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Volumn 112, Issue 9, 2015, Pages 2806-2811

Hybrid origins and the earliest stages of diploidization in the highly successful recent polyploid Capsella bursa-pastoris

Author keywords

Gene loss; Polyploidy; Population genomics; Speciation

Indexed keywords

ALLOPOLYPLOIDY; ANGIOSPERM; ARTICLE; CAPSELLA BURSAPASTORIS; CLINICAL EVALUATION; DEVELOPMENTAL STAGE; DIPLOIDY; GENE CONVERSION; GENE DUPLICATION; GENE EXPRESSION; GENE FLOW; GENE IDENTIFICATION; GENE INACTIVATION; GENE LOSS; GENE MUTATION; GENE SEQUENCE; GENE SILENCING; GENETIC ASSOCIATION; GENOME ANALYSIS; HETEROZYGOSITY; HYBRID; MOLECULAR EVOLUTION; NATURAL SELECTION; NONHUMAN; PARENT; PHYLOGENETIC TREE; PLANT DEVELOPMENT; PLANT GENOME; POLYPLOIDY; PRIORITY JOURNAL; QUANTITATIVE ANALYSIS; SELFING; SPECIES DISTRIBUTION; TETRAPLOIDY; CAPSELLA; CHIMERA; GENETIC SELECTION; GENETICS; MUTATION; PHYSIOLOGY;

EID: 84924083242     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1412277112     Document Type: Article
Times cited : (112)

References (47)
  • 1
    • 84874229463 scopus 로고    scopus 로고
    • Convergent gene loss following gene and genome duplications creates single-copy families in flowering plants
    • De Smet R, et al. (2013) Convergent gene loss following gene and genome duplications creates single-copy families in flowering plants. Proc Natl Acad Sci USA 110(8): 2898-2903.
    • (2013) Proc Natl Acad Sci USA , vol.110 , Issue.8 , pp. 2898-2903
    • De Smet, R.1
  • 2
    • 0034634395 scopus 로고    scopus 로고
    • The evolutionary fate and consequences of duplicate genes
    • Lynch M, Conery JS (2000) The evolutionary fate and consequences of duplicate genes. Science 290(5494): 1151-1155.
    • (2000) Science , vol.290 , Issue.5494 , pp. 1151-1155
    • Lynch, M.1    Conery, J.S.2
  • 3
    • 0034500239 scopus 로고    scopus 로고
    • Polyploid incidence and evolution
    • Otto SP, Whitton J (2000) Polyploid incidence and evolution. Annu Rev Genet 34: 401-437.
    • (2000) Annu Rev Genet , vol.34 , pp. 401-437
    • Otto, S.P.1    Whitton, J.2
  • 4
    • 84866449699 scopus 로고    scopus 로고
    • Fractionation, rearrangement and subgenome dominance
    • Sankoff D, Zheng C (2012) Fractionation, rearrangement and subgenome dominance. Bioinformatics 28(18):i402-i408.
    • (2012) Bioinformatics , vol.28 , Issue.18 , pp. i402-i408
    • Sankoff, D.1    Zheng, C.2
  • 5
    • 79952744855 scopus 로고    scopus 로고
    • Differentiation of the maize sub-genomes by genome dominance and both ancient and ongoing gene loss
    • Schnable JC, Springer NM, Freeling M (2011) Differentiation of the maize sub-genomes by genome dominance and both ancient and ongoing gene loss. Proc Natl Acad Sci USA 108(10): 4069-4074.
    • (2011) Proc Natl Acad Sci USA , vol.108 , Issue.10 , pp. 4069-4074
    • Schnable, J.C.1    Springer, N.M.2    Freeling, M.3
  • 6
    • 1542338594 scopus 로고    scopus 로고
    • Genomic duplication, fractionation and the origin of regulatory novelty
    • Langham RJ, et al. (2004) Genomic duplication, fractionation and the origin of regulatory novelty. Genetics 166(2): 935-945.
