International Mammalian Genome Society

The 16th International Mouse Genome Conference (2002)


MC Zody
Whitehead/MIT Center for Genome Research

1) Kamal M, 1) Jaffe D, 1) Butler J, 1) Gnerre S, 1) Mauceli E, 1) Karlsson E, 1) Mesirov JP, 1) Lander ES, 1) Lindblad-Toh K, 2) Mouse Genome Sequencing Consortium and Analysis Group
1) Whitehead/MIT Center for Genome Research, 2) Mouse Genome Sequencing Consortium and Analysis Group

Recognizing the importance of the mouse for biology, medicine, and comparative analysis, he Mouse Genome Sequencing Consortium (MGSC) has generated a whole genome shotgun assembly of the C57BL/6J mouse genome covering more than 95% of the euchromatic genome. The assembly has an N50 contig size of 25kb and an N50 scaffold size of 17Mb and is completely anchored to the mouse chromosomes through the genetic map. We present the details of this assembly and some analyses based on it.         We will present work in the areas of genome landscape, conserved synteny, and gene annotation. The term genome landscape refers to basic genome features such as GC content and CpG island distribution. The genomic landscape of the mouse differs significantly from that of the human genome, showing tighter GC distribution, fewer CpG islands, and less variation of features by chromosome.            The comparison of the mouse and human genomes has allowed a detailed analysis of conserved synteny between the two species. In addition to its usefulness as a framework for comparative studies, this detailed synteny map gives insight into the nature of structural changes in mammalian genomes.      Finally, Ensembl has produced automated annotation of over 22,000 mouse genes and determined human orthologs for a large number of these. Based on the results of mutliple gene finders, we estimate the total number of mouse genes to be between 26,000 and 28,000.

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