A Comparison of Whole-Genome Shotgun-Derived Mouse Chromosome 16 and the Human Genome

The high degree of similarity between the mouse and human genomes is demonstrated through analysis of the sequence of mouse chromosome 16 (Mmu 16), which was obtained as part of a whole-genome shotgun assembly of the mouse genome. The mouse genome is about 10% smaller than the human genome, owing to a lower repetitive DNA content. Comparison of the structure and protein-coding potential of Mmu 16 with that of the homologous segments of the human genome identifies regions of conserved synteny with human chromosomes (Hsa) 3, 8, 12, 16, 21, and 22. Gene content and order are highly conserved between Mmu 16 and the syntenic blocks of the human genome. Of the 731 predicted genes on Mmu 16, 509 align with orthologs on the corresponding portions of the human genome, 44 are likely paralogous to these genes, and 164 genes have homologs elsewhere in the human genome; there are 14 genes for which we could find no human counterpart.

William H. Majoros | Randall A. Bolanos | Ashwinikumar K. Naik | Kimberly A. Parker | Xiangqun H. Zheng | S. Salzberg | M. Adams | E. Myers | Z. Gu | K. Reinert | Peter W. Li | A. Halpern | A. Delcher | R. Mural | G. Sutton | S. Kravitz | K. Beeson | T. McIntosh | K. Remington | Y. Rogers | J. Venter | Hamilton O. Smith | S. Yooseph | J. Gocayne | G. L. Miklos | A. Głodek | J. Scott | R. Holt | C. Xiao | M. Yandell | D. Fasulo | G. Subramanian | Quan Chen | P. Guan | P. Amanatides | M. Barnstead | Soo H. Chin | C. Evans | S. Ferriera | C. Fosler | C. Kraft | C. Pfannkoch | Cynthia D. Sitter | J. Wortman | A. Gabrielian | J. Miller | D. Huson | D. Rusch | J. Zaveri | C. Mobarry | I. Dew | M. Flanigan | R. Bolanos | F. Lu | D. Nusskern | B. Shue | F. Zhong | N. Milshina | E. Venter | H. An | A. Center | C. Dahlke | L. Davenport | S. Dietz | K. Dodson | L. Doup | C. Evangelista | T. J. Heiman | J. Houck | T. Howland | C. Ibegwam | M. Jalali | C. Kodira | Z. Lai | Y. Lei | A. Levitsky | G. Merkulov | M. Moy | B. Murphy | K. Nelson | V. Puri | R. Strong | W. Zhong | Qing Zhang | Lin Chen | Joe Nadeau | Kendra Biddick | Kabir Chaturvedi | Z. Deng | Weiniu Gan | Rui-Ru Ji | Z. Ke | Zhenya Li | Jiayin Li | Jingtao Sun | Aihui Wang | Xin Wang | Jian Wang | R. Wides | A. Yao | J. Ye | Qi Zhao | Liansheng Zheng | Shiaoping C. Zhu | F. Ali | Amy L. Carver | Mingbo Cheng | S. Danaher | R. Desilets | Andres Gluecksmann | Britney Hart | Jason Haynes | C. Haynes | S. Hladun | Jeffery E. Johnson | Felecia Mann | David May | Linda P Moy | Eric C. Pratts | Hina-Ur-Razaq Qureshi | Matt Reardon | Deanna L. Romblad | Richard Scott | Erin Stewart | Ellen Suh | R. Thomas | Ni Ni Tint | Gary Wang | S. Williams | Monica S. Williams | Sandra M. Windsor | Keriellen Wolfe | David R. Allen | Parris Caulk | My D. Coyne | Michael Donnelly | H. Gire | Barry Gropman | Xiangjun Liu | John Lopez | Daniel S. Ma | Sean Murphy | M. Newman | Marc Nodell | Robert Sanders | Thomas J. Smith | A. Sprague | Mei Wang | Mitchell M. Wu | Ashley Xia | R. Qi | Xianghe Yan | Zhen-Yuan Wang | Chia-Chien Chiang | K. Woodford | D. Tompkins | D. Jacob | Ke Li | Danita Baldwin-Pitts | Shuang Cai | M. Carnes | Yen-Hui Chen | M. Crowder | Patrick Dullaghan | Jonathan Gray | Jeffery Hoover | D. Johns | Leslie D. Kline | Steven MacCawley | Anand Magoon | S. Mehta | Zubeda Nuri | A. Prudhomme | John C. Raley | Megan A. Regier | J. Schutz | M. Smallwood | Karena Sylvester | C. Tsonis | George S Wang | Alison Yao | A. Glodek | W. Majoros | D. May | D. Allen | Matthew Newman | Feroze Ali | Yen‐Hui Chen | Raymond Desilets | Harold C. Gire | Linda Moy | Sherita M. Williams | M. Regier | George Wang | Richard T. Scott | G. Miklos | Fu Lu | Lisa D Stephenson | Mary Barnstead | Shibu Yooseph | Chunlin Xiao

