Gene family evolution in green plants with emphasis on the origination and evolution of Arabidopsis thaliana genes

Plant Journal

Volumn 73, Issue 6, 2013, Pages 941-951

  Guo, Ya Long ^a,b  

^a INSTITUTE OF BOTANY   (China)

^b MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY   (Germany)

Author keywords

Arabidopsis thaliana; Evolutionary genomics; Gene family; Gene origination; Green plants

Indexed keywords

ARABIDOPSIS THALIANA; EVOLUTIONARY HISTORY; GENE FAMILIES; GENOMICS; GREEN PLANTS; NATURAL VARIATION; SIZE VARIATION; THALIANA;

BIOLOGY; PLANTS (BOTANY);

GENES;

ARABIDOPSIS PROTEIN;

ARABIDOPSIS; ARTICLE; GENETICS; MOLECULAR EVOLUTION; MULTIGENE FAMILY; PHYLOGENY; VIRIDIPLANTAE;

ARABIDOPSIS; ARABIDOPSIS PROTEINS; EVOLUTION, MOLECULAR; MULTIGENE FAMILY; PHYLOGENY; VIRIDIPLANTAE;

ARABIDOPSIS; ARABIDOPSIS THALIANA; MAMMALIA; VIRIDIPLANTAE;

EID: 84874935725     PISSN: 09607412     EISSN: 1365313X     Source Type: Journal    
DOI: 10.1111/tpj.12089     Document Type: Article

References (91)

