Nathans J, Piantanida TP, Eddy RL, Shows TB, Hogness DS. Molecular genetics of inherited variation in human color vision. Science. 1986;232:203–10.
Article
CAS
PubMed
Google Scholar
Iafrate AJ, Feuk L, Rivera MN, Listewnik ML, Donahoe PK, Qi Y, Scherer SW, Lee C. Detection of large-scale variation in the human genome. Nat Genet. 2004;36:949–51.
Article
CAS
PubMed
Google Scholar
Redon R, Ishikawa S, Fitch KR, Feuk L, Perry GH, Andrews TD, Fiegler H, Shapero MH, Carson AR, Chen W, et al. Global variation in copy number in the human genome. Nature. 2006;444:444–54.
Article
CAS
PubMed
PubMed Central
Google Scholar
Lupski JR. Structural variation in the human genome. N Engl J Med. 2007;356:1169–71.
Article
CAS
PubMed
Google Scholar
Feuk L, Carson AR, Scherer SW. Structural variation in the human genome. Nat Rev Genet. 2006;7:85–97.
Article
CAS
PubMed
Google Scholar
Sebat J, Lakshmi B, Troge J, Alexander J, Young J, Lundin P, Maner S, Massa H, Walker M, Chi M, et al. Large-scale copy number polymorphism in the human genome. Science. 2004;305:525–8.
Article
CAS
PubMed
Google Scholar
Freeman JL, Perry GH, Feuk L, Redon R, McCarroll SA, Altshuler DM, Aburatani H, Jones KW, Tyler-Smith C, Hurles ME, et al. Copy number variation: new insights in genome diversity. Genome Res. 2006;16:949–61.
Article
CAS
PubMed
Google Scholar
Springer NM, Ying K, Fu Y, Ji T, Yeh CT, Jia Y, Wu W, Richmond T, Kitzman J, Rosenbaum H, et al. Maize inbreds exhibit high levels of copy number variation (CNV) and presence/absence variation (PAV) in genome content. PLoS Genet. 2009;5:e1000734.
Article
PubMed
PubMed Central
Google Scholar
Hastings PJ, Lupski JR, Rosenberg SM, Ira G. Mechanisms of change in gene copy number. Nat Rev Genet. 2009;10:551–64.
Article
CAS
PubMed
PubMed Central
Google Scholar
Lupski JR. Genomic disorders: structural features of the genome can lead to DNA rearrangements and human disease traits. Trends Genet. 1998;14:417–22.
Article
CAS
PubMed
Google Scholar
Daley JM, Palmbos PL, Wu D, Wilson TE. Nonhomologous end joining in yeast. Annu Rev Genet. 2005;39:431–51.
Article
CAS
PubMed
Google Scholar
Lam KW, Jeffreys AJ. Processes of de novo duplication of human alpha-globin genes. Proc Natl Acad Sci U S A. 2007;104:10950–5.
Article
CAS
PubMed
PubMed Central
Google Scholar
Sweigert SE, Carroll D. Repair and recombination of X-irradiated plasmids in Xenopus laevis oocytes. Mol Cell Biol. 1990;10:5849–56.
Article
CAS
PubMed
PubMed Central
Google Scholar
Tanaka H, Yao MC. Palindromic gene amplification-an evolutionarily conserved role for DNA inverted repeats in the genome. Nat Rev Cancer. 2009;9:216–24.
Article
CAS
PubMed
Google Scholar
Lovett ST. Encoded errors: mutations and rearrangements mediated by misalignment at repetitive DNA sequences. Mol Microbiol. 2004;52:1243–53.
Article
CAS
PubMed
Google Scholar
Slack A, Thornton PC, Magner DB, Rosenberg SM, Hastings PJ. On the mechanism of gene amplification induced under stress in Escherichia coli. PLoS Genet. 2006;2:e48.
