publication . Article . Other literature type . 2012

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

Dan Vanderpool;
Open Access English
  • Published: 01 Aug 2012 Journal: BMC Genomics, volume 13, issue 1, page 403 (issn: 1471-2164, Copyright policy)
  • Publisher: Springer Nature
  • Country: Algeria
Abstract
<p>Abstract</p> <p>Background</p> <p>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 (<it>Tamias</it>) based on <it>de novo</it> transcriptome assemblies. We evaluated the performance of our approach across specimens from four chipmunk species.</p> <p>Results</p> <p>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...
Subjects
free text keywords: Life Sciences, Bi [BRII recipient], Biotechnology, Genetics, Methodology Article, Microarray-based exon capture, Phylogenetics, Population genomics, SNP identification, Tamias, Target enrichment, <it>Tamias</it>, TP248.13-248.65, QH426-470
Funded by
NSERC
Project
  • Funder: Natural Sciences and Engineering Research Council of Canada (NSERC)
38 references, page 1 of 3

Shendure, J, Hanlee, J. Next-generation DNA sequencing. Nat Biotech. 2008; 26: 1135-1145 [OpenAIRE] [DOI]

Good, JM. Reduced representation methods for subgenomic enrichment and next-generation sequencing. Methods Mol Biol. 2011; 772: 85-103 [PubMed]

Gilad, Y, Pritchard, JK, Thornton, K. Characterizing natural variation using next- generation sequencing technologies. Trends Genet. 2009; 25: 463-471 [OpenAIRE] [PubMed] [DOI]

Yi, X, Liang, Y, Huerta-Sanchez, E, Jin, X, Cuo, ZX, Pool, JE, Xu, X, Jiang, H, Vinckenbosch, N, Korneliussen, TS, Zheng, H, Liu, T, He, W, Li, K, Luo, R, Nie, X, Wu, H, Zhao, M, Cao, H, Zou, J, Shan, Y, Li, S, Yang, Q, Asan, null, Ni, P, Tian, G, Xu, J, Liu, X, Jiang, T, Wu, R, Zhou, G, Tang, M, Qin, J, Wang, T, Feng, S, Li, G, Huasang, null, Luosang, J, Wang, W, Chen, F, Wang, Y, Zheng, X, Li, Z, Bianba, Z, Yang, G, Wang, X, Tang, S, Gao, G, Chen, Y, Luo, Z, Gusang, L, Cao, Z, Zhang, Q, Ouyang, W, Ren, X, Liang, H, Zheng, H, Huang, Y, Li, J, Bolund, L, Kristiansen, K, Li, Y, Zhang, Y, Zhang, X, Li, R, Li, S, Yang, H, Nielsen, R, Wang, J, Wang, J. Sequencing of 50 human exomes reveals adaptation to high altitude. Science. 2010; 329: 75-78 [OpenAIRE] [PubMed] [DOI]

Smith, SA, Wilson, NG, Goetz, FE, Feehery, C, Andrade, SCS, Rouse, GW, Giribet, G, Dunn, CW. Resolving the evolutionary relationships of molluscs with phylogenomic tools. Nature. 2011; 480: 364-367 [OpenAIRE] [PubMed] [DOI]

Lemmon, A, Emme, S, Lemmon, E. Anchored hybrid enrichment for massively high-throughput phylogenomics. Syst Biol. 2012 [OpenAIRE] [DOI]

Hodges, E, Rooks, M, Xuan, Z, Bhattacharjee, A, Benjamin Gordon, D, Brizuela, L, Richard McCombie, W, Hannon, GJ. Hybrid selection of discrete genomic intervals on custom-designed microarrays for massively parallel sequencing. Nat Protoc. 2009; 4: 960-974 [OpenAIRE] [PubMed] [DOI]

Hohenlohe, PA, Amish, SJ, Catchen, JM, Allendorf, FW, Luikart, G. Next-generation RAD sequencing identifies thousands of SNPs for assessing hybridization between rainbow and westslope cutthroat trout. Mol Ecol Res. 2011; 11: 117-122 [OpenAIRE]