[1]  Cynthia Friedman,et al.  Different evolutionary processes shaped the mouse and human olfactory receptor gene families. , 2002, Human molecular genetics.

[2]  S. Firestein,et al.  The olfactory receptor gene superfamily of the mouse , 2002, Nature Neuroscience.

[3]  N. Grishin,et al.  Evolution of the regulators of G-protein signaling multigene family in mouse and human. , 2002, Genomics.

[4]  Sudhir Kumar,et al.  Mutation rates in mammalian genomes , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[5]  K. Lindblad-Toh,et al.  Progress in sequencing the mouse genome , 2001, Genesis.

[6]  S. P. Fodor,et al.  Evolutionarily conserved sequences on human chromosome 21. , 2001, Genome research.

[7]  W. Wasserman,et al.  A predictive model for regulatory sequences directing liver-specific transcription. , 2001, Genome research.

[8]  D. Gurwitz,et al.  Animal models and human genome diversity: the pitfalls of inbred mice. , 2001, Drug discovery today.

[9]  Paul Richardson,et al.  Human Chromosome 19 and Related Regions in Mouse: Conservative and Lineage-Specific Evolution , 2001, Science.

[10]  B. Birren,et al.  Analysis of the cat eye syndrome critical region in humans and the region of conserved synteny in mice: a search for candidate genes at or near the human chromosome 22 pericentromere. , 2001, Genome research.

[11]  T. Wiltshire,et al.  Use of comparative physical and sequence mapping to annotate mouse chromosome 16 and human chromosome 21. , 2001, Genomics.

[12]  Timothy B. Stockwell,et al.  The Sequence of the Human Genome , 2001, Science.

[13]  J. V. Moran,et al.  Initial sequencing and analysis of the human genome. , 2001, Nature.

[14]  P. Fontanillas,et al.  Developmental stability in house mice heterozygous for single Robertsonian fusions. , 2001, The Journal of heredity.

[15]  W. Miller,et al.  Divergent human and mouse orthologs of a novel gene (WBSCR15/Wbscr15) reside within the genomic interval commonly deleted in Williams syndrome , 2000, Cytogenetic and Genome Research.

[16]  C. Lawrence,et al.  Human-mouse genome comparisons to locate regulatory sites , 2000, Nature Genetics.

[17]  Roderic Guigó,et al.  Gff2ps: Visualizing Genomic Annotations , 2000, Bioinform..

[18]  W. Miller,et al.  Comparative genome sequence analysis of the Bpa/Str region in mouse and Man. , 2000, Genome research.

[19]  M. Hattori,et al.  The DNA sequence of human chromosome 21 , 2000, Nature.

[20]  V. Solovyev,et al.  Ab initio gene finding in Drosophila genomic DNA. , 2000, Genome research.

[21]  G M Rubin,et al.  A brief history of Drosophila's contributions to genome research. , 2000, Science.

