These authors contributed equally to this manuscript.
Characterization of duplicate gene evolution in the recent natural allopolyploid Tragopogon miscellus by next-generation sequencing and Sequenom iPLEX MassARRAY genotyping
Article first published online: 10 FEB 2010
DOI: 10.1111/j.1365-294X.2009.04469.x
© 2010 Blackwell Publishing Ltd
Issue

Molecular Ecology
Special Issue: Next Generation Molecular Ecology
Volume 19, Issue Supplement s1, pages 132–146, March 2010
Additional Information
How to Cite
BUGGS, R. J. A., CHAMALA, S., WU, W., GAO, L., MAY, G. D., SCHNABLE, P. S., SOLTIS, D. E., SOLTIS, P. S. and BARBAZUK, W. B. (2010), Characterization of duplicate gene evolution in the recent natural allopolyploid Tragopogon miscellus by next-generation sequencing and Sequenom iPLEX MassARRAY genotyping. Molecular Ecology, 19: 132–146. doi: 10.1111/j.1365-294X.2009.04469.x
R.J.A.B. uses molecular genetic and bioinformatics approaches to study duplicate gene evolution and the consequences of polyploidy. C.S. uses computational methods to investigate genome architecture and gene expression and alternative splicing, using next generation sequence technologies. W.W. is the manager of the Schnable lab where she conducts research on heterosis and carbon capturing crops. L.G. manages the Genomics Technologies Facility at Iowa State University. G.D.M.’s research focuses on comparative genomics for crop improvement applications. P.S. Schnable’s research focuses on structural and functional analyses of complex plant genomes, primarily maize. He was a co-PI on the maize genome sequencing project P.S. Soltis’ research interests include: plant phylogenetics, polyploidy, gene family evolution, phylogeography and conservation genetics. D.E.S. is interested in angiosperm phylogeny, genome doubling, floral developmental genetics, phylogeography and molecular cytogenetics. W.B.B uses bioinformatics and comparative and functional genomics to investigate plant genome structure and function, gene expression and alternative splicing.
- †
These authors contributed equally to this manuscript.
Publication History
- Issue published online: 10 FEB 2010
- Article first published online: 10 FEB 2010
- Received 1 June 2009; revision received 28 July 2009; accepted 6 August 2009
References
- , (2004) Exploring the genomic mysteries of polyploidy in cotton. Biological Journal of the Linnean Society, 82, 573–581.
- , (2005) Polyploidy and genome evolution in plants. Current Opinion in Plant Biology, 8, 135–141.
- , , , (2003) Genes duplicated by polyploidy show unequal contributions to the transcriptome and organ-specific reciprocal silencing. Proceedings of the National Academy of Sciences of the United States of America, 100, 4649–4654.
- , , (2004) Spartina anglica C. E. Hubbard: a natural model system for analysing early evolutionary changes that affect allopolyploid genomes. Biological Journal of the Linnean Society, 82, 475–484.
- , , , , (2007) SNP discovery via 454 transcriptome sequencing. Plant Journal, 51, 910–918.
- , , (2006) Homoeologous gene silencing in hexaploid wheat. Plant Journal, 47, 897–906.
- (2008) Towards natural polyploid model organisms. Molecular Ecology, 17, 1875–1876.
- , (2007) Ecological differentiation and diploid superiority across a moving ploidy contact zone. Evolution, 61, 125–140.
- , , et al. (2009) Gene loss and silencing in Tragopogon miscellus (Asteraceae): comparison of natural and synthetic allotetraploids. Heredity, 103, 73–81.
- , , , (2010) Assembly-free comparative genomics of short-read sequence data discovers the needles in the haystack. Molecular Ecology, 19 (Suppl. 1), 146–160.
- , (2008) Short read fragment assembly of bacterial genomes. Genome Research, 18, 324–330.
- , , et al. (2009) Reciprocal silencing, transcriptional bias and functional divergence of homeologs in polyploid cotton (Gossypium). Genetics, 182, 503–517.