    • (2004) Genetics , vol.166 , Issue.2 , pp. 935-945
    • Langham, R.J.1
  • 7
    • 84898052115 scopus 로고    scopus 로고
    • Origin, inheritance, and gene regulatory consequences of genome dominance in polyploids
    • Woodhouse MR, et al. (2014) Origin, inheritance, and gene regulatory consequences of genome dominance in polyploids. Proc Natl Acad Sci USA 111(14): 5283-5288.
    • (2014) Proc Natl Acad Sci USA , vol.111 , Issue.14 , pp. 5283-5288
    • Woodhouse, M.R.1
  • 8
    • 78650334271 scopus 로고    scopus 로고
    • Homoeolog-specific retention and use in allotetraploid arabidopsis suecica depends on parent of origin and network partners
    • Chang PL, Dilkes BP, McMahon M, Comai L, Nuzhdin SV (2010) Homoeolog-specific retention and use in allotetraploid Arabidopsis suecica depends on parent of origin and network partners. Genome Biol 11(12): R125.
    • (2010) Genome Biol , vol.11 , Issue.12 , pp. R125
    • Chang, P.L.1    Dilkes, B.P.2    McMahon, M.3    Comai, L.4    Nuzhdin, S.V.5
  • 9
    • 84862777707 scopus 로고    scopus 로고
    • Rapid, repeated, and clustered loss of duplicate genes in allopolyploid plant populations of independent origin
    • Buggs RJA, et al. (2012) Rapid, repeated, and clustered loss of duplicate genes in allopolyploid plant populations of independent origin. Curr Biol 22(3): 248-252.
    • (2012) Curr Biol , vol.22 , Issue.3 , pp. 248-252
    • Buggs, R.J.A.1
  • 10
    • 0032422925 scopus 로고    scopus 로고
    • Pathways, mechanisms, and rates of polyploid formation in flowering plants
    • Ramsey J, Schemske DW (1998) Pathways, mechanisms, and rates of polyploid formation in flowering plants. Annu Rev Ecol Syst 29: 467-501.
    • (1998) Annu Rev Ecol Syst , vol.29 , pp. 467-501
    • Ramsey, J.1    Schemske, D.W.2
  • 11
    • 33645389485 scopus 로고    scopus 로고
    • Mechanisms of genomic rearrangements and gene expression changes in plant polyploids
    • Chen ZJ, Ni Z (2006) Mechanisms of genomic rearrangements and gene expression changes in plant polyploids. BioEssays 28(3): 240-252.
    • (2006) BioEssays , vol.28 , Issue.3 , pp. 240-252
    • Chen, Z.J.1    Ni, Z.2
  • 12
    • 0345071423 scopus 로고    scopus 로고
    • Genes duplicated by polyploidy show unequal contributions to the transcriptome and organ-specific reciprocal silencing
    • Adams KL, Cronn R, Percifield R, Wendel JF (2003) Genes duplicated by polyploidy show unequal contributions to the transcriptome and organ-specific reciprocal silencing. Proc Natl Acad Sci USA 100(8): 4649-4654.
    • (2003) Proc Natl Acad Sci USA , vol.100 , Issue.8 , pp. 4649-4654
    • Adams, K.L.1    Cronn, R.2    Percifield, R.3    Wendel, J.F.4
  • 13
    • 79953789287 scopus 로고    scopus 로고
    • Transcriptomic shock generates evolutionary novelty in a newly formed, natural allopolyploid plant
    • Buggs RJA, et al. (2011) Transcriptomic shock generates evolutionary novelty in a newly formed, natural allopolyploid plant. Curr Biol 21(7): 551-556.
    • (2011) Curr Biol , vol.21 , Issue.7 , pp. 551-556
    • Buggs, R.J.A.1
  • 14
    • 84902983437 scopus 로고    scopus 로고
    • The legacy of diploid progenitors in allopolyploid gene expression patterns
    • Buggs RJA, et al. (2014) The legacy of diploid progenitors in allopolyploid gene expression patterns. Philos Trans R Soc Lond B Biol Sci 369(1648): 20130354.
