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Start Over Author "Chow, William" Journal genome research
6 results on '"Chow, William"'

1. Repeat associated mechanisms of genome evolution and function revealed by the Mus caroli and Mus pahari genomes

Author

Thybert, David, primary, Roller, Maša, additional, Navarro, Fábio C.P., additional, Fiddes, Ian, additional, Streeter, Ian, additional, Feig, Christine, additional, Martin-Galvez, David, additional, Kolmogorov, Mikhail, additional, Janoušek, Václav, additional, Akanni, Wasiu, additional, Aken, Bronwen, additional, Aldridge, Sarah, additional, Chakrapani, Varshith, additional, Chow, William, additional, Clarke, Laura, additional, Cummins, Carla, additional, Doran, Anthony, additional, Dunn, Matthew, additional, Goodstadt, Leo, additional, Howe, Kerstin, additional, Howell, Matthew, additional, Josselin, Ambre-Aurore, additional, Karn, Robert C., additional, Laukaitis, Christina M., additional, Jingtao, Lilue, additional, Martin, Fergal, additional, Muffato, Matthieu, additional, Nachtweide, Stefanie, additional, Quail, Michael A., additional, Sisu, Cristina, additional, Stanke, Mario, additional, Stefflova, Klara, additional, Van Oosterhout, Cock, additional, Veyrunes, Frederic, additional, Ward, Ben, additional, Yang, Fengtang, additional, Yazdanifar, Golbahar, additional, Zadissa, Amonida, additional, Adams, David J., additional, Brazma, Alvis, additional, Gerstein, Mark, additional, Paten, Benedict, additional, Pham, Son, additional, Keane, Thomas M., additional, Odom, Duncan T., additional, and Flicek, Paul, additional

Published
2018
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2. Evaluation of GRCh38 and de novo haploid genome assemblies demonstrates the enduring quality of the reference assembly

Author

Schneider, Valerie A., primary, Graves-Lindsay, Tina, additional, Howe, Kerstin, additional, Bouk, Nathan, additional, Chen, Hsiu-Chuan, additional, Kitts, Paul A., additional, Murphy, Terence D., additional, Pruitt, Kim D., additional, Thibaud-Nissen, Françoise, additional, Albracht, Derek, additional, Fulton, Robert S., additional, Kremitzki, Milinn, additional, Magrini, Vincent, additional, Markovic, Chris, additional, McGrath, Sean, additional, Steinberg, Karyn Meltz, additional, Auger, Kate, additional, Chow, William, additional, Collins, Joanna, additional, Harden, Glenn, additional, Hubbard, Timothy, additional, Pelan, Sarah, additional, Simpson, Jared T., additional, Threadgold, Glen, additional, Torrance, James, additional, Wood, Jonathan M., additional, Clarke, Laura, additional, Koren, Sergey, additional, Boitano, Matthew, additional, Peluso, Paul, additional, Li, Heng, additional, Chin, Chen-Shan, additional, Phillippy, Adam M., additional, Durbin, Richard, additional, Wilson, Richard K., additional, Flicek, Paul, additional, Eichler, Evan E., additional, and Church, Deanna M., additional

Published
2017
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3. The pig X and Y Chromosomes: structure, sequence, and evolution

Author

Skinner, Benjamin M., primary, Sargent, Carole A., additional, Churcher, Carol, additional, Hunt, Toby, additional, Herrero, Javier, additional, Loveland, Jane E., additional, Dunn, Matt, additional, Louzada, Sandra, additional, Fu, Beiyuan, additional, Chow, William, additional, Gilbert, James, additional, Austin-Guest, Siobhan, additional, Beal, Kathryn, additional, Carvalho-Silva, Denise, additional, Cheng, William, additional, Gordon, Daria, additional, Grafham, Darren, additional, Hardy, Matt, additional, Harley, Jo, additional, Hauser, Heidi, additional, Howden, Philip, additional, Howe, Kerstin, additional, Lachani, Kim, additional, Ellis, Peter J.I., additional, Kelly, Daniel, additional, Kerry, Giselle, additional, Kerwin, James, additional, Ng, Bee Ling, additional, Threadgold, Glen, additional, Wileman, Thomas, additional, Wood, Jonathan M.D., additional, Yang, Fengtang, additional, Harrow, Jen, additional, Affara, Nabeel A., additional, and Tyler-Smith, Chris, additional