Article
PubMed
PubMed Central
Google Scholar
Lupski JR. Genomic rearrangements and sporadic disease. Nat Genet. 2007;39:S43–7.
Article
CAS
PubMed
Google Scholar
Perry GH, Dominy NJ, Claw KG, Lee AS, Fiegler H, Redon R, Werner J, Villanea FA, Mountain JL, Misra R, et al. Diet and the evolution of human amylase gene copy number variation. Nat Genet. 2007;39:1256–60.
Article
CAS
PubMed
PubMed Central
Google Scholar
Frank B, Bermejo JL, Hemminki K, Sutter C, Wappenschmidt B, Meindl A, Kiechle-Bahat M, Bugert P, Schmutzler RK, Bartram CR, Burwinkel B. Copy number variant in the candidate tumor suppressor gene MTUS1 and familial breast cancer risk. Carcinogenesis. 2007;28:1442–5.
Article
CAS
PubMed
Google Scholar
Cook DE, Lee TG, Guo X, Melito S, Wang K, Bayless AM, Wang J, Hughes TJ, Willis DK, Clemente TE, et al. Copy number variation of multiple genes at Rhg1 mediates nematode resistance in soybean. Science. 2012;338:1206–9.
Article
CAS
PubMed
Google Scholar
Wang L, Xu L, Liu X, Zhang T, Li N, Hayel H, Zhang Y, Yan H, Zhao K, Liu GE, Zhang L. Copy number variation-based genome wide association study reveals additional variants contributing to meat quality in Swine. Sci Rep. 2015;5:12535.
Article
CAS
PubMed
PubMed Central
Google Scholar
Dumas L, Kim YH, Karimpour-Fard A, Cox M, Hopkins J, Pollack JR, Sikela JM. Gene copy number variation spanning 60 million years of human and primate evolution. Genome Res. 2007;17:1266–77.
Article
CAS
PubMed
PubMed Central
Google Scholar
Swanson-Wagner RA, Eichten SR, Kumari S, Tiffin P, Stein JC, Ware D, Springer NM. Pervasive gene content variation and copy number variation in maize and its undomesticated progenitor. Genome Res. 2010;20:1689–99.
Article
CAS
PubMed
PubMed Central
Google Scholar
DeBolt S. Copy number variation shapes genome diversity in Arabidopsis over immediate family generational scales. Genome Biol Evol. 2010;2:441–53.
Article
PubMed
PubMed Central
Google Scholar
McHale LK, Haun WJ, Xu WW, Bhaskar PB, Anderson JE, Hyten DL, Gerhardt DJ, Jeddeloh JA, Stupar RM. Structural variants in the soybean genome localize to clusters of biotic stress-response genes. Plant Physiol. 2012;159:1295–308.
Article
CAS
PubMed
PubMed Central
Google Scholar
Munoz-Amatriain M, Eichten SR, Wicker T, Richmond TA, Mascher M, Steuernagel B, Scholz U, Ariyadasa R, Spannagl M, Nussbaumer T, et al. Distribution, functional impact, and origin mechanisms of copy number variation in the barley genome. Genome Biol. 2013;14:R58.
Article
PubMed
PubMed Central
Google Scholar
Bai Z, Chen J, Liao Y, Wang M, Liu R, Ge S, Wing RA, Chen M. The impact and origin of copy number variations in the Oryza species. BMC Genomics. 2016;17:261.
Article
PubMed
PubMed Central
Google Scholar
Pinosio S, Giacomello S, Faivre-Rampant P, Taylor G, Jorge V, Le Paslier MC, Zaina G, Bastien C, Cattonaro F, Marroni F, et al. Characterization of the poplar pan-genome by genome-wide identification of structural variation. Mol Biol Evol. 2016;33(10):2706–19.
Article
CAS
PubMed
PubMed Central
Google Scholar
Carter NP. Methods and strategies for analyzing copy number variation using DNA microarrays. Nat Genet. 2007;39:S16–21.
