and Speciation

2006

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“…Since the approximate distance between these matches is known, these BAC clones are more informative in comparative studies to identify putative orthologous regions (Zhao et al 2001(Zhao et al , 2004. According to the positions of the two paired-end matches in the rice genome, these BACs can be placed into six different classes (Fig.…”

Section: Resultsmentioning

confidence: 99%

Structural characterization of Brachypodium genome and its syntenic relationship with rice and wheat

et al. 2009

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Brachypodium distachyon (Brachypodium) has been recently recognized as an emerging model system for both comparative and functional genomics in grass species. In this study, 55,221 repeat masked Brachypodium BAC end sequences (BES) were used for comparative analysis against the 12 rice pseudomolecules. The analysis revealed that *26.4% of BES have significant matches with the rice genome and 82.4% of the matches were homologous to known genes. Further analysis of paired-end BES and *1.0 Mb sequences from nine selected BACs proved to be useful in revealing conserved regions and regions that have undergone considerable genomic changes. Differential gene amplification, insertions/deletions and inversions appeared to be the common evolutionary events that caused variations of microcolinearity at different orthologous genomic regions. It was found that *17% of genes in the two genomes are not colinear in the orthologous regions. Analysis of BAC sequences also revealed higher gene density (*9 kb/gene) and lower repeat DNA content (*13.1%) in Brachypodium when compared to the orthologous rice regions, consistent with the smaller size of the Brachypodium genome. The 119 annotated Brachypodium genes were BLASTN compared against the wheat EST database and deletion bin mapped wheat ESTs. About 77% of the genes retrieved significant matches in the EST database, while 9.2% matched to the bin mapped ESTs. In some cases, genes in single Brachypodium BACs matched to multiple ESTs that were mapped to the same deletion bins, suggesting that the Brachypodium genome will be useful for ordering wheat ESTs within the deletion bins and developing specific markers at targeted regions in the wheat genome.

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“…Supplement L compares MGRA and inferCARs on simulated data and illustrates that MGRA generates more accurate ancestral reconstructions for all choices of parameters. However, analyzing all these tools on simulated data may generate over-optimistic results since RBM does not reflect the realities of mammalian evolution (Bailey et al 2004;van der Wind et al 2004;Zhao et al 2004;Murphy et al 2005;Webber and Kikuta et al 2007;Mehan et al 2007). We therefore decided to analyze the differences between MGRA and inferCARs reconstructions and to further track evidence for each such difference in a case-by-case fashion.…”

Section: Benchmarking Mgramentioning

confidence: 99%

Breakpoint graphs and ancestral genome reconstructions

Alekseyev¹,

Pevzner²

2009

Genome Res.

121

130

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Recently completed whole-genome sequencing projects marked the transition from gene-based phylogenetic studies to phylogenomics analysis of entire genomes. We developed an algorithm MGRA for reconstructing ancestral genomes and used it to study the rearrangement history of seven mammalian genomes: human, chimpanzee, macaque, mouse, rat, dog, and opossum. MGRA relies on the notion of the multiple breakpoint graphs to overcome some limitations of the existing approaches to ancestral genome reconstructions. MGRA also generates the rearrangement-based characters guiding the phylogenetic tree reconstruction when the phylogeny is unknown.

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Human, Mouse, and Rat Genome Large-Scale Rearrangements: Stability Versus Speciation

Cited by 134 publications

References 61 publications

Chromosome Inversions, Local Adaptation and Speciation

Chromosome Inversions, Local Adaptation and Speciation

Structural characterization of Brachypodium genome and its syntenic relationship with rice and wheat

Breakpoint graphs and ancestral genome reconstructions

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