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Transcriptome-based exon capture enables highly cost-effective comparative genomic data collection at moderate evolutionary scales.

Bi K, Vanderpool D, Singhal S, Linderoth T, Moritz C, Good JM - BMC Genomics (2012)

Bottom Line: There was no decrease in coverage among chipmunk species, which showed up to 1.5% sequence divergence in coding regions.Final assemblies yielded over ten thousand orthologous loci (~3.6 Mb) with thousands of fixed and polymorphic SNPs among species identified.Our study demonstrates the potential of a transcriptome-enabled, multiplexed, exon capture method to create thousands of informative markers for population genomic and phylogenetic studies in non-model species across the tree of life.

View Article: PubMed Central - HTML - PubMed

Affiliation: Museum of Vertebrate Zoology, University of California, Berkeley, CA 94720-3160, USA. kebi@berkeley.edu

ABSTRACT

Background: To date, exon capture has largely been restricted to species with fully sequenced genomes, which has precluded its application to lineages that lack high quality genomic resources. We developed a novel strategy for designing array-based exon capture in chipmunks (Tamias) based on de novo transcriptome assemblies. We evaluated the performance of our approach across specimens from four chipmunk species.

Results: We selectively targeted 11,975 exons (~4 Mb) on custom capture arrays, and enriched over 99% of the targets in all libraries. The percentage of aligned reads was highly consistent (24.4-29.1%) across all specimens, including in multiplexing up to 20 barcoded individuals on a single array. Base coverage among specimens and within targets in each species library was uniform, and the performance of targets among independent exon captures was highly reproducible. There was no decrease in coverage among chipmunk species, which showed up to 1.5% sequence divergence in coding regions. We did observe a decline in capture performance of a subset of targets designed from a much more divergent ground squirrel genome (30 My), however, over 90% of the targets were also recovered. Final assemblies yielded over ten thousand orthologous loci (~3.6 Mb) with thousands of fixed and polymorphic SNPs among species identified.

Conclusions: Our study demonstrates the potential of a transcriptome-enabled, multiplexed, exon capture method to create thousands of informative markers for population genomic and phylogenetic studies in non-model species across the tree of life.

Show MeSH
Specificity of exon capture in the four chipmunk species. Specificity denotes the percentage of cleaned reads aligned within the targets over the total reads aligned to the consensus assemblies. The number of individual libraries barcoded and pooled on the same array varies for different species, while the overall specificity among the 31 specimens is similar. Each column represents an individual library.
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Figure 2: Specificity of exon capture in the four chipmunk species. Specificity denotes the percentage of cleaned reads aligned within the targets over the total reads aligned to the consensus assemblies. The number of individual libraries barcoded and pooled on the same array varies for different species, while the overall specificity among the 31 specimens is similar. Each column represents an individual library.

Mentions: We retrieved the complete Tamias mitochondrial genome and all 7 nuclear control loci from all 31 individual libraries. For the targeted T. alpinus exons and for all libraries, the sensitivity, or percentage of exons that were covered by at least one read, was greater than 99%, which is consistent with other exome capture studies (e.g. [7,20]). For the 20 T. alpinus samples, the specificity, or the percentage of mapped reads that map to target regions, ranged from 24.4% to 27.7% with an average of 25.6%. Similar specificity was observed in the other chipmunk species: 27.6% in T. amoenus, 27.2% in T. ruficaudus, and 29.1% in T. striatus (Figure 2).


Transcriptome-based exon capture enables highly cost-effective comparative genomic data collection at moderate evolutionary scales.

Bi K, Vanderpool D, Singhal S, Linderoth T, Moritz C, Good JM - BMC Genomics (2012)

Specificity of exon capture in the four chipmunk species. Specificity denotes the percentage of cleaned reads aligned within the targets over the total reads aligned to the consensus assemblies. The number of individual libraries barcoded and pooled on the same array varies for different species, while the overall specificity among the 31 specimens is similar. Each column represents an individual library.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3472323&req=5

Figure 2: Specificity of exon capture in the four chipmunk species. Specificity denotes the percentage of cleaned reads aligned within the targets over the total reads aligned to the consensus assemblies. The number of individual libraries barcoded and pooled on the same array varies for different species, while the overall specificity among the 31 specimens is similar. Each column represents an individual library.
Mentions: We retrieved the complete Tamias mitochondrial genome and all 7 nuclear control loci from all 31 individual libraries. For the targeted T. alpinus exons and for all libraries, the sensitivity, or percentage of exons that were covered by at least one read, was greater than 99%, which is consistent with other exome capture studies (e.g. [7,20]). For the 20 T. alpinus samples, the specificity, or the percentage of mapped reads that map to target regions, ranged from 24.4% to 27.7% with an average of 25.6%. Similar specificity was observed in the other chipmunk species: 27.6% in T. amoenus, 27.2% in T. ruficaudus, and 29.1% in T. striatus (Figure 2).

Bottom Line: There was no decrease in coverage among chipmunk species, which showed up to 1.5% sequence divergence in coding regions.Final assemblies yielded over ten thousand orthologous loci (~3.6 Mb) with thousands of fixed and polymorphic SNPs among species identified.Our study demonstrates the potential of a transcriptome-enabled, multiplexed, exon capture method to create thousands of informative markers for population genomic and phylogenetic studies in non-model species across the tree of life.

View Article: PubMed Central - HTML - PubMed

Affiliation: Museum of Vertebrate Zoology, University of California, Berkeley, CA 94720-3160, USA. kebi@berkeley.edu

ABSTRACT

Background: To date, exon capture has largely been restricted to species with fully sequenced genomes, which has precluded its application to lineages that lack high quality genomic resources. We developed a novel strategy for designing array-based exon capture in chipmunks (Tamias) based on de novo transcriptome assemblies. We evaluated the performance of our approach across specimens from four chipmunk species.

Results: We selectively targeted 11,975 exons (~4 Mb) on custom capture arrays, and enriched over 99% of the targets in all libraries. The percentage of aligned reads was highly consistent (24.4-29.1%) across all specimens, including in multiplexing up to 20 barcoded individuals on a single array. Base coverage among specimens and within targets in each species library was uniform, and the performance of targets among independent exon captures was highly reproducible. There was no decrease in coverage among chipmunk species, which showed up to 1.5% sequence divergence in coding regions. We did observe a decline in capture performance of a subset of targets designed from a much more divergent ground squirrel genome (30 My), however, over 90% of the targets were also recovered. Final assemblies yielded over ten thousand orthologous loci (~3.6 Mb) with thousands of fixed and polymorphic SNPs among species identified.

Conclusions: Our study demonstrates the potential of a transcriptome-enabled, multiplexed, exon capture method to create thousands of informative markers for population genomic and phylogenetic studies in non-model species across the tree of life.

Show MeSH