- , , et al. (2004) The development of an Arabidopsis model system for genome-wide analysis of polyploidy effects. Biological Journal of the Linnean Society, 82, 689–700.
- , , , , (2008) RNAi of met1 reduces DNA methylation and induces genome-specific changes in gene expression and centromeric small RNA accumulation in Arabidopsis allopolyploids. Genetics, 178, 1845–1858.
- , , et al. (2006) Sequencing Medicago truncatula expressed sequenced tags using 454 Life Sciences technology. BMC Genomics, 7, 272.
- , , et al. (2008) Analysis of the Pythium ultimum transcriptome using Sanger and pyrosequencing approaches. BMC Genomics, 9, 542.
- , (1999) Mating systems of diploid and allotetraploid populations of Tragopogon (Asteraceae). I. Natural populations. Heredity, 82, 237–244.
- , (2000) Mating systems of diploid and allotetraploid populations of Tragopogon (Asteraceae). II. Artificial populations. Heredity, 84, 410–415. Direct Link:
- , , et al. (2005) Allopolyploidy in wheat induces rapid and heritable alterations in DNA methylation patterns of cellular genes and mobile elements. Russian Journal of Genetics, 41, 890–896.
- , (1987) Genomic plant DNA preparation from fresh tissue-CTAB method. Phytochemical Bulletin, 19, 11–15.
- , , et al. (2007) A TNF region haplotype offers protection from typhoid fever in Vietnamese patients. Human Genetics, 122, 51–61.
- (2008) Sequencing goes 454 and takes large-scale genomics into the wild. Molecular Ecology, 17, 1629–1631.
- , , , , , , (2010) Rapid evolution and selection inferred from the transcriptomes of sympatric crater lake cichlid fishes. Molecular Ecology, 19 (Suppl. 1), 197–211.
- , , , (2007) Gene discovery and annotation using LCM-454 transcriptome sequencing. Genome Research, 17, 69–73.
- , , (2008) Transcript profiling by 3′-untranslated region sequencing resolves expression of gene families. Plant Physiology, 146, 32–44.
- , , et al. (1997) Rapid elimination of low-copy DNA sequences in polyploid wheat: a possible mechanism for differentiation of homoeologous chromosomes. Genetics, 147, 1381–1387.
- , , , , , , , , , , , , , , , , (2010) Characterization of a hotspot for mimicry: Assembly of a butterfly wing transcriptome to genomic sequence at the HMYb/Sb locus. Molecular Ecology, 19 (Suppl. 1), 240–254.
- , , , (2008) Duplicate gene expression in allopolyploid Gossypium reveals two temporally distinct phases of expression evolution. BMC Biology, 6, 16.
- , , , (2009) Coordinated and fine-scale control of homoeologous gene expression in allotetraploid cotton. Journal of Heredity, 100, 487–490.
- , , (2009) SNP genotyping using the Sequenom MassARRAY iPLEX platform. Current Protocols in Human Genetics, 60, 2.12.11–12.12.18.
- , , , , (2007) Genomic changes in resynthesized Brassica napus and their effect on gene expression and phenotype. Plant Cell, 19, 3403–3417.
- , , , , , , , , , (2010) A genetic basis for the phenotypic differentiation between siscowet and lean lake trout (Salvelinus namaycush). Molecular Ecology, 19 (Suppl. 1), 176–196.
- , , et al. (2004) Allelic variation of gene expression in maize hybrids. Plant Cell, 16, 1707–1716.
- (2001) Automation in genotyping of single nucleotide polymorphisms. Human Mutation, 17, 475–492.
- , (2010) Genome-wide analysis of alternative splicing evolution among Mus subspecies. Molecular Ecology, 19 (Suppl. 1), 228–239.
- , , et al. (2005) Development of anonymous cDNA microarrays to study changes to the Senecio floral transcriptome during hybrid speciation. Molecular Ecology, 14, 2493–2510.
