Every genome sequence needs a good map
- Harris A. Lewin1,2,4,
- Denis M. Larkin1,
- Joan Pontius3 and
- Stephen J. O'Brien3
- 1 Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA;
- 2 Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Ilinois 61801, USA;
- 3 Laboratory of Genomic Diversity, National Cancer Institute, Frederick, Maryland 21702, USA
This extract was created in the absence of an abstract.
High-resolution physical maps of vertebrate species’ chromosomes empower comparative genomics discovery and are indispensable for sequence assembly precision. Beginning in 2003, the NIH–NHGRI launched an initiative that designated 24 species of mammals for low-coverage whole-genome sequencing in order to provide evolutionary context to human genome annotation (Green 2007) (http://www.genome.gov/25521745). Four principal goals were anticipated for the bold sequencing initiative: (1) to discover evolutionarily conserved sequence motifs, particularly outside of protein-coding genes, which are responsible for regulatory and other critical genomic functions; (2) to provide a framework for reconstruction of genome organization, content, and dynamics that have occurred during the mammalian radiations; (3) to empower new models of human disease and heritable phenotypes; and (4) to provide a starting point for assessment of the expansion, contraction, and adaptation of gene families in different evolutionary lineages.
Although the new mammal sequences have been eagerly anticipated, it is now becoming evident that draft and even “finished” genome sequence of evolutionarily divergent species by themselves can fail to provide sufficient granularity for confident comparison of genome organization and structure to fulfill goals 2–4 listed above. We suggest here to look “back to the future” in developing high-resolution chromosome-based physical maps as an essential and cost-effective framework for the annotation and evolutionary analysis of mammalian and other vertebrate genomes. Independent physical maps in concert with draft or complete sequence assemblies will greatly empower the precise view of comparative genome organization by facilitating the correct ordering of genic and nongenic DNA segments on chromosomes for whole-genome alignments. Accurate comparative physical maps enable discovery of conserved chromosome segments and evolutionary breakpoint regions (EBRs) that are useful for reconstructing the origins of mammalian genomes and the evolutionary forces that molded them (Murphy et al. 2005a; Larkin et al. 2009).
Genetic maps have formed the bedrock of …