    • (2014) Philos Trans R Soc Lond B Biol Sci , vol.369 , Issue.1648
    • Buggs, R.J.A.1
  • 15
    • 84857625124 scopus 로고    scopus 로고
    • 'Missing link' species capsella orientalis and capsella thracica elucidate evolution of model plant genus capsella (Brassicaceae)
    • Hurka H, Friesen N, German DA, Franzke A, Neuffer B (2012) 'Missing link' species Capsella orientalis and Capsella thracica elucidate evolution of model plant genus Capsella (Brassicaceae). Mol Ecol 21(5): 1223-1238.
    • (2012) Mol Ecol , vol.21 , Issue.5 , pp. 1223-1238
    • Hurka, H.1    Friesen, N.2    German, D.A.3    Franzke, A.4    Neuffer, B.5
  • 16
    • 84862792837 scopus 로고    scopus 로고
    • Coalescent-based analysis distinguishes between allo- and autopolyploid origin in shepherd's purse (Capsella bursa-pastoris)
    • St Onge KR, et al. (2012) Coalescent-based analysis distinguishes between allo- and autopolyploid origin in Shepherd's Purse (Capsella bursa-pastoris). Mol Biol Evol 29(7): 1721-1733.
    • (2012) Mol Biol Evol , vol.29 , Issue.7 , pp. 1721-1733
    • St. Onge, K.R.1
  • 17
    • 0030916073 scopus 로고    scopus 로고
    • Evolutionary processes in the genus capsella (Brassicaceae)
    • Hurka H, Neuffer B (1997) Evolutionary processes in the genus Capsella (Brassicaceae). Plant Syst Evol 206(1-4): 295-316.
    • (1997) Plant Syst Evol , vol.206 , Issue.1-4 , pp. 295-316
    • Hurka, H.1    Neuffer, B.2
  • 18
    • 65249150257 scopus 로고    scopus 로고
    • Recent speciation associated with the evolution of selfing in capsella
    • Foxe JP, et al. (2009) Recent speciation associated with the evolution of selfing in Capsella. Proc Natl Acad Sci USA 106(13): 5241-5245.
    • (2009) Proc Natl Acad Sci USA , vol.106 , Issue.13 , pp. 5241-5245
    • Foxe, J.P.1
  • 19
    • 65249092034 scopus 로고    scopus 로고
    • Recent speciation of capsella rubella from capsella grandiflora, associated with loss of self-incompatibility and an extreme bottleneck
    • Guo Y-L, et al. (2009) Recent speciation of Capsella rubella from Capsella grandiflora, associated with loss of self-incompatibility and an extreme bottleneck. Proc Natl Acad Sci USA 106(13): 5246-5251.
    • (2009) Proc Natl Acad Sci USA , vol.106 , Issue.13 , pp. 5246-5251
    • Guo, Y.-L.1
  • 20
    • 84884692797 scopus 로고    scopus 로고
    • Genomic identification of founding haplotypes reveals the history of the selfing species capsella rubella
    • Brandvain Y, Slotte T, Hazzouri KM, Wright SI, Coop G (2013) Genomic identification of founding haplotypes reveals the history of the selfing species Capsella rubella. PLoS Genet 9(9): e1003754.
    • (2013) PLoS Genet , vol.9 , Issue.9
    • Brandvain, Y.1    Slotte, T.2    Hazzouri, K.M.3    Wright, S.I.4    Coop, G.5
  • 21
    • 84879686532 scopus 로고    scopus 로고
    • The capsella rubella genome and the genomic consequences of rapid mating system evolution
    • Slotte T, et al. (2013) The Capsella rubella genome and the genomic consequences of rapid mating system evolution. Nat Genet 45(7): 831-835.