1. Adams, K.L. and Wendel, J.F. (2005) Polyploidy and genome evolution in plants. Curr. Opin. Plant Biol. 8, 135-141. (Pubitemid 40323541)
2. Alba, M.M. and Castresana, J. (2005) Inverse relationship between evolutionary rate and age of mammalian genes. Mol. Biol. Evol. 22, 598-606. (Pubitemid 40299509)
3. Banks, J.A., Nishiyama, T., Hasebe, M. et al. (2011) The Selaginella genome identifies genetic changes associated with the evolution of vascular plants. Science, 332, 960-963.
4. Beilstein, M.A., Nagalingum, N.S., Clements, M.D., Manchester, S.R. and Mathews, S. (2010) Dated molecular phylogenies indicate a Miocene origin for Arabidopsis thaliana. Proc. Natl Acad. Sci. USA, 107, 18724-18728.
5. Blanc, G. and Wolfe, K.H. (2004) Widespread paleopolyploidy in model plant species inferred from age distributions of duplicate genes. Plant Cell, 16, 1667-1678. (Pubitemid 38908767)
6. Buschiazzo, E., Ritland, C., Bohlmann, J. and Ritland, K. (2012) Slow but not low: genomic comparisons reveals slower evolutionary rate and higher dN/dS in conifers compared to angiosperms. BMC Evol. Biol. 12, 8.
7. Cai, J.J., Borenstein, E., Chen, R. and Petrov, D.A. (2009) Similarly strong purifying selection acts on human disease genes of all evolutionary ages. Genome Biol. Evol. 1, 131-144.
8. Carroll, S., Wetherbee, S. and Grenier, J. (2001) From DNA to Diversity. Oxford, UK: Blackwell Science.
9. Chardon, F. and Damerval, C. (2005) Phylogenomic analysis of the PEBP gene family in cereals. J. Mol. Evol. 61, 579-590. (Pubitemid 41598604)
10. Chen, S., Zhang, Y.E. and Long, M. (2010) New genes in Drosophila quickly become essential. Science, 330, 1682-1685.
11. Conesa, A., Gotz, S., Garcia-Gomez, J.M., Terol, J., Talon, M. and Robles, M. (2005) Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics, 21, 3674-3676. (Pubitemid 41264107)
12. David, L.A. and Alm, E.J. (2011) Rapid evolutionary innovation during an Archaean genetic expansion. Nature, 469, 93-96.
13. De Bie, T., Cristianini, N., Demuth, J.P. and Hahn, M.W. (2006) CAFE: a computational tool for the study of gene family evolution. Bioinformatics, 22, 1269-1271. (Pubitemid 43779021)
14. De Bodt, S., Maere, S. and Van de Peer, Y. (2005) Genome duplication and the origin of angiosperms. Trends Ecol. Evol. 20, 591-597. (Pubitemid 41502811)
15. De Smet, R. and Van De Peer, Y. (2012) Redundancy and rewiring of genetic networks following genome-wide duplication events. Curr. Opin. Plant Biol. 15, 168-176.
16. Demuth, J.P. and Hahn, M.W. (2009) The life and death of gene families. BioEssays, 31, 29-39.
17. Demuth, J.P., De Bie, T., Stajich, J.E., Cristianini, N. and Hahn, M.W. (2006) The evolution of mammalian gene families. PLoS ONE, 1, e85.
18. Domazet-Loso, T. and Tautz, D. (2003) An evolutionary analysis of orphan genes in Drosophila. Genome Res. 13, 2213-2219. (Pubitemid 37265985)
19. Domazet-Loso, T. and Tautz, D. (2008) An ancient evolutionary origin of genes associated with human genetic diseases. Mol. Biol. Evol. 25, 2699-2707.
20. Domazet-Loso, T. and Tautz, D. (2010a) A phylogenetically based transcriptome age index mirrors ontogenetic divergence patterns. Nature, 468, 815-818.
21. Domazet-Loso, T. and Tautz, D. (2010b) Phylostratigraphic tracking of cancer genes suggests a link to the emergence of multicellularity in metazoa. BMC Biol. 8, 66.
22. Domazet-Loso, T., Brajkovic, J. and Tautz, D. (2007) A phylostratigraphy approach to uncover the genomic history of major adaptations in metazoan lineages. Trends Genet. 23, 533-539. (Pubitemid 350052349)
23. Doyle, J.J., Flagel, L.E., Paterson, A.H., Rapp, R.A., Soltis, D.E., Soltis, P.S. and Wendel, J.F. (2008) Evolutionary genetics of genome merger and doubling in plants. Annu. Rev. Genet. 42, 443-461.
24. Drosophila 12 Genomes Consortium. (2007) Evolution of genes and genomes on the Drosophila phylogeny. Nature, 450, 203-218.
25. Enright, A.J., Van Dongen, S. and Ouzounis, C.A. (2002) An efficient algorithm for large-scale detection of protein families. Nucleic Acids Res. 30, 1575-1584. (Pubitemid 34679732)
