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Methods: Physical map-assisted whole-genome shotgun sequence assemblies
- René L. Warren,
- Dmitry Varabei,
- Darren Platt,
- Xiaoqiu Huang,
- David Messina,
- Shiaw-Pyng Yang,
- James W. Kronstad,
- Martin Krzywinski,
- Wesley C. Warren,
- John W. Wallis,
- LaDeana W. Hillier,
- Asif T. Chinwalla,
- Jacqueline E. Schein,
- Asim S. Siddiqui,
- Marco A. Marra,
- Richard K. Wilson,
- and Steven J.M. Jones
Genome Res. June 2006 16: 768-775; doi:10.1101/gr.5090606
....A. , Holt R.A. , et al. ( 2001 ) The sequence of the human . Science 291 : 1304 – 1351 . ↵ Wallis J.W. , Aerts J. , Groenen M.A. , Crooijmans R.P. , Layman D. , Graves T.A. , Scheer D.E. , Kremitzki C. , Fedele M.J. , Mudd N.K. , et al. ( 2004 ) A physical map of the chicken . Nature 432 : 761 – 764...
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RESOURCE: A BAC- and BIBAC-Based Physical Map of the Soybean Genome
- Chengcang Wu,
- Shuku Sun,
- Padmavathi Nimmakayala,
- Felipe A. Santos,
- Khalid Meksem,
- Rachael Springman,
- Kejiao Ding,
- David A. Lightfoot,
- and Hong-Bin Zhang
Genome Res. February 2004 14: 319-326; Published in Advance January 12, 2004, doi:10.1101/gr.1405004
...map. Nat. Genet. 18 : 345 -349. ↵ Ren, C., Lee, M.-K., Yan, B., Ding, K., Cox, B., Romanov, M.N., Price, J.A., Dodgson, J.B., and Zhang, H.-B. 2003 . A BAC-based physical map of the chicken . Genome Res. 13 : 2754 -2758. ↵ Salimath, S.S. and Bhattacharyya, M.K. 1999 . Generation of a soybean BAC...
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Resource: Upgrading short-read animal genome assemblies to chromosome level using comparative genomics and a universal probe set
- Joana Damas,
- Rebecca O'Connor,
- Marta Farré,
- Vasileios Panagiotis E. Lenis,
- Henry J. Martell,
- Anjali Mandawala,
- Katie Fowler,
- Sunitha Joseph,
- Martin T. Swain,
- Darren K. Griffin,
- and Denis M. Larkin
Genome Res. May 2017 27: 875-884; Published in Advance November 30, 2016, doi:10.1101/gr.213660.116
...chromosome coordinates using the UCSC Genome Browser liftOver tool (Kent et al. 2002) with a minimum ratio of remapped bases >0.1. For each BAC clone mapped to the chicken chromosomes, various genomic features selected to estimate the probability of clones to hybridizewithmetaphase chromosomes in distant...
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LETTER: Comparative analysis of chicken chromosome 28 provides new clues to the evolutionary fragility of gene-rich vertebrate regions
- Laurie Gordon,
- Shan Yang,
- Mary Tran-Gyamfi,
- Dan Baggott,
- Mari Christensen,
- Aaron Hamilton,
- Richard Crooijmans,
- Martien Groenen,
- Susan Lucas,
- Ivan Ovcharenko,
- and Lisa Stubbs
Genome Res. November 2007 17: 1603-1613; Published in Advance October 5, 2007, doi:10.1101/gr.6775107
...Generating BAC-based chicken sequence Contiguous BAC maps spanning GGA28- and HSA19q-related regions of GGA11 We isolated overlapping BAC clones from libraries derived from DNA of red jungle fowl (JF), G. gallus gallus , and the White Leghorn (WL) domestic strain, G. gallus domesticus , using probes designed...
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PERSPECTIVE: The opossum genome: Insights and opportunities from an alternative mammal
- Paul B. Samollow
Genome Res. August 2008 18: 1199-1215; doi:10.1101/gr.065326.107
...with the general structural conservatism exhibited by metatherian chromosomes in general (see following section). Chromosome structure and evolution Comparison of synteny relationships in the opossum with those of human, dog, mouse, rat, and chicken enabled construction of a five-way multispecies synteny map...