Published
2015
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4. Repeat associated mechanisms of genome evolution and function revealed by the Mus caroliand Mus paharigenomes

Author

Thybert, David, Roller, Maša, Navarro, Fšábio C.P., Fiddes, Ian, Streeter, Ian, Feig, Christine, Martin-Galvez, David, Kolmogorov, Mikhail, Janoušáášek, Všááclav, Akanni, Wasiu, Aken, Bronwen, Aldridge, Sarah, Chakrapani, Varshith, Chow, William, Clarke, Laura, Cummins, Carla, Doran, Anthony, Dunn, Matthew, Goodstadt, Leo, Howe, Kerstin, Howell, Matthew, Josselin, Ambre-Aurore, Karn, Robert C., Laukaitis, Christina M., Jingtao, Lilue, Martin, Fergal, Muffato, Matthieu, Nachtweide, Stefanie, Quail, Michael A., Sisu, Cristina, Stanke, Mario, Stefflova, Klara, Van Oosterhout, Cock, Veyrunes, Frederic, Ward, Ben, Yang, Fengtang, Yazdanifar, Golbahar, Zadissa, Amonida, Adams, David J., Brazma, Alvis, Gerstein, Mark, Paten, Benedict, Pham, Son, Keane, Thomas M., Odom, Duncan T., and Flicek, Paul

Abstract

Understanding the mechanisms driving lineage-specific evolution in both primates and rodents has been hindered by the lack of sister clades with a similar phylogenetic structure having high-quality genome assemblies. Here, we have created chromosome-level assemblies of the Mus caroliand Mus paharigenomes. Together with the Mus musculusand Rattus norvegicusgenomes, this set of rodent genomes is similar in divergence times to the Hominidae (human-chimpanzee-gorilla-orangutan). By comparing the evolutionary dynamics between the Muridae and Hominidae, we identified punctate events of chromosome reshuffling that shaped the ancestral karyotype of Mus musculusand Mus carolibetween 3 and 6 million yr ago, but that are absent in the Hominidae. Hominidae show between four- and sevenfold lower rates of nucleotide change and feature turnover in both neutral and functional sequences, suggesting an underlying coherence to the Muridae acceleration. Our system of matched, high-quality genome assemblies revealed how specific classes of repeats can play lineage-specific roles in related species. Recent LINE activity has remodeled protein-coding loci to a greater extent across the Muridae than the Hominidae, with functional consequences at the species level such as reproductive isolation. Furthermore, we charted a Muridae-specific retrotransposon expansion at unprecedented resolution, revealing how a single nucleotide mutation transformed a specific SINE element into an active CTCF binding site carrier specifically in Mus caroli, which resulted in thousands of novel, species-specific CTCF binding sites. Our results show that the comparison of matched phylogenetic sets of genomes will be an increasingly powerful strategy for understanding mammalian biology.

Published
2018
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5. The pig X and Y Chromosomes: structure, sequence, and evolution

Author

Skinner, Benjamin M., Sargent, Carole A., Churcher, Carol, Hunt, Toby, Herrero, Javier, Loveland, Jane E., Dunn, Matt, Louzada, Sandra, Fu, Beiyuan, Chow, William, Gilbert, James, Austin-Guest, Siobhan, Beal, Kathryn, Carvalho-Silva, Denise, Cheng, William, Gordon, Daria, Grafham, Darren, Hardy, Matt, Harley, Jo, Hauser, Heidi, Howden, Philip, Howe, Kerstin, Lachani, Kim, Ellis, Peter J.I., Kelly, Daniel, Kerry, Giselle, Kerwin, James, Ng, Bee Ling, Threadgold, Glen, Wileman, Thomas, Wood, Jonathan M.D., Yang, Fengtang, Harrow, Jen, Affara, Nabeel A., and Tyler-Smith, Chris

