Development and analysis of a germline BAC resource for the sea lamprey, a vertebrate that undergoes substantial chromatin diminution |
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Authors: | Jeramiah J Smith Andrew B Stuart Tatjana Sauka-Spengler Sandra W Clifton Chris T Amemiya |
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Institution: | 1. Benaroya Research Institute at Virginia Mason, 1201 Ninth Avenue, Seattle, WA, 98101-2795, USA 2. California Institute of Technology, Pasadena, CA, 92125, USA 3. Washington University School of Medicine Genome Center, St. Louis, MO, 63108, USA
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Abstract: | Over the last several years, the sea lamprey (Petromyzon marinus) has grown substantially as a model for understanding the evolutionary fundaments and capacity of vertebrate developmental
and genome biology. Recent work on the lamprey genome has resulted in a preliminary assembly of the lamprey genome and led
to the realization that nearly all somatic cell lineages undergo extensive programmed rearrangements. Here we describe the
development of a bacterial artificial chromosome (BAC) resource for lamprey germline DNA and use sequence information from
this resource to probe the subchromosomal structure of the lamprey genome. The arrayed germline BAC library represents ∼10×
coverage of the lamprey genome. Analyses of BAC-end sequences reveal that the lamprey genome possesses a high content of repetitive
sequences (relative to human), which show strong clustering at the subchromosomal level. This pattern is not unexpected given
that the sea lamprey genome is dispersed across a large number of chromosomes (n ∼ 99) and suggests a low-copy DNA targeting strategy for efficiently generating informative paired-BAC-end linkages from
highly repetitive genomes. This library therefore represents a new and biologically informed resource for understanding the
structure of the lamprey genome and the biology of programmed genome rearrangement. |
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