Homology-Driven Assembly of a Sequence-Ready Mouse BAC Contig Map Spanning Regions Related to the 46-Mb Gene-Rich Euchromatic Segments of Human Chromosome 19

Kim, Joomyeong; Gordon, Laurie; Dehal, Paramvir; Badri, Hummy; Christensen, Mari; Groza, Matthew; Ha, Chi; Hammond, Sha S.; Vargas, Michelle; Wehri, Edward; Wagner, Mark C.; Olsen, Anne S.; Stubbs, Lisa

doi:10.1006/geno.2001.6521

Cited by 34 publications

(16 citation statements)

References 26 publications

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“…We focused first on regions that have undergone rearrangements in more recent evolutionary time by examining human-mouse (H/M) EBRs. Most HSA19p H/M rearrangements correspond to interchromosomal translocation events that occurred specifically in the rodent lineage Kim et al 2001). GGA28 sequence is informative for 9 HSBs flanking one or both sides of 6 H/M major synteny breaks (Supplemental Fig.…”

Section: Human-mouse Synteny Breaks Provide Evidence For Breakpoint Rmentioning

confidence: 99%

“…To screen three libraries, one from G. gallus domesticus ‫ן5.5(‬ Wageningen chicken BAC library, Crooijmans et al 2000) and two from G. gallus gallus ‫ן8.4(‬ Texas A&M chicken BAC library, segment 1, Ren et al 2003; ‫ן11‬ CHORI-261, BACPAC Resources, http://bacpac.chori.org/ chicken261.htm), 32 P-labeled DNA probes were hybridized in pools of 20 to high-density filters, then rescreened individually as previously described (Ashworth et al 1995;Ross et al 1999;Kim et al 2001). BACs were restriction fingerprinted and manually assembled into maps (Kim et al 2001;Grimwood et al 2004, Supplemental Methods). Finally, isolated islands of gene-poor GGA11 were joined, and the telomeric end of GGA28 was extended, after identifying spanning BAC clones from the Washington University fpc fingerprints (Wallis et al 2004).…”

Section: Bac Mappingmentioning

confidence: 99%

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Comparative analysis of chicken chromosome 28 provides new clues to the evolutionary fragility of gene-rich vertebrate regions

Gordon¹,

Yang²,

Tran-Gyamfi³

et al. 2007

Genome Res.

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The chicken genome draft sequence has provided a valuable resource for studies of an important agricultural and experimental model species and an important data set for comparative analysis. However, some of the most gene-rich segments are missing from chicken genome draft assemblies, limiting the analysis of a substantial number of genes and preventing a closer look at regions that are especially prone to syntenic rearrangements. To facilitate the functional and evolutionary analysis of one especially gene-rich, rearrangement-prone genomic region, we analyzed sequence from BAC clones spanning chicken microchromosome GGA28; as a complement we also analyzed a gene-sparse, stable region from GGA11. In these two regions we documented the conservation and lineage-specific gain and loss of protein-coding genes and precisely mapped the locations of 31 major human-chicken syntenic breakpoints. Altogether, we identified 72 lineage-specific genes, many of which are found at or near syntenic breaks, implicating evolutionary breakpoint regions as major sites of genetic innovation and change. Twenty-two of the 31 breakpoint regions have been reused repeatedly as rearrangement breakpoints in vertebrate evolution. Compared with stable GC-matched regions, GGA28 is highly enriched in CpG islands, as are break-prone intervals identified elsewhere in the chicken genome; evolutionary breakpoints are further enriched in GC content and CpG islands, highlighting a potential role for these features in genome instability. These data support the hypothesis that chromosome rearrangements have not occurred randomly over the course of vertebrate evolution but are focused preferentially within "fragile" regions with unusual DNA sequence characteristics.

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Section: Human-mouse Synteny Breaks Provide Evidence For Breakpoint Rmentioning

confidence: 99%

Section: Bac Mappingmentioning

confidence: 99%

Comparative analysis of chicken chromosome 28 provides new clues to the evolutionary fragility of gene-rich vertebrate regions

Gordon¹,

Yang²,

Tran-Gyamfi³

et al. 2007

Genome Res.