Article
CAS
PubMed
PubMed Central
Google Scholar
Olshen AB, Venkatraman ES, Lucito R, Wigler M. Circular binary segmentation for the analysis of array-based DNA copy number data. Biostatistics. 2004;5:557–72.
Article
PubMed
Google Scholar
Price TS, Regan R, Mott R, Hedman A, Honey B, Daniels RJ, Smith L, Greenfield A, Tiganescu A, Buckle V, et al. SW-ARRAY: a dynamic programming solution for the identification of copy-number changes in genomic DNA using array comparative genome hybridization data. Nucleic Acids Res. 2005;33:3455–64.
Article
CAS
PubMed
PubMed Central
Google Scholar
De La Torre AR, Wang T, Jaquish B, Aitken SN. Adaptation and exogenous selection in a Picea glauca x Picea engelmannii hybrid zone: implications for forest management under climate change. New Phytol. 2014;201:687–99.
Article
Google Scholar
Birol I, Raymond A, Jackman SD, Pleasance S, Coope R, Taylor GA, Yuen MM, Keeling CI, Brand D, Vandervalk BP, et al. Assembling the 20 Gb white spruce (Picea glauca) genome from whole-genome shotgun sequencing data. Bioinformatics. 2013;29:1492–7.
Article
CAS
PubMed
PubMed Central
Google Scholar
Warren RL, Keeling CI, Yuen MM, Raymond A, Taylor GA, Vandervalk BP, Mohamadi H, Paulino D, Chiu R, Jackman SD, et al. Improved white spruce (Picea glauca) genome assemblies and annotation of large gene families of conifer terpenoid and phenolic defense metabolism. Plant J. 2015;83:189–212.
Article
CAS
PubMed
Google Scholar
Nystedt B, Street NR, Wetterbom A, Zuccolo A, Lin YC, Scofield DG, Vezzi F, Delhomme N, Giacomello S, Alexeyenko A, et al. The Norway spruce genome sequence and conifer genome evolution. Nature. 2013;497:579–84.
Article
CAS
PubMed
Google Scholar
Rigault P, Boyle B, Lepage P, Cooke JEK, Bousquet J, MacKay JJ. A white spruce gene catalog for conifer genome analyses. Plant Physiol. 2011;157:14–28.
Article
CAS
PubMed
PubMed Central
Google Scholar
Stival Sena J, Giguere I, Boyle B, Rigault P, Birol I, Zuccolo A, Ritland K, Ritland C, Bohlmann J, Jones S, et al. Evolution of gene structure in the conifer Picea glauca: a comparative analysis of the impact of intron size. BMC Plant Biol. 2014;14:95.
Article
PubMed
PubMed Central
Google Scholar
Raherison E, Rigault P, Caron S, Poulin PL, Boyle B, Verta JP, Giguere I, Bomal C, Bohlmann J, MacKay J. Transcriptome profiling in conifers and the PiceaGenExpress database show patterns of diversification within gene families and interspecific conservation in vascular gene expression. BMC Genomics. 2012;13:434.
Article
CAS
PubMed
PubMed Central
Google Scholar
Smyth GK: Limma: linear models for microarray data. In Bioinformatics and computational biology solutions using R and Bioconductor. New York: Springer; 2005. p. 397–420.
Pavy N, Pelgas B, Laroche J, Rigault P, Isabel N, Bousquet J. A spruce gene map infers ancient plant genome reshuffling and subsequent slow evolution in the gymnosperm lineage leading to extant conifers. BMC Biol. 2012;10:1.
Article
Google Scholar
Pelgas B, Beauseigle S, Achere V, Jeandroz S, Bousquet J, Isabel N. Comparative genome mapping among Picea glauca, P-mariana x P-rubens and P-abies, and correspondence with other Pinaceae. Theor Appl Genet. 2006;113:1371–93.