[22]  Stephen M. Mount,et al.  The genome sequence of Drosophila melanogaster. , 2000, Science.

[23]  B. Roe,et al.  Comparative sequence analysis of 634 kb of the mouse chromosome 16 region of conserved synteny with the human velocardiofacial syndrome region on chromosome 22q11.2. , 2000, Genomics.

[24]  Eugene W. Myers,et al.  A whole-genome assembly of Drosophila. , 2000, Science.

[25]  Donna R. Maglott,et al.  NCBI's LocusLink and RefSeq , 2000, Nucleic Acids Res..

[26]  Donna K. Slonim,et al.  Radiation hybrid map of the mouse genome , 1999, Nature Genetics.

[27]  E. Simpson,et al.  Revised nomenclature for strain 129 mice , 1999, Mammalian Genome.

[28]  B. Roe,et al.  Sequence-ready physical map of the mouse Chromosome 16 region with conserved synteny to the human Velocardiofacial syndrome region on 22q11.2 , 1999, Mammalian Genome.

[29]  R J Mural,et al.  Current status of computational gene finding: a perspective. , 1999, Methods in enzymology.

[30]  S. Salzberg,et al.  Alignment of whole genomes. , 1999, Nucleic acids research.

[31]  T. Dragani,et al.  The gene encoding the transcriptional repressor BERF-1 maps to a region of conserved synteny on mouse chromosome 16 and human chromosome 3 and a related pseudogene maps to mouse chromosome 8 , 1999, Cytogenetic and Genome Research.

[32]  M. Boguski,et al.  Evolutionary parameters of the transcribed mammalian genome: an analysis of 2,820 orthologous rodent and human sequences. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[33]  C. Epstein,et al.  Ts1Cje, a partial trisomy 16 mouse model for Down syndrome, exhibits learning and behavioral abnormalities. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[34]  J. Yu,et al.  Stch maps to mouse chromosome 16, extending the conserved synteny with human chromosome 21. , 1998, Genomics.

[35]  Muriel T. Davisson,et al.  Genetic variation among 129 substrains and its importance for targeted mutagenesis in mice , 1997, Nature Genetics.

[36]  S. Karlin,et al.  Prediction of complete gene structures in human genomic DNA. , 1997, Journal of molecular biology.

[37]  D. Sankoff,et al.  Landmarks in the Rosetta Stone of mammalian comparative maps , 1997, Nature Genetics.

[38]  G Bernardi,et al.  The gene distribution of the human genome. , 1996, Gene.

[39]  E. Uberbacher,et al.  Discovering and understanding genes in human DNA sequence using GRAIL. , 1996, Methods in enzymology.

[40]  A. Lengeling,et al.  Chloride channel 2 gene (Clc2) maps to chromosome 16 of the mouse, extending a region of conserved synteny with human chromosome 3q. , 1995, Genetical research.

[41]  R. Bronson,et al.  A mouse model for Down syndrome exhibits learning and behaviour deficits , 1995, Nature Genetics.

[42]  B. Koop,et al.  Human and rodent DNA sequence comparisons: a mosaic model of genomic evolution. , 1995, Trends in genetics : TIG.

[43]  Ping Liu,et al.  Smooth muscle myosin heavy chain locus (MYH11) maps to 16p13.13-p13.12 and establishes a new region of conserved synteny between human 16p and mouse 16. , 1993, Genomics.

[44]  E. Myers,et al.  Basic local alignment search tool. , 1990, Journal of molecular biology.

[45]  J. Nadeau,et al.  Lengths of chromosomal segments conserved since divergence of man and mouse. , 1984, Proceedings of the National Academy of Sciences of the United States of America.

[46]  G. Bernardi,et al.  The major components of the mouse and human genomes. 2. Reassociation kinetics. , 1981, European journal of biochemistry.

[47]  R. Britten,et al.  Repetitive and Non-Repetitive DNA Sequences and a Speculation on the Origins of Evolutionary Novelty , 1971, The Quarterly Review of Biology.