The sea lamprey, Petromyzon marinus, is an emerging nonmammalian model organism that satisfactorily meets the criteria for PA-07-457. The genome has been sequenced to 9.1X coverage and an assembly is publicly available. The impetus for this proposal is based on our observations concerning the dynamic nature of the sea lamprey genome. We have recently shown that P. marinus undergoes substantial chromatin diminution with as much as 20% of its somatic genome being discarded during early embryogenesis. Extensive preliminary data presented in this proposal confirm these losses and importantly corroborate our prior observations that large swaths of protein-coding sequences are also being developmentally eliminated. These findings uncover a severe deficiency in the available lamprey genome sequence assembly. In this application we propose to generate and assemble DNA sequences from the P. marinus germline that will provide an overall improved genome assembly for this species. The proposed work fills a major gap in sequence knowledge for this organism and is therefore critical to nearly every lab that utilizes lamprey as a primary model or as a reference for understanding basal features of vertebrate development, physiology, or genome biology. By developing seeded assemblies of unsampled regions, improving contiguity of the somatic and germline genome assemblies, cross-informing existing clone resources, and annotating the location of expressed sequences within constant and modified regions of the genome, we stand to dramatically improve the utility of existing lamprey genome resources for the community and to learn much about programmed genome rearrangement in this nonmammalian model system.

Public Health Relevance

The lamprey is an emerging nonmammalian model organism that has been utilized extensively to study many vertebrate-specific characteristics, including those of human health relevance. The inadequacy of the lamprey genome sequence, however, is highly problematic for researchers studying this organism. Development of an improved lamprey genome sequence is thus imperative for the community.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Resource-Related Research Projects (R24)
Project #
5R24GM095471-04
Application #
8634119
Study Section
Genomics, Computational Biology and Technology Study Section (GCAT)
Program Officer
Carter, Anthony D
Project Start
2011-04-01
Project End
2015-03-31
Budget Start
2014-04-01
Budget End
2015-03-31
Support Year
4
Fiscal Year
2014
Total Cost
$328,900
Indirect Cost
$149,173
Name
Benaroya Research Institute at Virginia Mason
Department
Type
DUNS #
076647908
City
Seattle
State
WA
Country
United States
Zip Code
98101
Smith, Jeramiah J; Kuraku, Shigehiro; Holt, Carson et al. (2013) Sequencing of the sea lamprey (Petromyzon marinus) genome provides insights into vertebrate evolution. Nat Genet 45:415-21, 421e1-2