Faircloth, BC, McCormack, JE, Crawford, NG, Harvey, MG, Brumfield, RT, Glenn, TC. Ultraconserved elements anchor thousands of genetic markers spanning multiple evolutionary timescales. Syst Biol. 2012 [OpenAIRE] [DOI]

Cosart, T, Beja-Pereira, A, Chen, S, Ng, SB, Shendure, J, Luikart, G. Exome-wide DNA capture and next generation sequencing in domestic and wild species. BMC Genomics. 2011; 12: 347 [OpenAIRE] [PubMed] [DOI]

Gnirke, A, Melnikov, A, Maguire, J, Rogov, P, LeProust, EM, Brockman, W, Fennell, T, Giannoukos, G, Fisher, S, Russ, C, Gabriel, S, Jaffe, DB, Lander, ES, Nusbaum, C. Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing. Nat Biotechnol. 2009; 27: 182-189 [OpenAIRE] [PubMed] [DOI]

George, RD, McVicker, G, Diederich, R, Ng, SB, MacKenzie, AP, Swanson, WJ, Shendure, J, Thomas, JH. Trans genomic capture and sequencing of primate exomes reveals new targets of positive selection. Genome Res. 2011; 21: 1686-1694 [OpenAIRE] [PubMed] [DOI]

Good, JM, Hird, S, Reid, N, Demboski, JR, Steppan, SJ, Martin-Nims, TR, Sullivan, J. Ancient hybridization and mitochondrial capture between two species of chipmunks. Mol Ecol. 2008; 17: 1313-1327 [OpenAIRE] [PubMed] [DOI]

Reid, N, Demboski, JR, Sullivan, J. Phylogeny estimation of the radiation western American chipmunk (Tamias) in the face of introgression using reproductive protein genes. Syst Biol. 2012; 61: 44-62 [OpenAIRE] [PubMed] [DOI]

Surget-Groba, Y, Montoya-Burgos, JI. Optimization of de novo transcriptome assembly from next-generation sequencing data. Genome Res. 2010; 20: 1432-1440 [OpenAIRE] [PubMed] [DOI]

38 references, page 1 of 3
Abstract
<p>Abstract</p> <p>Background</p> <p>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 (<it>Tamias</it>) based on <it>de novo</it> transcriptome assemblies. We evaluated the performance of our approach across specimens from four chipmunk species.</p> <p>Results</p> <p>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...
Subjects
free text keywords: Life Sciences, Bi [BRII recipient], Biotechnology, Genetics, Methodology Article, Microarray-based exon capture, Phylogenetics, Population genomics, SNP identification, Tamias, Target enrichment, <it>Tamias</it>, TP248.13-248.65, QH426-470
Funded by
NSERC
Project
  • Funder: Natural Sciences and Engineering Research Council of Canada (NSERC)
38 references, page 1 of 3

Shendure, J, Hanlee, J. Next-generation DNA sequencing. Nat Biotech. 2008; 26: 1135-1145 [OpenAIRE] [DOI]

Good, JM. Reduced representation methods for subgenomic enrichment and next-generation sequencing. Methods Mol Biol. 2011; 772: 85-103 [PubMed]

Gilad, Y, Pritchard, JK, Thornton, K. Characterizing natural variation using next- generation sequencing technologies. Trends Genet. 2009; 25: 463-471 [OpenAIRE] [PubMed] [DOI]