Self Cite

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“…Comparative sequence analysis of the MMU7 and MMU8 regions (identified by cytogenetic studies as harboring duplicated segments) was facilitated by extensive data generated by mapping and sequencing of the syntenic regions of HSA19 Kim et al 2001). In particular, these regions were scrutinized for the presence of dpA (details are available as supplementary material at www.genome.…”

Section: Characterization Of the Duplicated Segments On Mmu5 And Mmu6mentioning

confidence: 99%

Pericentromeric Duplications in the Laboratory Mouse

et al. 2002

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Duplications have long been postulated to be an important mechanism by which genomes evolve. Interspecies genomic comparisons are one method by which the origin and molecular mechanism of duplications can be inferred. By comparative mapping in human, mouse, and rat, we previously found evidence for a recent chromosome-fission event that occurred in the mouse lineage. Cytogenetic mapping revealed that the genomic segments flanking the fission site appeared to be duplicated, with copies residing near the centromere of multiple mouse chromosomes. Here we report the mapping and sequencing of the regions of mouse chromosomes 5 and 6 involved in this chromosome-fission event as well as the results of comparative sequence analysis with the orthologous human and rat genomic regions. Our data indicate that the duplications associated with mouse chromosomes 5 and 6 are recent and that the resulting duplicated segments share significant sequence similarity with a series of regions near the centromeres of the mouse chromosomes previously identified by cytogenetic mapping. We also identified pericentromeric duplicated segments shared between mouse chromosomes 5 and 1. Finally, novel mouse satellite sequences as well as putative chimeric transcripts were found to be associated with the duplicated segments. Together, these findings demonstrate that pericentromeric duplications are not restricted to primates and may be a common mechanism for genome evolution in mammals.

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“…Specifically, the locations and sequences of genes in the human genome can be used to guide map construction in other species through the computational detection of or-thologous sequences. This has proven to be effective for both long-range comparative mapping and the construction of sequence-ready BAC contig maps for targeted regions of interest Kim et al 2001). For example, human genomic sequence can be used to identify orthologous mouse sequences, which in turn can be used to design small, oligonucleotide-based "overgo" probes (Vollrath 1999) for use in isolating orthologous mouse BACs.…”

mentioning

confidence: 99%

Parallel Construction of Orthologous Sequence-Ready Clone Contig Maps in Multiple Species

Thomas

Prasad²,

Summers³

et al. 2002

Genome Res.

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Comparison is a fundamental tool for analyzing DNA sequence. Interspecies sequence comparison is particularly powerful for inferring genome function and is based on the simple premise that conserved sequences are likely to be important. Thus, the comparison of a genomic sequence with its orthologous counterpart from another species is increasingly becoming an integral component of genome analysis. In ideal situations, such comparisons are performed with orthologous sequences from multiple species. To facilitate multispecies comparative sequence analysis, a robust and scalable strategy for simultaneously constructing sequence-ready bacterial artificial chromosome (BAC) contig maps from targeted genomic regions has been developed. Central to this approach is the generation and utilization of "universal" oligonucleotide-based hybridization probes ("overgo" probes), which are designed from sequences that are highly conserved between distantly related species. Large collections of these probes are used en masse to screen BAC libraries from multiple species in parallel, with the isolated clones assembled into physical contig maps. To validate the effectiveness of this strategy, efforts were focused on the construction of BAC-based physical maps from multiple mammalian species (chimpanzee, baboon, cat, dog, cow, and pig). Using available human and mouse genomic sequence and a newly developed computer program (soop) to design the requisite probes, sequence-ready maps were constructed in all species for a series of targeted regions totaling ∼16 Mb in the human genome. The described approach can be used to facilitate the multispecies comparative sequencing of targeted genomic regions and can be adapted for constructing BAC contig maps in other vertebrates.

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Homology-Driven Assembly of a Sequence-Ready Mouse BAC Contig Map Spanning Regions Related to the 46-Mb Gene-Rich Euchromatic Segments of Human Chromosome 19

Cited by 34 publications

References 26 publications

Comparative analysis of chicken chromosome 28 provides new clues to the evolutionary fragility of gene-rich vertebrate regions

Comparative analysis of chicken chromosome 28 provides new clues to the evolutionary fragility of gene-rich vertebrate regions

Pericentromeric Duplications in the Laboratory Mouse

Parallel Construction of Orthologous Sequence-Ready Clone Contig Maps in Multiple Species

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