    • (2013) Nat Genet , vol.45 , Issue.7 , pp. 831-835
    • Slotte, T.1
  • 22
    • 84920175965 scopus 로고    scopus 로고
    • Evolution of the mating system in the genus capsella (Brassicaceae)
    • ed Glaubrecht M (Springer, Berlin)
    • Paetsch M, Mayland-Quellhorst S, Hurka H, Neuffer B (2010) Evolution of the mating system in the genus Capsella (Brassicaceae). Evolution in Action, ed Glaubrecht M (Springer, Berlin), pp 77-100.
    • (2010) Evolution in Action , pp. 77-100
    • Paetsch, M.1    Mayland-Quellhorst, S.2    Hurka, H.3    Neuffer, B.4
  • 23
    • 33749035459 scopus 로고    scopus 로고
    • Evolution of the self-incompatibility system in the brassicaceae: Identification of S-locus receptor kinase (SRK) in self-incompatible capsella grandiflora
    • Paetsch M, Mayland-Quellhorst S, Neuffer B (2006) Evolution of the self-incompatibility system in the Brassicaceae: Identification of S-locus receptor kinase (SRK) in self-incompatible Capsella grandiflora. Heredity (Edinb) 97(4): 283-290.
    • (2006) Heredity (Edinb) , vol.97 , Issue.4 , pp. 283-290
    • Paetsch, M.1    Mayland-Quellhorst, S.2    Neuffer, B.3
  • 24
    • 33751228457 scopus 로고    scopus 로고
    • Intrageneric phylogeny of capsella (Brassicaceae) and the origin of the tetraploid C. Bursa-pastoris based on chloroplast and nuclear DNA sequences
    • Slotte T, Ceplitis A, Neuffer B, Hurka H, Lascoux M (2006) Intrageneric phylogeny of Capsella (Brassicaceae) and the origin of the tetraploid C. bursa-pastoris based on chloroplast and nuclear DNA sequences. Am J Bot 93(11): 1714-1724.
    • (2006) Am J Bot , vol.93 , Issue.11 , pp. 1714-1724
    • Slotte, T.1    Ceplitis, A.2    Neuffer, B.3    Hurka, H.4    Lascoux, M.5
  • 25
    • 84881028642 scopus 로고    scopus 로고
    • An atlas of over 90,000 conserved noncoding sequences provides insight into crucifer regulatory regions
    • Haudry A, et al. (2013) An atlas of over 90,000 conserved noncoding sequences provides insight into crucifer regulatory regions. Nat Genet 45(8): 891-898.
    • (2013) Nat Genet , vol.45 , Issue.8 , pp. 891-898
    • Haudry, A.1
  • 26
    • 0024618031 scopus 로고
    • Aspartate aminotransferase isozymes in the genus capsella (Brassicaceae): Subcellular location, gene duplication, and polymorphism
    • Hurka H, Freundner S, Brown AH, Plantholt U (1989) Aspartate aminotransferase isozymes in the genus Capsella (Brassicaceae): Subcellular location, gene duplication, and polymorphism. Biochem Genet 27(1-2): 77-90.
    • (1989) Biochem Genet , vol.27 , Issue.1-2 , pp. 77-90
    • Hurka, H.1    Freundner, S.2    Brown, A.H.3    Plantholt, U.4
  • 27
    • 0001139997 scopus 로고
    • Evolution of the tetraploid capsella bursa-pastoris (Brassicaceae): Isoelectric-focusing analysis of rubisco
    • Mummenhoff K, Hurka H (1990) Evolution of the tetraploid Capsella bursa-pastoris (Brassicaceae): Isoelectric-focusing analysis of Rubisco. Plant Syst Evol 172(1-4): 205-213.
    • (1990) Plant Syst Evol , vol.172 , Issue.1-4 , pp. 205-213
    • Mummenhoff, K.1    Hurka, H.2
  • 28
    • 84923602999 scopus 로고    scopus 로고
    • Inferring the mode of origin of polyploid species from next-generation sequence data
    • Roux C, Pannell JR (2015) Inferring the mode of origin of polyploid species from next-generation sequence data. Mol Ecol, 10.1111/mec.13078.