26. Fawcett, J.A., Rouze, P. and Van de Peer, Y. (2012) Higher intron loss rate in Arabidopsis thaliana than A. lyrata is consistent with stronger selection for a smaller genome. Mol. Biol. Evol. 29, 849-859.
27. Flagel, L.E. and Wendel, J.F. (2009) Gene duplication and evolutionary novelty in plants. New Phytol. 183, 557-564.
28. Freeling, M. (2009) Bias in plant gene content following different sorts of duplication: tandem, whole-genome, segmental, or by transposition. Annu. Rev. Plant Biol. 60, 433-453.
29. Gaut, B. (2002) Evolutionary dynamics of grass genomes. New Phytol. 154, 15-28. (Pubitemid 34294328)
30. Gaut, B.S., Yang, L., Takuno, S. and Eguiarte, L.E. (2011) The patterns and causes of variation in plant nucleotide substitution rates. Annu. Rev. Ecol. Evol. Syst. 42, 245-266.
31. Gene Ontology Consortium. (2004) The Gene Ontology (GO) database and informatics resource. Nucleic Acids Res. 32, D258-D261.
32. Gu, X., Wang, Y. and Gu, J. (2002) Age distribution of human gene families shows significant roles of both large- and small-scale duplications in vertebrate evolution. Nat. Genet. 31, 205-209.
33. Guo, Y.L., Fitz, J., Schneeberger, K., Ossowski, S., Cao, J. and Weigel, D. (2011a) Genome-wide comparison of nucleotide-binding site-leucine-rich repeat-encoding genes in Arabidopsis. Plant Physiol. 157, 757-769.
34. Guo, Y.L., Zhao, X., Lanz, C. and Weigel, D. (2011b) Evolution of the S-locus region in Arabidopsis thaliana relatives. Plant Physiol. 157, 937-946.
35. Hahn, M.W., De Bie, T., Stajich, J.E., Nguyen, C. and Cristianini, N. (2005) Estimating the tempo and mode of gene family evolution from comparative genomic data. Genome Res. 15, 1153-1160. (Pubitemid 41126871)
36. Hahn, M.W., Han, M.V. and Han, S.G. (2007) Gene family evolution across 12 Drosophila genomes. PLoS Genet. 3, e197.
37. Hollister, J.D., Smith, L.M., Guo, Y.L., Ott, F., Weigel, D. and Gaut, B.S. (2011) Transposable elements and small RNAs contribute to gene expression divergence between Arabidopsis thaliana and Arabidopsis lyrata. Proc. Natl Acad. Sci. USA, 108, 2322-2327.
38. Hu, T.T., Pattyn, P., Bakker, E.G. et al. (2011) The Arabidopsis lyrata genome sequence and the basis of rapid genome size change. Nat. Genet. 43, 476-481. International Rice Genome Sequencing Project. (2005) The map-based sequence of the rice genome. Nature, 436, 793-800.
39. Jiao, Y., Wickett, N.J., Ayyampalayam, S. et al. (2011) Ancestral polyploidy in seed plants and angiosperms. Nature, 473, 97-100.
40. Kellogg, E.A. (2001) Evolutionary history of the grasses. Plant Physiol. 125, 1198-1205. (Pubitemid 32224610)
41. Kersting, A.R., Bornberg-Bauer, E., Moore, A.D. and Grath, S. (2012) Dynamics and adaptive benefits of protein domain emergence and arrangements during plant genome evolution. Genome Biol. Evol. 4, 316-329.
42. Kim, S., Soltis, P.S., Wall, K. and Soltis, D.E. (2006) Phylogeny and domain evolution in the APETALA2-like gene family. Mol. Biol. Evol. 23, 107-120. (Pubitemid 41785958)
43. Koh, J., Soltis, P.S. and Soltis, D.E. (2010) Homeolog loss and expression changes in natural populations of the recently and repeatedly formed allotetraploid Tragopogon mirus (Asteraceae). BMC Genomics, 11, 97.
44. Lander, E.S., Linton, L.M., Birren, B. et al. International Human Genome Sequencing Consortium. (2001) Initial sequencing and analysis of the human genome. Nature, 409, 860-921. (Pubitemid 32165345)
45. Lang, D., Weiche, B., Timmerhaus, G., Richardt, S., Riano-Pachon, D.M., Correa, L.G., Reski, R., Mueller-Roeber, B. and Rensing, S.A. (2010) Genome- wide phylogenetic comparative analysis of plant transcriptional regulation: a timeline of loss, gain, expansion, and correlation with complexity. Genome Biol. Evol. 2, 488-503.
46. Larracuente, A.M., Sackton, T.B., Greenberg, A.J., Wong, A., Singh, N.D., Sturgill, D., Zhang, Y., Oliver, B. and Clark, A.G. (2008) Evolution of protein- coding genes in Drosophila. Trends Genet. 24, 114-123.
