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Development and analysis of a germline BAC resource for the sea lamprey, a vertebrate that undergoes substantial chromatin diminution

Smith, Jeramiah J. and Stuart, Andrew B. and Sauka-Spengler, Tatjana and Clifton, Sandra W. and Amemiya, Chris T. (2010) Development and analysis of a germline BAC resource for the sea lamprey, a vertebrate that undergoes substantial chromatin diminution. Chromosoma, 119 (4). pp. 381-389. ISSN 0009-5915. https://resolver.caltech.edu/CaltechAUTHORS:20100817-095634397

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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.


Item Type:Article
Related URLs:
URLURL TypeDescription
http://dx.doi.org/10.1007/s00412-010-0263-z DOIUNSPECIFIED
http://www.springerlink.com/content/l33784853329h121/PublisherUNSPECIFIED
ORCID:
AuthorORCID
Smith, Jeramiah J.0000-0001-5333-5531
Sauka-Spengler, Tatjana0000-0001-9289-0263
Additional Information:© 2010 Springer-Verlag. Received: 17 December 2009. Revised: 27 January 2010. Accepted: 28 January 2010. Published online: 2 March 2010. This work was supported by the National Institutes of Health [grant number GM079492] and the National Science Foundation [grant number MCB-0719558] to CTA. This work was supported by the National Institutes of Health [grant number T32- HG00035, F32-GM087919] to JJS. Its contents are solely the responsibility of the authors and do not necessarily represent the official views of NIH.
Funders:
Funding AgencyGrant Number
NIHGM079492
NIHT32-HG00035
NIHF32-GM087919
NSFMCB-0719558
Issue or Number:4
Record Number:CaltechAUTHORS:20100817-095634397
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20100817-095634397
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:19469
Collection:CaltechAUTHORS
Deposited By: Tony Diaz
Deposited On:17 Aug 2010 18:32
Last Modified:09 Mar 2020 13:19

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