- , , et al. (2006) Transcriptome shock after interspecific hybridization in Senecio is ameliorated by genome duplication. Current Biology, 16, 1652–1659.
- , , et al. (2008) Whole-genome sequencing and variant discovery in C. elegans. Nature Methods, 5, 183–188.
- , (2008) The new paradigm of flow cell sequencing. Genome Research, 18, 839–846.
- (2008) Sequencing breakthroughs for genomic ecology and evolutionary biology. Molecular Ecology Resources, 8, 3–17.
- , , , (2007) Genome-wide mapping of in vivo protein-DNA interactions. Science, 316, 1497–1502.
- , , , , (2004) Evolutionary dynamics and preferential expression of homeologous 18S-5.8S-26S nuclear ribosomal genes in natural and artificial Glycine allopolyploids. Molecular Biology and Evolution, 21, 1409–1421.
- , , , , (2007) Plant Systematics: A Phylogenetic Approach, 3rd edn. Sinauer, Sunderland, MA.
- , , (2002) Gene loss, silencing and activation in a newly synthesized wheat allotetraploid. Genetics, 160, 1651–1659.
- , (1927) Chromosomenzahlen und systematische Gruppierung der Rumex-Arten. Zeitschrift für Zellforschung und mikroskopische Anatomie, 4, 475–481.
- , (2009) Allelic imbalance sequencing reveals that single-nucleotide polymorphisms frequently alter microRNA-directed repression. Nature Biotechnology, 27, 472–477.
- , , et al. (2004) Phylogeny and diversification of B-function MADS-box genes in angiosperms: evolutionary and functional implications of a 260-million-year-old duplication. American Journal of Botany, 91, 2102–2118.
- , , et al. (2005) Rapid concerted evolution of nuclear ribosomal DNA in two Tragopogon allopolyploids of recent and recurrent origin. Genetics, 169, 931–944.
- (2001) Methods for genotyping single nucleotide polymorphisms. Annual Review of Genomics and Human Genetics, 2, 235–258.
- , (2004) Genetic and epigenetic reprogramming of the wheat genome upon allopolyploidization. Biological Journal of the Linnean Society, 82, 607–613.
- , , , (2004) Genome evolution in allotetraploid Nicotiana. Biological Journal of the Linnean Society, 82, 599–606.
- , , et al. (2008) Rapid chromosome evolution in recently formed polyploids in Tragopogon (Asteraceae). PLoS ONE, 3, e3353.
- , , et al. (2009) High-throughput genetic mapping of mutants via quantitative SNP-typing. Genetics (submitted).
- , (2000) The evolutionary fate and consequences of duplicate genes. Science, 290, 1151–1155.
- , , et al. Genome sequencing in microfabricated high-density picolitre reactors. Nature, 437, 376–380.
- , , et al. (1999) A general approach to single-nucleotide polymorphism discovery. Nature Genetics, 23, 452–456.
- , , et al. (2007) Concerted evolution of rDNA in recently formed Tragopogon allotetraploids is typically associated with an inverse correlation between gene copy number and expression. Genetics, 176, 2509–2519.
- , , et al. (2005) Phylogeny of Tragopogon L. (Asteraceae) based on internal and external transcribed spacer sequence data. International Journal of Plant Sciences, 166, 117–133.
- , , et al. (2008) High-throughput gene and SNP discovery in Eucalyptus grandis, an uncharacterized genome. BMC Genomics, 9, 312.
- , , (1991) Ownbey Tragopogons– 40 years later. American Journal of Botany, 78, 1586–1600.
- (1950) Natural hybridization and amphiploidy in the genus Tragopogon. American Journal of Botany, 37, 487–499.
- , , et al. (2008) 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, 9, 21.
- , , et al. (2007) Differential impact of retrotransposon populations on the genome of allotetraploid tobacco (Nicotiana tabacum). Molecular Genetics and Genomics, 278, 1–15.
