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Extracting functional trends from whole genome duplication events using comparative genomics.

Hermansen RA, Hvidsten TR, Sandve SR, Liberles DA - Biol Proced Online (2016)

Bottom Line: The number of species with completed genomes, including those with evidence for recent whole genome duplication events has exploded.The recently sequenced Atlantic salmon genome has been through two rounds of whole genome duplication since the divergence of teleost fish from the lineage that led to amniotes.This quadrupoling of the number of potential genes has led to complex patterns of retention and loss among gene families.

View Article: PubMed Central - PubMed

Affiliation: Department of Molecular Biology, University of Wyoming, Laramie, WY 82071 USA ; Center for Computational Genetics and Genomics and Department of Biology, Temple University, Philadelphia, PA 19122 USA.

ABSTRACT

Background: The number of species with completed genomes, including those with evidence for recent whole genome duplication events has exploded. The recently sequenced Atlantic salmon genome has been through two rounds of whole genome duplication since the divergence of teleost fish from the lineage that led to amniotes. This quadrupoling of the number of potential genes has led to complex patterns of retention and loss among gene families.

Results: Methods have been developed to characterize the interplay of duplicate gene retention processes across both whole genome duplication events and additional smaller scale duplication events. Further, gene expression divergence data has become available as well for Atlantic salmon and the closely related, pre-whole genome duplication pike and methods to describe expression divergence are also presented. These methods for the characterization of duplicate gene retention and gene expression divergence that have been applied to salmon are described.

Conclusions: With the growth in available genomic and functional data, the opportunities to extract functional inference from large scale duplicates using comparative methods have expanded dramatically. Recently developed methods that further this inference for duplicated genes have been described.

No MeSH data available.


Related in: MedlinePlus

In comparison with an outgroup species that is pre-duplication, the divergence of duplicate gene expression states is shown across four conditions, consistent with conservation, neofunctionalization and subfunctionalization. Neofunctionalized states may or may not retain redundancy in ancestral states (such as states A and B in this figure)
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Fig3: In comparison with an outgroup species that is pre-duplication, the divergence of duplicate gene expression states is shown across four conditions, consistent with conservation, neofunctionalization and subfunctionalization. Neofunctionalized states may or may not retain redundancy in ancestral states (such as states A and B in this figure)

Mentions: With decreasing sequencing costs, publication of larger gene expression datasets encompassing multiple species is increasing [50, 51]. Such datasets (like ENCODE [50]) allow us to analyze duplicate expression evolution in a phylogenetic framework and enable inference of ancestral gene regulation and ultimately to classify the direction of expression evolution; i.e. if duplicates have partitioned ancestral regulation among themselves (subfunctionalization) or if duplicates have evolved novel regulation which was not present pre-duplication (neofunctionalization) (Fig. 3). The best practice for studying expression evolution after WGD using a multi-species data sets is to generate expression data from diploid sister outgroup(s), and either assume diploid expression pattern to be identical to ancestral pre-duplicated states (if only a single diploid outgroup is available), or infer ancestral expression regulation states over a gene tree phylogeny, for example through parsimony or model based approaches (if multiple diploid sister species are available).Fig. 3


Extracting functional trends from whole genome duplication events using comparative genomics.

Hermansen RA, Hvidsten TR, Sandve SR, Liberles DA - Biol Proced Online (2016)

In comparison with an outgroup species that is pre-duplication, the divergence of duplicate gene expression states is shown across four conditions, consistent with conservation, neofunctionalization and subfunctionalization. Neofunctionalized states may or may not retain redundancy in ancestral states (such as states A and B in this figure)
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4862183&req=5

Fig3: In comparison with an outgroup species that is pre-duplication, the divergence of duplicate gene expression states is shown across four conditions, consistent with conservation, neofunctionalization and subfunctionalization. Neofunctionalized states may or may not retain redundancy in ancestral states (such as states A and B in this figure)
Mentions: With decreasing sequencing costs, publication of larger gene expression datasets encompassing multiple species is increasing [50, 51]. Such datasets (like ENCODE [50]) allow us to analyze duplicate expression evolution in a phylogenetic framework and enable inference of ancestral gene regulation and ultimately to classify the direction of expression evolution; i.e. if duplicates have partitioned ancestral regulation among themselves (subfunctionalization) or if duplicates have evolved novel regulation which was not present pre-duplication (neofunctionalization) (Fig. 3). The best practice for studying expression evolution after WGD using a multi-species data sets is to generate expression data from diploid sister outgroup(s), and either assume diploid expression pattern to be identical to ancestral pre-duplicated states (if only a single diploid outgroup is available), or infer ancestral expression regulation states over a gene tree phylogeny, for example through parsimony or model based approaches (if multiple diploid sister species are available).Fig. 3

Bottom Line: The number of species with completed genomes, including those with evidence for recent whole genome duplication events has exploded.The recently sequenced Atlantic salmon genome has been through two rounds of whole genome duplication since the divergence of teleost fish from the lineage that led to amniotes.This quadrupoling of the number of potential genes has led to complex patterns of retention and loss among gene families.

View Article: PubMed Central - PubMed

Affiliation: Department of Molecular Biology, University of Wyoming, Laramie, WY 82071 USA ; Center for Computational Genetics and Genomics and Department of Biology, Temple University, Philadelphia, PA 19122 USA.

ABSTRACT

Background: The number of species with completed genomes, including those with evidence for recent whole genome duplication events has exploded. The recently sequenced Atlantic salmon genome has been through two rounds of whole genome duplication since the divergence of teleost fish from the lineage that led to amniotes. This quadrupoling of the number of potential genes has led to complex patterns of retention and loss among gene families.

Results: Methods have been developed to characterize the interplay of duplicate gene retention processes across both whole genome duplication events and additional smaller scale duplication events. Further, gene expression divergence data has become available as well for Atlantic salmon and the closely related, pre-whole genome duplication pike and methods to describe expression divergence are also presented. These methods for the characterization of duplicate gene retention and gene expression divergence that have been applied to salmon are described.

Conclusions: With the growth in available genomic and functional data, the opportunities to extract functional inference from large scale duplicates using comparative methods have expanded dramatically. Recently developed methods that further this inference for duplicated genes have been described.

No MeSH data available.


Related in: MedlinePlus