Yi, X, Liang, Y, Huerta-Sanchez, E, Jin, X, Cuo, ZX, Pool, JE, Xu, X, Jiang, H, Vinckenbosch, N, Korneliussen, TS, Zheng, H, Liu, T, He, W, Li, K, Luo, R, Nie, X, Wu, H, Zhao, M, Cao, H, Zou, J, Shan, Y, Li, S, Yang, Q, Asan, null, Ni, P, Tian, G, Xu, J, Liu, X, Jiang, T, Wu, R, Zhou, G, Tang, M, Qin, J, Wang, T, Feng, S, Li, G, Huasang, null, Luosang, J, Wang, W, Chen, F, Wang, Y, Zheng, X, Li, Z, Bianba, Z, Yang, G, Wang, X, Tang, S, Gao, G, Chen, Y, Luo, Z, Gusang, L, Cao, Z, Zhang, Q, Ouyang, W, Ren, X, Liang, H, Zheng, H, Huang, Y, Li, J, Bolund, L, Kristiansen, K, Li, Y, Zhang, Y, Zhang, X, Li, R, Li, S, Yang, H, Nielsen, R, Wang, J, Wang, J. Sequencing of 50 human exomes reveals adaptation to high altitude. Science. 2010; 329: 75-78 [OpenAIRE] [PubMed] [DOI]

Smith, SA, Wilson, NG, Goetz, FE, Feehery, C, Andrade, SCS, Rouse, GW, Giribet, G, Dunn, CW. Resolving the evolutionary relationships of molluscs with phylogenomic tools. Nature. 2011; 480: 364-367 [OpenAIRE] [PubMed] [DOI]

Lemmon, A, Emme, S, Lemmon, E. Anchored hybrid enrichment for massively high-throughput phylogenomics. Syst Biol. 2012 [OpenAIRE] [DOI]

Hodges, E, Rooks, M, Xuan, Z, Bhattacharjee, A, Benjamin Gordon, D, Brizuela, L, Richard McCombie, W, Hannon, GJ. Hybrid selection of discrete genomic intervals on custom-designed microarrays for massively parallel sequencing. Nat Protoc. 2009; 4: 960-974 [OpenAIRE] [PubMed] [DOI]

Hohenlohe, PA, Amish, SJ, Catchen, JM, Allendorf, FW, Luikart, G. Next-generation RAD sequencing identifies thousands of SNPs for assessing hybridization between rainbow and westslope cutthroat trout. Mol Ecol Res. 2011; 11: 117-122 [OpenAIRE]

Faircloth, BC, McCormack, JE, Crawford, NG, Harvey, MG, Brumfield, RT, Glenn, TC. Ultraconserved elements anchor thousands of genetic markers spanning multiple evolutionary timescales. Syst Biol. 2012 [OpenAIRE] [DOI]

Cosart, T, Beja-Pereira, A, Chen, S, Ng, SB, Shendure, J, Luikart, G. Exome-wide DNA capture and next generation sequencing in domestic and wild species. BMC Genomics. 2011; 12: 347 [OpenAIRE] [PubMed] [DOI]

Gnirke, A, Melnikov, A, Maguire, J, Rogov, P, LeProust, EM, Brockman, W, Fennell, T, Giannoukos, G, Fisher, S, Russ, C, Gabriel, S, Jaffe, DB, Lander, ES, Nusbaum, C. Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing. Nat Biotechnol. 2009; 27: 182-189 [OpenAIRE] [PubMed] [DOI]

George, RD, McVicker, G, Diederich, R, Ng, SB, MacKenzie, AP, Swanson, WJ, Shendure, J, Thomas, JH. Trans genomic capture and sequencing of primate exomes reveals new targets of positive selection. Genome Res. 2011; 21: 1686-1694 [OpenAIRE] [PubMed] [DOI]

Good, JM, Hird, S, Reid, N, Demboski, JR, Steppan, SJ, Martin-Nims, TR, Sullivan, J. Ancient hybridization and mitochondrial capture between two species of chipmunks. Mol Ecol. 2008; 17: 1313-1327 [OpenAIRE] [PubMed] [DOI]

Reid, N, Demboski, JR, Sullivan, J. Phylogeny estimation of the radiation western American chipmunk (Tamias) in the face of introgression using reproductive protein genes. Syst Biol. 2012; 61: 44-62 [OpenAIRE] [PubMed] [DOI]

Surget-Groba, Y, Montoya-Burgos, JI. Optimization of de novo transcriptome assembly from next-generation sequencing data. Genome Res. 2010; 20: 1432-1440 [OpenAIRE] [PubMed] [DOI]

38 references, page 1 of 3
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