CiteULike

Delicious

Connotea

Citation for Study 12669

Citation title: "Anchored hybrid enrichment for massively high-throughput phylogenomics".

Study name: "Anchored hybrid enrichment for massively high-throughput phylogenomics".

This study is part of submission 12669 (Status: Published).

Citation

Lemmon A.R., Lemmon E., & Emme S. 2012. Anchored hybrid enrichment for massively high-throughput phylogenomics. Systematic Biology, .

Authors

• Lemmon A.R. (submitter) 8504454393
• Lemmon E.
• Emme S.

Abstract

The field of phylogenetics is on the cusp of a major revolution, enabled by new methods of data collection that leverage both genomic resources and recent advances in DNA sequencing. Previous phylogenetic work has required labor-intensive marker development coupled with single-locus PCR and DNA sequencing on a clade-by-clade and marker-by-marker basis. Here, we present a new, cost-efficient, and rapid approach to obtaining data from hundreds of genes for potentially hundreds of individuals for deep and shallow phylogenetic studies in any system. Specifically, we designed probes for target enrichment of >500 loci in highly-conserved anchor regions of vertebrate genomes (flanked by less conserved regions) from five model species and tested enrichment efficiency in non-model species up to 250 million years divergent from the nearest model. We found that hybrid enrichment using conserved probes (anchored enrichment) can recover a large number of unlinked loci that are useful at a diversity of phylogenetic timescales. This new approach has the potential to not only expedite resolution of deep-scale portions of the Tree of Life but also to greatly accelerate resolution of the large number of shallow clades that remain unresolved. The combination of low cost (<1% of the cost of traditional Sanger sequencing and 5% of the cost of high-throughput amplicon sequencing for projects on the scale of 500 loci x 100 individuals) and rapid data collection (less than two weeks of laboratory time) are expected to make this approach tractable even for researchers working on systems with limited or non-existent genomic resources.

Keywords

anchored enrichment, sequence capture, hybrid enrichment, highly-conserved regions, ultraconserved elements, anchor regions, phylogenetics, phylogeography

External links

About this resource

• Canonical resource URI: http://purl.org/phylo/treebase/phylows/study/TB2:S12669
• Other versions: Nexus NeXML
• Show BibTeX reference

  		@ARTICLE{TreeBASE2Ref20665,
  	 author = {Alan Richard Lemmon and Emily M.  Lemmon and Sandra  Emme},
  	 title = {Anchored hybrid enrichment for massively high-throughput phylogenomics},
  	 year = {2012},
  	 keywords = {anchored enrichment, sequence capture, hybrid enrichment, highly-conserved regions, ultraconserved elements, anchor regions, phylogenetics, phylogeography},
  	 doi = {},
  	 url = {http://},
  	 pmid = {},
  	 journal = {Systematic Biology},
  	 volume = {},
  	 number = {},
  	 pages = {},
  	 abstract = {The field of phylogenetics is on the cusp of a major revolution, enabled by new methods of data collection that leverage both genomic resources and recent advances in DNA sequencing. Previous phylogenetic work has required labor-intensive marker development coupled with single-locus PCR and DNA sequencing on a clade-by-clade and marker-by-marker basis. Here, we present a new, cost-efficient, and rapid approach to obtaining data from hundreds of genes for potentially hundreds of individuals for deep and shallow phylogenetic studies in any system. Specifically, we designed probes for target enrichment of >500 loci in highly-conserved anchor regions of vertebrate genomes (flanked by less conserved regions) from five model species and tested enrichment efficiency in non-model species up to 250 million years divergent from the nearest model. We found that hybrid enrichment using conserved probes (anchored enrichment) can recover a large number of unlinked loci that are useful at a diversity of phylogenetic timescales. This new approach has the potential to not only expedite resolution of deep-scale portions of the Tree of Life but also to greatly accelerate resolution of the large number of shallow clades that remain unresolved. The combination of low cost (<1% of the cost of traditional Sanger sequencing and 5% of the cost of high-throughput amplicon sequencing for projects on the scale of 500 loci x 100 individuals) and rapid data collection (less than two weeks of laboratory time) are expected to make this approach tractable even for researchers working on systems with limited or non-existent genomic resources.}
  }
  		

• Show RIS reference

  		TY  - JOUR
  ID  - 20665
  AU  - Lemmon,Alan Richard
  AU  - Lemmon,Emily M. 
  AU  - Emme,Sandra 
  T1  - Anchored hybrid enrichment for massively high-throughput phylogenomics
  PY  - 2012
  KW  - anchored enrichment
  KW  - sequence capture
  KW  - hybrid enrichment
  KW  - highly-conserved regions
  KW  - ultraconserved elements
  KW  - anchor regions
  KW  - phylogenetics
  KW  - phylogeography
  UR  - http://dx.doi.org/
  N2  - The field of phylogenetics is on the cusp of a major revolution, enabled by new methods of data collection that leverage both genomic resources and recent advances in DNA sequencing. Previous phylogenetic work has required labor-intensive marker development coupled with single-locus PCR and DNA sequencing on a clade-by-clade and marker-by-marker basis. Here, we present a new, cost-efficient, and rapid approach to obtaining data from hundreds of genes for potentially hundreds of individuals for deep and shallow phylogenetic studies in any system. Specifically, we designed probes for target enrichment of >500 loci in highly-conserved anchor regions of vertebrate genomes (flanked by less conserved regions) from five model species and tested enrichment efficiency in non-model species up to 250 million years divergent from the nearest model. We found that hybrid enrichment using conserved probes (anchored enrichment) can recover a large number of unlinked loci that are useful at a diversity of phylogenetic timescales. This new approach has the potential to not only expedite resolution of deep-scale portions of the Tree of Life but also to greatly accelerate resolution of the large number of shallow clades that remain unresolved. The combination of low cost (<1% of the cost of traditional Sanger sequencing and 5% of the cost of high-throughput amplicon sequencing for projects on the scale of 500 loci x 100 individuals) and rapid data collection (less than two weeks of laboratory time) are expected to make this approach tractable even for researchers working on systems with limited or non-existent genomic resources.
  L3  - 
  JF  - Systematic Biology
  VL  - 
  IS  - 
  ER  -