Journal article
The Possibility of De Novo Assembly of the Genome and Population Genomics of the Mangrove Rivulus, Kryptolebias marmoratus
Integrative and comparative biology, Vol.52(6), pp.737-742
12/2012
Handle:
https://hdl.handle.net/2376/106126
PMCID: PMC3501098
PMID: 22723055
Abstract
How organisms adapt to the range of environments they encounter is a fundamental question in biology. Elucidating the genetic basis of adaptation is a difficult task, especially when the targets of selection are not known. Emerging sequencing technologies and assembly algorithms facilitate the genomic dissection of adaptation and population differentiation in a vast array of organisms. Here we describe the attributes of
Kryptolebias marmoratus
, one of two known self-fertilizing hermaphroditic vertebrates that make this fish an attractive genetic system and a model for understanding the genomics of adaptation. Long periods of selfing have resulted in populations composed of many distinct naturally homozygous strains with a variety of identifiable, and apparently heritable, phenotypes. There also is strong population genetic structure across a diverse range of mangrove habitats, making this a tractable system in which to study differentiation both within and among populations. The ability to rear
K. marmoratus
in the laboratory contributes further to its value as a model for understanding the genetic drivers for adaptation. To date, microsatellite markers distinguish wild isogenic strains but the naturally high homozygosity improves the quality of
de novo
assembly of the genome and facilitates the identification of genetic variants associated with phenotypes. Gene annotation can be accomplished with RNA-sequencing data in combination with
de novo
genome assembly. By combining genomic information with extensive laboratory-based phenotyping, it becomes possible to map genetic variants underlying differences in behavioral, life-history, and other potentially adaptive traits. Emerging genomic technologies provide the required resources for establishing
K. marmoratus
as a new model organism for behavioral genetics and evolutionary genetics research.
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Details
- Title
- The Possibility of De Novo Assembly of the Genome and Population Genomics of the Mangrove Rivulus, Kryptolebias marmoratus
- Creators
- Joanna L Kelley - Department of Genetics, Stanford University, 300 Pasteur Drive, Lane Building, L301, Stanford, CA, 94305, USAMuh-Ching Yee - Department of Genetics, Stanford University, 300 Pasteur Drive, Lane Building, L301, Stanford, CA, 94305, USAClarence Lee - Department of Genetics, Stanford University, 300 Pasteur Drive, Lane Building, L301, Stanford, CA, 94305, USAElizabeth Levandowsky - Department of Genetics, Stanford University, 300 Pasteur Drive, Lane Building, L301, Stanford, CA, 94305, USAMinita Shah - Department of Genetics, Stanford University, 300 Pasteur Drive, Lane Building, L301, Stanford, CA, 94305, USATimothy Harkins - Department of Genetics, Stanford University, 300 Pasteur Drive, Lane Building, L301, Stanford, CA, 94305, USARyan L Earley - Department of Genetics, Stanford University, 300 Pasteur Drive, Lane Building, L301, Stanford, CA, 94305, USACarlos D Bustamante - Department of Genetics, Stanford University, 300 Pasteur Drive, Lane Building, L301, Stanford, CA, 94305, USA
- Publication Details
- Integrative and comparative biology, Vol.52(6), pp.737-742
- Academic Unit
- Kelley Lab; Biological Sciences, School of
- Publisher
- Oxford University Press
- Identifiers
- 99900546955901842
- Language
- English
- Resource Type
- Journal article