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Comparison of taxon-specific versus general locus sets for targeted sequence capture in plant phylogenomics.


ABSTRACT: Premise of the Study:Targeted sequence capture can be used to efficiently gather sequence data for large numbers of loci, such as single-copy nuclear loci. Most published studies in plants have used taxon-specific locus sets developed individually for a clade using multiple genomic and transcriptomic resources. General locus sets can also be developed from loci that have been identified as single-copy and have orthologs in large clades of plants. Methods:We identify and compare a taxon-specific locus set and three general locus sets (conserved ortholog set [COSII], shared single-copy nuclear [APVO SSC] genes, and pentatricopeptide repeat [PPR] genes) for targeted sequence capture in Buddleja (Scrophulariaceae) and outgroups. We evaluate their performance in terms of assembly success, sequence variability, and resolution and support of inferred phylogenetic trees. Results:The taxon-specific locus set had the most target loci. Assembly success was high for all locus sets in Buddleja samples. For outgroups, general locus sets had greater assembly success. Taxon-specific and PPR loci had the highest average variability. The taxon-specific data set produced the best-supported tree, but all data sets showed improved resolution over previous non-sequence capture data sets. Discussion:General locus sets can be a useful source of sequence capture targets, especially if multiple genomic resources are not available for a taxon.

SUBMITTER: Chau JH 

PROVIDER: S-EPMC5895190 | biostudies-literature | 2018 Mar

REPOSITORIES: biostudies-literature

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Comparison of taxon-specific versus general locus sets for targeted sequence capture in plant phylogenomics.

Chau John H JH   Rahfeldt Wolfgang A WA   Olmstead Richard G RG  

Applications in plant sciences 20180331 3


<h4>Premise of the study</h4>Targeted sequence capture can be used to efficiently gather sequence data for large numbers of loci, such as single-copy nuclear loci. Most published studies in plants have used taxon-specific locus sets developed individually for a clade using multiple genomic and transcriptomic resources. General locus sets can also be developed from loci that have been identified as single-copy and have orthologs in large clades of plants.<h4>Methods</h4>We identify and compare a  ...[more]

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