47. Leseberg, C.H., Li, A., Kang, H., Duvall, M. and Mao, L. (2006) Genome-wide analysis of the MADS-box gene family in Populus trichocarpa. Gene, 378, 84-94. (Pubitemid 44108468)
48. Li, X., Duan, X., Jiang, H. et al. (2006) Genome-wide analysis of basic/helixloop- helix transcription factor family in rice and Arabidopsis. Plant Physiol. 141, 1167-1184. (Pubitemid 44223270)
49. Liao, B.Y., Weng, M.P. and Zhang, J. (2010) Impact of extracellularity on the evolutionary rate of mammalian proteins. Genome Biol. Evol. 2, 39-43.
50. Lynch, M. and Conery, J.S. (2000) The evolutionary fate and consequences of duplicate genes. Science, 290, 1151-1155.
51. Lynch, M. and Conery, J.S. (2003) The evolutionary demography of duplicate genes. J. Struct. Funct. Genomics, 3, 35-44. (Pubitemid 36460242)
52. Maere, S., De Bodt, S., Raes, J., Casneuf, T., Van Montagu, M., Kuiper, M. and Van de Peer, Y. (2005) Modeling gene and genome duplications in eukaryotes. Proc. Natl Acad. Sci. USA, 102, 5454-5459. (Pubitemid 40530279)
53. Magallon, S.A. and Sanderson, M.J. (2005) Angiosperm divergence times: the effect of genes, codon positions, and time constraints. Evolution, 59, 1653-1670. (Pubitemid 41266771)
54. McLysaght, A., Hokamp, K. and Wolfe, K.H. (2002) Extensive genomic duplication during early chordate evolution. Nat. Genet. 31, 200-204.
55. Merchant, S.S., Prochnik, S.E., Vallon, O. et al. (2007) The Chlamydomonas genome reveals the evolution of key animal and plant functions. Science, 318, 245-250.
56. Milinkovitch, M.C., Helaers, R., Depiereux, E., Tzika, A.C. and Gabaldon, T. (2010) 2x genomes - depth does matter. Genome Biol. 11, R16.
57. Nei, M. and Rooney, A.P. (2005) Concerted and birth-and-death evolution of multigene families. Annu. Rev. Genet. 39, 121-152. (Pubitemid 43011110)
58. Ouyang, S., Zhu, W., Hamilton, J. et al. (2007) The TIGR Rice Genome Annotation Resource: improvements and new features. Nucleic Acids Res. 35, D883-D887. (Pubitemid 46056327)
59. Paterson, A.H., Bowers, J.E., Bruggmann, R. et al. (2009) The Sorghum bicolor genome and the diversification of grasses. Nature, 457, 551-556.
60. Porter, B.W., Paidi, M., Ming, R., Alam, M., Nishijima, W.T. and Zhu, Y.J. (2009) Genome-wide analysis of Carica papaya reveals a small NBS resistance gene family. Mol. Genet. Genomics, 281, 609-626.
61. Prachumwat, A. and Li, W.H. (2008) Gene number expansion and contraction in vertebrate genomes with respect to invertebrate genomes. Genome Res. 18, 221-232. (Pubitemid 351240732)
62. Proost, S., Pattyn, P., Gerats, T. and Van De Peer, Y. (2011) Journey through the past: 150 million years of plant genome evolution. Plant J. 66, 58-65.
63. Rensing, S.A., Lang, D., Zimmer, A.D. et al. (2007) The Physcomitrella genome reveals evolutionary insights into the conquest of land by plants. Science, 319, 64-69.
64. Rhesus Macaque Genome Sequencing and Analysis Consortium. (2007) Evolutionary and biomedical insights from the rhesus macaque genome. Science, 316, 222-234.
65. Schmid, M., Davison, T.S., Henz, S.R., Pape, U.J., Demar, M., Vingron, M., Scholkopf, B., Weigel, D. and Lohmann, J.U. (2005) A gene expression map of Arabidopsis thaliana development. Nat. Genet. 37, 501-506. (Pubitemid 40617278)
66. Schneider, A., Souvorov, A., Sabath, N., Landan, G., Gonnet, G.H. and Graur, D. (2009) Estimates of positive Darwinian selection are inflated by errors in sequencing, annotation, and alignment. Genome Biol. Evol. 1, 114-118.
67. Shiu, S.H., Karlowski, W.M., Pan, R., Tzeng, Y.H., Mayer, K.F. and Li, W.H. (2004) Comparative analysis of the receptor-like kinase family in Arabidopsis and rice. Plant Cell, 16, 1220-1234. (Pubitemid 38641516)
68. Simillion, C., Vandepoele, K., Van Montagu, M.C., Zabeau, M. and Van de Peer, Y. (2002) The hidden duplication past of Arabidopsis thaliana. Proc. Natl Acad. Sci. USA, 99, 13627-13632. (Pubitemid 35215431)