Article
CAS
PubMed
Google Scholar
Pavy N, Pelgas B, Beauseigle S, Blais S, Gagnon F, Gosselin I, Lamothe M, Isabel N, Bousquet J. Enhancing genetic mapping of complex genomes through the design of highly-multiplexed SNP arrays: application to the large and unsequenced genomes of white spruce and black spruce. BMC Genomics. 2008;9:21.
Article
PubMed
PubMed Central
Google Scholar
Pelgas B, Bousquet J, Meirmans PG, Ritland K, Isabel N. QTL mapping in white spruce: gene maps and genomic regions underlying adaptive traits across pedigrees, years and environments. BMC Genomics. 2011;12:145.
Article
PubMed
PubMed Central
Google Scholar
Prunier J, Pelgas B, Gagnon F, Desponts M, Isabel N, Beaulieu J, Bousquet J. The genomic architecture and association genetics of adaptive characters using a candidate SNP approach in boreal black spruce. BMC Genomics. 2013;14:368.
Article
CAS
PubMed
PubMed Central
Google Scholar
Carvalho B, Ouwerkerk E, Meijer GA, Ylstra B. High resolution microarray comparative genomic hybridisation analysis using spotted oligonucleotides. J Clin Pathol. 2004;57:644–6.
Article
CAS
PubMed
PubMed Central
Google Scholar
Brewer C, Holloway S, Zawalnyski P, Schinzel A, FitzPatrick D. A chromosomal duplication map of malformations: regions of suspected haplo-and triplolethality-and tolerance of segmental aneuploidy-in humans. Am J Hum Genet. 1999;64:1702–8.
Article
CAS
PubMed
PubMed Central
Google Scholar
Santuari L, Pradervand S, Amiguet-Vercher A-M, Thomas J, Dorcey E, Harshman K, Xenarios I, Juenger TE, Hardtke CS. Substantial deletion overlap among divergent Arabidopsis genomes revealed by intersection of short reads and tiling arrays. Genome Biol. 2010;11:1.
Article
Google Scholar
Graubert TA, Cahan P, Edwin D, Selzer RR, Richmond TA, Eis PS, Shannon WD, Li X, McLeod HL, Cheverud JM. A high-resolution map of segmental DNA copy number variation in the mouse genome. PLoS Genet. 2007;3:e3.
Article
PubMed
PubMed Central
Google Scholar
Guryev V, Saar K, Adamovic T, Verheul M, Van Heesch SA, Cook S, Pravenec M, Aitman T, Jacob H, Shull JD. Distribution and functional impact of DNA copy number variation in the rat. Nat Genet. 2008;40:538–45.
Article
CAS
PubMed
Google Scholar
Perry GH, Yang F, Marques-Bonet T, Murphy C, Fitzgerald T, Lee AS, Hyland C, Stone AC, Hurles ME, Tyler-Smith C. Copy number variation and evolution in humans and chimpanzees. Genome Res. 2008;18:1698–710.
Article
CAS
PubMed
PubMed Central
Google Scholar
Neale DB, Wegrzyn JL, Stevens KA, Zimin AV, Puiu D, Crepeau MW, Cardeno C, Koriabine M, Holtz-Morris AE, Liechty JD. Decoding the massive genome of loblolly pine using haploid DNA and novel assembly strategies. Genome Biol. 2014;15:1.
Article
Google Scholar
Perry GH, Tchinda J, McGrath SD, Zhang J, Picker SR, Cáceres AM, Iafrate AJ, Tyler-Smith C, Scherer SW, Eichler EE. Hotspots for copy number variation in chimpanzees and humans. Proc Natl Acad Sci. 2006;103:8006–11.
Article
CAS
PubMed
PubMed Central
Google Scholar
De Smith AJ, Tsalenko A, Sampas N, Scheffer A, Yamada NA, Tsang P, Ben-Dor A, Yakhini Z, Ellis RJ, Bruhn L. Array CGH analysis of copy number variation identifies 1284 new genes variant in healthy white males: implications for association studies of complex diseases. Hum Mol Genet. 2007;16:2783–94.