Abstract

We have generated an improved assembly and gene annotation of the pig X Chromosome, and a first draft assembly of the pig Y Chromosome, by sequencing BAC and fosmid clones from Duroc animals and incorporating information from optical mapping and fiber-FISH. The X Chromosome carries 1033 annotated genes, 690 of which are protein coding. Gene order closely matches that found in primates (including humans) and carnivores (including cats and dogs), which is inferred to be ancestral. Nevertheless, several protein-coding genes present on the human X Chromosome were absent from the pig, and 38 pig-specific X-chromosomal genes were annotated, 22 of which were olfactory receptors. The pig Y-specific Chromosome sequence generated here comprises 30 megabases (Mb). A 15-Mb subset of this sequence was assembled, revealing two clusters of male-specific low copy number genes, separated by an ampliconic region including the HSFYgene family, which together make up most of the short arm. Both clusters contain palindromes with high sequence identity, presumably maintained by gene conversion. Many of the ancestral X-related genes previously reported in at least one mammalian Y Chromosome are represented either as active genes or partial sequences. This sequencing project has allowed us to identify genes—both single copy and amplified—on the pig Y Chromosome, to compare the pig X and Y Chromosomes for homologous sequences, and thereby to reveal mechanisms underlying pig X and Y Chromosome evolution.

Published
2016
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6. Sequencing and analysis of 10,967 full-length cDNA clones from Xenopus laevis and Xenopus tropicalis reveals post-tetraploidization transcriptome remodeling.

Author

Morin RD, Chang E, Petrescu A, Liao N, Griffith M, Chow W, Kirkpatrick R, Butterfield YS, Young AC, Stott J, Barber S, Babakaiff R, Dickson MC, Matsuo C, Wong D, Yang GS, Smailus DE, Wetherby KD, Kwong PN, Grimwood J, Brinkley CP 3rd, Brown-John M, Reddix-Dugue ND, Mayo M, Schmutz J, Beland J, Park M, Gibson S, Olson T, Bouffard GG, Tsai M, Featherstone R, Chand S, Siddiqui AS, Jang W, Lee E, Klein SL, Blakesley RW, Zeeberg BR, Narasimhan S, Weinstein JN, Pennacchio CP, Myers RM, Green ED, Wagner L, Gerhard DS, Marra MA, Jones SJ, and Holt RA

Subjects
Animals, Evolution, Molecular, Gene Expression, Genes, Duplicate, Genome, Molecular Sequence Data, Open Reading Frames genetics, Phylogeny, Sequence Homology, Nucleic Acid, Base Sequence, Gene Library, Polyploidy, Xenopus genetics, Xenopus laevis genetics
Abstract

Sequencing of full-insert clones from full-length cDNA libraries from both Xenopus laevis and Xenopus tropicalis has been ongoing as part of the Xenopus Gene Collection Initiative. Here we present 10,967 full ORF verified cDNA clones (8049 from X. laevis and 2918 from X. tropicalis) as a community resource. Because the genome of X. laevis, but not X. tropicalis, has undergone allotetraploidization, comparison of coding sequences from these two clawed (pipid) frogs provides a unique angle for exploring the molecular evolution of duplicate genes. Within our clone set, we have identified 445 gene trios, each comprised of an allotetraploidization-derived X. laevis gene pair and their shared X. tropicalis ortholog. Pairwise dN/dS, comparisons within trios show strong evidence for purifying selection acting on all three members. However, dN/dS ratios between X. laevis gene pairs are elevated relative to their X. tropicalis ortholog. This difference is highly significant and indicates an overall relaxation of selective pressures on duplicated gene pairs. We have found that the paralogs that have been lost since the tetraploidization event are enriched for several molecular functions, but have found no such enrichment in the extant paralogs. Approximately 14% of the paralogous pairs analyzed here also show differential expression indicative of subfunctionalization.

Published
2006
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