69. Singh, N.D., Larracuente, A.M., Sackton, T.B. and Clark, A.G. (2009) Comparative genomics on the Drosophila phylogenetic tree. Annu. Rev. Ecol. Evol. Syst. 40, 459-480.
70. Slotte, T., Bataillon, T., Hansen, T.T., St Onge, K., Wright, S.I. and Schierup, M.H. (2011) Genomic determinants of protein evolution and polymorphism in Arabidopsis. Genome Biol. Evol. 3, 1210-1219.
71. Soltis, D.E., Albert, V.A., Leebens-Mack, J., Bell, C.D., Paterson, A.H., Zheng, C., Sankoff, D., Depamphilis, C.W., Wall, P.K. and Soltis, P.S. (2009) Polyploidy and angiosperm diversification. Am. J. Bot. 96, 336-348.
72. Suyama, M., Torrents, D. and Bork, P. (2006) PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments. Nucleic Acids Res. 34, W609-W612. (Pubitemid 44529842)
73. Tautz, D. and Domazet-Loso, T. (2011) The evolutionary origin of orphan genes. Nat. Rev. Genet. 12, 692-702. The Arabidopsis Genome Initiative. (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature, 408, 796-815.
74. Tuskan, G.A., Difazio, S., Jansson, S. et al. (2006) The genome of black cottonwood, Populus trichocarpa (Torr. & Gray). Science, 313, 1596-1604. (Pubitemid 44414027)
75. Van Bel, M., Proost, S., Wischnitzki, E., Movahedi, S., Scheerlinck, C., Van de Peer, Y. and Vandepoele, K. (2012) Dissecting plant genomes with the PLAZA comparative genomics platform. Plant Physiol. 158, 590-600.
76. Van De Peer, Y. (2011) A mystery unveiled. Genome Biol. 12, 113.
77. Van De Peer, Y., Maere, S. and Meyer, A. (2009) The evolutionary significance of ancient genome duplications. Nat. Rev. Genet. 10, 725-732.
78. Van Dongen, S. (2000) Graph clustering by flow simulation. PhD Thesis, University of Utrecht, The Netherlands.
79. Warringer, J. and Blomberg, A. (2006) Evolutionary constraints on yeast protein size. BMC Evol. Biol. 6, 61.
80. Wellman, C.H., Osterloff, P.L. and Mohiuddin, U. (2003) Fragments of the earliest land plants. Nature, 425, 282-285. (Pubitemid 37158401)
81. Wikström, N., Savolainen, V. and Chase, M.W. (2001) Evolution of the angiosperms: calibrating the family tree. Proc. Biol. Sci. 268, 2211-2220. (Pubitemid 33032897)
82. Woodhouse, M.R., Tang, H. and Freeling, M. (2011) Different genes families in Arabidopsis thaliana transposed in different epochs and at different frequencies throughout the rosids. Plant Cell, 23, 4241-4253.
83. Yang, Z. (1997) PAML: a program package for phylogenetic analysis by maximum likelihood. Comput. Appl. Biosci. 13, 555-556. (Pubitemid 27480216)
84. Yang, L. and Gaut, B.S. (2011) Factors that contribute to variation in evolutionary rate among Arabidopsis Genes. Mol. Biol. Evol. 28, 2359-2369.
85. Yang, X., Jawdy, S., Tschaplinski, T.J. and Tuskan, G.A. (2009) Genomewide identification of lineage-specific genes in Arabidopsis, Oryza and Populus. Genomics, 93, 473-480.
86. Yang, L., Takuno, S., Waters, E.R. and Gaut, B.S. (2011) Lowly expressed genes in Arabidopsis thaliana bear the signature of possible pseudogenization by promoter degradation. Mol. Biol. Evol. 28, 1193-1203.
87. Zhang, Y.E., Vibranovski, M.D., Krinsky, B.H. and Long, M. (2010a) Agedependent chromosomal distribution of male-biased genes in Drosophila. Genome Res. 20, 1526-1533.
88. Zhang, Y.E., Vibranovski, M.D., Landback, P., Marais, G.A. and Long, M. (2010b) Chromosomal redistribution of male-biased genes in mammalian evolution with two bursts of gene gain on the X chromosome. PLoS Biol. 8, e1000494.
89. Zhang, Y.E., Landback, P., Vibranovski, M.D. and Long, M. (2011) Accelerated recruitment of new brain development genes into the human genome. PLoS Biol. 9, e1001179.
90. Zhang, X.C., Wang, Z., Zhang, X., Le, M.H., Sun, J., Xu, D., Cheng, J. and Stacey, G. (2012) Evolutionary dynamics of protein domain architecture in plants. BMC Evol. Biol. 12, 6.
91. Zimmer, A., Lang, D., Richardt, S., Frank, W., Reski, R. and Rensing, S.A. (2007) Dating the early evolution of plants: detection and molecular clock analyses of orthologs. Mol. Genet. Genomics, 278, 393-402. (Pubitemid 47437683)