- , , , , (2000) The TIGR gene indices: reconstruction and representation of expressed gene sequences. Nucleic Acids Research, 28, 141–145.
- , , (2010) Mining transcriptome sequences towards identifying adaptive single nucleotide polymorphisms in lake whitefish species pairs (Coregonus spp. Salmonidae). Molecular Ecology, 19 (Suppl. 1), 114–130.
- , , , , (2008) Life: The Science of Biology, 8th edn. Macmillan, New York.
- , , et al. (2009) Gene mapping in the wild with SNPs: guidelines and future directions. Genetica, 136, 97–107.
- , (1989) Allopolyploid speciation in Tragopogon: insights from chloroplast DNA. American Journal of Botany, 76, 14–18.
- , (1999) Polyploidy: recurrent formation and genome evolution. Trends in Ecology & Evolution, 14, 348–352.
- , , , (1995) Genetic variation in Tragopogon species: additional origins of the allotetraploids T. mirus and T. miscellus (Compositae). American Journal of Botany, 82, 1329–1341.
- , , et al. (2004a) Recent and recurrent polyploidy in Tragopogon (Asteraceae): cytogenetic, genomic and genetic comparisons. Biological Journal of the Linnean Society, 82, 485–501.
- , , (2004b) Advances in the study of polyploidy since plant speciation. New Phytologist, 161, 173–191.
- , , , (1995) Rapid genome change in synthetic polyploids of Brassica and its implications for polyploid evolution. Proceedings of the National Academy of Sciences of the United States of America, 92, 7719–7723.
- (1942) Polyploid complexes in relation to ecology and the history of floras. American Naturalist, 76, 36–45.
- , (2006) Cis-transcriptional variation in maize inbred lines B73 and Mo17 leads to additive expression patterns in the F-1 hybrid. Genetics, 173, 2199–2210.
- , , et al. (2009) Widespread paternal genomic imprinting of trans-eQTL influences gene expression patterns in maize hybrids. Science, 326, 1118–1120.
- , , et al. (2006) Evolution and expression of homeologous loci in Tragopogon miscellus (Asteraceae), a recent and reciprocally formed allopolyploid. Genetics, 173, 1599–1611.
- , , , , (2009a) On the road to diploidization? Homoeolog loss in independently formed populations of the allopolyploid Tragopogon miscellus (Asteraceae). BMC Plant Biology, 9, 80.
- , , et al. (2009b) Synthetic polyploids of Tragopogon miscellus and T. mirus (Asteraceae): 60 Years after Ownbey’s discovery. American Journal of Botany, 96, 979–988.
- , (2006) Polyploidy and crop improvement. Crop Science, 46, S3–S14.
- , , , , , , (2010) Genome-wide SNP detection in the great tit Parus major using high throughput sequencing. Molecular Ecology, 19 (Suppl. 1), 88–98.
- , , et al. (2008) SNP discovery and allele frequency estimation by deep sequencing of reduced representation libraries. Nature Methods, 5, 247–252.
- , , et al. (2008) Rapid transcriptome characterization for a nonmodel organism using 454 pyrosequencing. Molecular Ecology, 17, 1636–1647.
- , , et al. (2006) Genomewide nonadditive gene regulation in Arabidopsis allotetraploids. Genetics, 172, 507–517.
- , , (2009) RNA-Seq: a revolutionary tool for transcriptomics. Nature Reviews Genetics, 10, 57–63.
- , , , , , , (2010) Finding a (pine) needle in a haystack: Chloroplast genome sequence divergence in rare and widespread pines. Molecular Ecology, 19 (Suppl. 1), 100–114.
- , , , , , (2010) Nucleotide divergence versus gene expression differentiation: comparative transcriptome sequencing in natural isolates from the carrion crow and its hybrid zone with the hooded crow. Molecular Ecology, 19 (Suppl. 1), 162–175.

1365-294X/asset/MEC_centre.gif?v=1&s=a3addb330bee9658564df3325c89548d75a4238d)