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RESOURCE: The Oryza bacterial artificial chromosome library resource: Construction and analysis of 12 deep-coverage large-insert BAC libraries that represent the 10 genome types of the genus Oryza
- Jetty S.S. Ammiraju,
- Meizhong Luo,
- José L. Goicoechea,
- Wenming Wang,
- Dave Kudrna,
- Christopher Mueller,
- Jayson Talag,
- HyeRan Kim,
- Nicholas B. Sisneros,
- Barbara Blackmon,
- Eric Fang,
- Jeffery B. Tomkins,
- Darshan Brar,
- David MacKill,
- Susan McCouch,
- Nori Kurata,
- Georgina Lambert,
- David W. Galbraith,
- K. Arumuganathan,
- Kiran Rao,
- Jason G. Walling,
- Navdeep Gill,
- Yeisoo Yu,
- Phillip SanMiguel,
- Carol Soderlund,
- Scott Jackson,
- and Rod A. Wing
Genome Res. January 2006 16: 140-147; Published in Advance December 12, 2005, doi:10.1101/gr.3766306
...experimental system for the genus Oryza by developing comparative BAC-based physical maps of all 10 types of the genus to study evolution, organization, domestication, gene regulatory networks, and crop improvement ( Wing et al. 2005 ). As a first step toward achieving this goal, we report the construction...
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LETTER: Integration of Cot Analysis, DNA Cloning, and High-Throughput Sequencing Facilitates Genome Characterization and Gene Discovery
- Daniel G. Peterson,
- Stefan R. Schulze,
- Erica B. Sciara,
- Scott A. Lee,
- John E. Bowers,
- Alexander Nagel,
- Ning Jiang,
- Deanne C. Tibbitts,
- Susan R. Wessler,
- and Andrew H. Paterson
Genome Res. May 1, 2002 12: 795-807; Published in Advance April 12, 2002, doi:10.1101/gr.226102
..., (4) Cot clones can be used to augment the information content of both molecular and physical maps, and (5) sequencing of clones from Cot libraries may represent a means by which the diversity of sequences found in a can be efficiently “captured”. Effectiveness of Cot-Based Cloning The three Cot...
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Research: Positive selection in noncoding genomic regions of vocal learning birds is associated with genes implicated in vocal learning and speech functions in humans
- James A. Cahill,
- Joel Armstrong,
- Alden Deran,
- Carolyn J. Khoury,
- Benedict Paten,
- David Haussler,
- and Erich D. Jarvis
Genome Res. November 2021 31: 2035-2049; Published in Advance October 19, 2021, doi:10.1101/gr.275989.121
...of ∼70% of the best annotated , the chicken, to most other species (28 of the remaining 32 species) (Fig. 2A,B). This is a more than twofold improvement over previous avian whole- comparative studies (Zhang et al. 2014) that recovered 31.6% of the chicken in the alignment with the same proportion...
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Methods: Efficient high-resolution deletion discovery in Caenorhabditis elegans by array comparative genomic hybridization
- Jason S. Maydan,
- Stephane Flibotte,
- Mark L. Edgley,
- Joanne Lau,
- Rebecca R. Selzer,
- Todd A. Richmond,
- Nathan J. Pofahl,
- James H. Thomas,
- and Donald G. Moerman
Genome Res. March 2007 17: 337-347; Published in Advance January 31, 2007, doi:10.1101/gr.5690307
..., isolated in England, to the wild-type strain CB4856 that was isolated on one of the Hawaiian Islands and to a strain isolated on the island of Madeira (JU258). We chose the Hawaiian strain because it is a popular strain for single nucleotide polymorphism (SNP) mapping, as it has many sequence variations...
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LETTER: An intermediate grade of finished genomic sequence suitable for comparative analyses
- Robert W. Blakesley,
- Nancy F. Hansen,
- James C. Mullikin,
- Pamela J. Thomas,
- Jennifer C. McDowell,
- Baishali Maskeri,
- Alice C. Young,
- Beatrice Benjamin,
- Shelise Y. Brooks,
- Bradley I. Coleman,
- Jyoti Gupta,
- Shi-Ling Ho,
- Eric M. Karlins,
- Quino L. Maduro,
- Sirintorn Stantripop,
- Cyrus Tsurgeon,
- Jennifer L. Vogt,
- Michelle A. Walker,
- Catherine A. Masiello,
- Xiaobin Guan,
- NISC Comparative Sequencing Program,
- Gerard G. Bouffard,
- and Eric D. Green
Genome Res. November 2004 14: 2235-2244; Published in Advance October 12, 2004, doi:10.1101/gr.2648404
...examined the sequence of the large genomic interval encompassing the CFTR gene ( Thomas et al. 2003 )—the same region from which virtually all of the above-analyzed BACs were derived—in four available whole- sequence assemblies (mouse, rat, chicken, and chimpanzee). In all four assemblies, the greater CFTR...

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