    • (2015) Mol Ecol
    • Roux, C.1    Pannell, J.R.2
  • 29
    • 84904275522 scopus 로고    scopus 로고
    • Mating system shifts and transposable element evolution in the plant genus capsella
    • Ågren JA, et al. (2014) Mating system shifts and transposable element evolution in the plant genus Capsella. BMC Genomics 15: 602.
    • (2014) BMC Genomics , vol.15 , pp. 602
    • Ågren, J.A.1
  • 30
    • 84907587760 scopus 로고    scopus 로고
    • Evidence for widespread positive and negative selection in coding and conserved noncoding regions of capsella grandiflora
    • Williamson RJ, et al. (2014) Evidence for widespread positive and negative selection in coding and conserved noncoding regions of Capsella grandiflora. PLoS Genet 10(9): e1004622.
    • (2014) PLoS Genet , vol.10 , Issue.9
    • Williamson, R.J.1
  • 32
    • 77954741256 scopus 로고    scopus 로고
    • Following tetraploidy in maize, a short deletion mechanism removed genes preferentially from one of the two homologs
    • Woodhouse MR, et al. (2010) Following tetraploidy in maize, a short deletion mechanism removed genes preferentially from one of the two homologs. PLoS Biol 8(6): e1000409.
    • (2010) PLoS Biol , vol.8 , Issue.6
    • Woodhouse, M.R.1
  • 33
    • 34547108086 scopus 로고    scopus 로고
    • Common sequence polymorphisms shaping genetic diversity in arabidopsis thaliana
    • Clark RM, et al. (2007) Common sequence polymorphisms shaping genetic diversity in Arabidopsis thaliana. Science 317(5836): 338-342.
    • (2007) Science , vol.317 , Issue.5836 , pp. 338-342
    • Clark, R.M.1
  • 34
    • 70350694443 scopus 로고    scopus 로고
    • Pindel: A pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads
    • Ye K, Schulz MH, Long Q, Apweiler R, Ning Z (2009) Pindel: A pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads. Bioinformatics 25(21): 2865-2871.
    • (2009) Bioinformatics , vol.25 , Issue.21 , pp. 2865-2871
    • Ye, K.1    Schulz, M.H.2    Long, Q.3    Apweiler, R.4    Ning, Z.5
  • 35
    • 84881026985 scopus 로고    scopus 로고
    • Massive genomic variation and strong selection in arabidopsis thaliana lines from Sweden
    • Long Q, et al. (2013) Massive genomic variation and strong selection in Arabidopsis thaliana lines from Sweden. Nat Genet 45(8): 884-890.
    • (2013) Nat Genet , vol.45 , Issue.8 , pp. 884-890
    • Long, Q.1
  • 36
    • 75949087420 scopus 로고    scopus 로고
    • VirtualPlant: A software platform to support systems biology research
    • Katari MS, et al. (2010) VirtualPlant: A software platform to support systems biology research. Plant Physiol 152(2): 500-515.
    • (2010) Plant Physiol , vol.152 , Issue.2 , pp. 500-515
    • Katari, M.S.1
  • 37
    • 84901818848 scopus 로고    scopus 로고
    • Dosage, duplication, and diploidization: Clarifying the interplay of multiple models for duplicate gene evolution over time
    • Conant GC, Birchler JA, Pires JC (2014) Dosage, duplication, and diploidization: Clarifying the interplay of multiple models for duplicate gene evolution over time. Curr Opin Plant Biol 19: 91-98.
    • (2014) Curr Opin Plant Biol , vol.19 , pp. 91-98
    • Conant, G.C.1    Birchler, J.A.2    Pires, J.C.3
  • 38
    • 0041732005 scopus 로고    scopus 로고
    • Plant polyploidy: Gene expression and genetic redundancy
    • Gottlieb LD (2003) Plant polyploidy: Gene expression and genetic redundancy. Heredity (Edinb) 91(2): 91-92.