Article
PubMed
Google Scholar
Clop A, Vidal O, Amills M. Copy number variation in the genomes of domestic animals. Anim Genet. 2012;43:503–17.
Article
CAS
PubMed
Google Scholar
He T, Pausas JG, Belcher CM, Schwilk DW, Lamont BB. Fire‐adapted traits of Pinus arose in the fiery Cretaceous. New Phytol. 2012;194:751–9.
Article
PubMed
Google Scholar
Nienstaedt H, Zasada JC. Picea glauca (Moench) Voss, White Spruce. In Silvics of North America. Volume 1: USDA. 1990. p. 227–37.
Google Scholar
Viereck L, Johnston W. Picea mariana (Mill.) BSP, Black spruce. In Silvics of North America. Volume 1: USDA. 1990. p. 227–37.
Google Scholar
Knox AK, Dhillon T, Cheng H, Tondelli A, Pecchioni N, Stockinger EJ. CBF gene copy number variation at Frost Resistance-2 is associated with levels of freezing tolerance in temperate-climate cereals. Theor Appl Genet. 2010;121:21–35.
Article
PubMed
Google Scholar
Morgenstern EK. Genetic variation in seedlings of picea mariana (Mill.) BSP. : I. Correlation with ecological factors. Silvae Genetica. 1969. p. 18.
Google Scholar
Nienstaedt H. Inheritance and correlations of frost injury, growth, flowering, and cone characteristics in white spruce, Picea glauca (Moench) Voss. Can J For Res. 1984;15:498–504.
Article
Google Scholar
Prunier J, Gerardi S, Laroche J, Beaulieu J, Bousquet J. Parallel and lineage-specific molecular adaptation to climate in boreal black spruce. Mol Ecol. 2012;21:4270–86.
Article
CAS
PubMed
Google Scholar
Lynch M, Conery JS. The origins of genome complexity. Science. 2003;302:1401–4.
Article
CAS
PubMed
Google Scholar
Wray GA. The evolutionary significance of cis-regulatory mutations. Nat Rev Genet. 2007;8:206–16.
Article
CAS
PubMed
Google Scholar
Alkan C, Coe BP, Eichler EE. Genome structural variation discovery and genotyping. Nat Rev Genetics. 2011;12(5):363–76.
Article
CAS
PubMed
Google Scholar
Dong J, Feng Y, Kumar D, Zhang W, Zhu T, Luo MC, Messing J. Analysis of tandem gene copies in maize chromosomal regions reconstructed from long sequence reads. Proc Natl Acad Sci U S A. 2016;2016:201608775.
Google Scholar
Mak AC, Lai YY, Lam ET, Kwok TP, Leung AK, Poon A, Mostovoy Y, Hastie AR, Stedman W, Anantharaman T, et al. Genome-wide structural variation detection by genome mapping on nanochannel arrays. Genetics. 2016;202(1):351–62.
Article
CAS
PubMed
Google Scholar
Marioni JC, Thorne NP, Valsesia A, Fitzgerald T, Redon R, Fiegler H, Andrews TD, Stranger BE, Lynch AG, Dermitzakis ET. Breaking the waves: improved detection of copy number variation from microarray-based comparative genomic hybridization. Genome Biol. 2007;8:1.
Article
Google Scholar
Medina I, Carbonell J, Pulido L, Madeira SC, Goetz S, Conesa A, Tárraga J, Pascual-Montano A, Nogales-Cadenas R, Santoyo J. Babelomics: an integrative platform for the analysis of transcriptomics, proteomics and genomic data with advanced functional profiling. Nucleic Acids Res. 2010;38:W210–3.
Article
CAS
PubMed
PubMed Central
Google Scholar