    • (2003) Heredity (Edinb) , vol.91 , Issue.2 , pp. 91-92
    • Gottlieb, L.D.1
  • 39
    • 37249042614 scopus 로고    scopus 로고
    • Joint inference of the distribution of fitness effects of deleterious mutations and population demography based on nucleotide polymorphism frequencies
    • Keightley PD, Eyre-Walker A (2007) Joint inference of the distribution of fitness effects of deleterious mutations and population demography based on nucleotide polymorphism frequencies. Genetics 177(4): 2251-2261.
    • (2007) Genetics , vol.177 , Issue.4 , pp. 2251-2261
    • Keightley, P.D.1    Eyre-Walker, A.2
  • 40
    • 0002594984 scopus 로고
    • A rapid DNA isolation procedure for small quantities of fresh leaf tissue
    • Doyle JJ, Doyle JL (1987) A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochem Bull 19: 11-15.
    • (1987) Phytochem Bull , vol.19 , pp. 11-15
    • Doyle, J.J.1    Doyle, J.L.2
  • 41
    • 78349238864 scopus 로고    scopus 로고
    • Ray: Simultaneous assembly of reads from a mix of high-throughput sequencing technologies
    • Boisvert S, Laviolette F, Corbeil J (2010) Ray: Simultaneous assembly of reads from a mix of high-throughput sequencing technologies. J Comput Biol 17(11): 1519-1533.
    • (2010) J Comput Biol , vol.17 , Issue.11 , pp. 1519-1533
    • Boisvert, S.1    Laviolette, F.2    Corbeil, J.3
  • 42
    • 79956307251 scopus 로고    scopus 로고
    • Stampy: A statistical algorithm for sensitive and fast mapping of illumina sequence reads
    • Lunter G, Goodson M (2011) Stampy: A statistical algorithm for sensitive and fast mapping of Illumina sequence reads. Genome Res 21(6): 936-939.
    • (2011) Genome Res , vol.21 , Issue.6 , pp. 936-939
    • Lunter, G.1    Goodson, M.2
  • 43
    • 49549099085 scopus 로고    scopus 로고
    • HapCUT: An efficient and accurate algorithm for the haplotype assembly problem
    • Bansal V, Bafna V (2008) HapCUT: An efficient and accurate algorithm for the haplotype assembly problem. Bioinformatics 24(16):i153-i159.
    • (2008) Bioinformatics , vol.24 , Issue.16 , pp. i153-i159
    • Bansal, V.1    Bafna, V.2
  • 44
    • 79955483667 scopus 로고    scopus 로고
    • A framework for variation discovery and genotyping using next-generation DNA sequencing data
    • DePristo MA, et al. (2011) A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat Genet 43(5): 491-498.
    • (2011) Nat Genet , vol.43 , Issue.5 , pp. 491-498
    • DePristo, M.A.1
  • 45
    • 84899553363 scopus 로고    scopus 로고
    • RAxML version 8: A tool for phylogenetic analysis and post-analysis of large phylogenies
    • Stamatakis A (2014) RAxML version 8: A tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30(9): 1312-1313.
    • (2014) Bioinformatics , vol.30 , Issue.9 , pp. 1312-1313
    • Stamatakis, A.1
  • 46
    • 84881041428 scopus 로고    scopus 로고
    • SLiM: Simulating evolution with selection and linkage
    • Messer PW (2013) SLiM: Simulating evolution with selection and linkage. Genetics 194(4): 1037-1039.
    • (2013) Genetics , vol.194 , Issue.4 , pp. 1037-1039
    • Messer, P.W.1
  • 47
    • 84862506964 scopus 로고    scopus 로고
    • A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of drosophila melanogaster strain w1118; iso-2; iso-3
    • Cingolani P, et al. (2012) A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3. Fly (Austin) 6(2): 80-92.
    • (2012) Fly (Austin) , vol.6 , Issue.2 , pp. 80-92
    • Cingolani, P.1


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