MCScanX: A toolkit for detection and evolutionary analysis of gene synteny and collinearity

Nucleic Acids Research

Volumn 40, Issue 7, 2012, Pages

  Wang, Yupeng ^a   Tang, Haibao ^a,b   Debarry, Jeremy D ^a   Tan, Xu ^a   Li, Jingping ^a   Wang, Xiyin ^a,c   Lee, Tae Ho ^a   Jin, Huizhe ^a   Marler, Barry ^a   Guo, Hui ^a   Kissinger, Jessica C ^a,d   Paterson, Andrew H ^a,d  

^a UNIVERSITY OF GEORGIA   (United States)

^b J CRAIG VENTER INSTITUTE   (United States)

^c HEBEI UNITED UNIVERSITY   (China)

^d University of Georgia   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ADAPTATION; ALGORITHM; ARTICLE; CHROMOSOME; CHROMOSOME STRUCTURE; COLLINEAR BLOCK; COMPUTER PROGRAM; GENE; GENE DUPLICATION; GENOME; MULTIGENE FAMILY; NONHUMAN; PLANT GENOME; PRIORITY JOURNAL; SYNTENY; TAXON;

ALGORITHMS; ANGIOSPERMS; EVOLUTION, MOLECULAR; GENE DUPLICATION; GENE ORDER; GENOME, PLANT; GENOMICS; MULTIGENE FAMILY; SOFTWARE; SYNTENY;

EID: 84860137835     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkr1293     Document Type: Article

References (73)

1. Coghlan, A., Eichler, E.E., Oliver, S.G., Paterson, A.H. and Stein, L. (2005) Chromosome evolution in eukaryotes: a multi-kingdom perspective. Trends Genet., 21, 673-682. (Pubitemid 41608690)
2. Dietrich, F.S., Voegeli, S., Brachat, S., Lerch, A., Gates, K., Steiner, S., Mohr, C., Pohlmann, R., Luedi, P., Choi, S.D. et al. (2004) The Ashbya gossypii genome as a tool for mapping the ancient Saccharomyces cerevisiae genome. Science, 304, 304-307. (Pubitemid 38452185)
3. Dujon, B., Sherman, D., Fischer, G., Durrens, P., Casaregola, S., Lafontaine, I., De Montigny, J., Marck, C., Neuveglise, C., Talla, E. et al. (2004) Genome evolution in yeasts. Nature, 430, 35-44. (Pubitemid 38915217)
4. Nakatani, Y., Takeda, H., Kohara, Y. and Morishita, S. (2007) Reconstruction of the vertebrate ancestral genome reveals dynamic genome reorganization in early vertebrates. Genome Res., 17, 1254-1265. (Pubitemid 47360900)
5. Salse, J., Abrouk, M., Bolot, S., Guilhot, N., Courcelle, E., Faraut, T., Waugh, R., Close, T.J., Messing, J. and Feuillet, C. (2009) Reconstruction of monocotelydoneous proto-chromosomes reveals faster evolution in plants than in animals. Proc. Natl Acad. Sci. USA, 106, 14908-14913.
6. Bowers, J.E., Chapman, B.A., Rong, J. and Paterson, A.H. (2003) Unravelling angiosperm genome evolution by phylogenetic analysis of chromosomal duplication events. Nature, 422, 433-438. (Pubitemid 36411396)
7. Hufton, A.L., Groth, D., Vingron, M., Lehrach, H., Poustka, A.J. and Panopoulou, G. (2008) Early vertebrate whole genome duplications were predated by a period of intense genome rearrangement. Genome Res., 18, 1582-1591.
8. Otto, S.P. and Whitton, J. (2000) Polyploid incidence and evolution. Annu. Rev. Genet., 34, 401-437. (Pubitemid 32065927)
9. Ranz, J.M., Casals, F. and Ruiz, A. (2001) How malleable is the eukaryotic genomë Extreme rate of chromosomal rearrangement in the genus Drosophila. Genome Res., 11, 230-239. (Pubitemid 32166532)
10. Bourque, G., Pevzner, P.A. and Tesler, G. (2004) Reconstructing the genomic architecture of ancestral mammals: lessons from human, mouse, and rat genomes. Genome Res., 14, 507-516. (Pubitemid 38500221)
11. Debarry, J.D. and Kissinger, J.C. (2011) Jumbled genomes: missing Apicomplexan synteny. Mol. Biol. Evol., 28, 2855-2871.
12. Vandepoele, K., Saeys, Y., Simillion, C., Raes, J. and Van De Peer, Y. (2002) The automatic detection of homologous regions (ADHoRe) and its application to microcolinearity between Arabidopsis and rice. Genome Res., 12, 1792-1801. (Pubitemid 35363684)
13. Luc, N., Risler, J.L., Bergeron, A. and Raffinot, M. (2003) Gene teams: a new formalization of gene clusters for comparative genomics. Comput. Biol. Chem., 27, 59-67.
14. Hampson, S., McLysaght, A., Gaut, B (Pubitemid 36621759)
15. Ling, X., He, X. and Xin, D. (2009) Detecting gene clusters under evolutionary constraint in a large number of genomes. Bioinformatics, 25, 571-577.
16. Vergara, I.A. and Chen, N. (2009) Using OrthoCluster for the detection of synteny blocks among multiple genomes. Curr. Protoc. Bioinform., 27, 6.10.1-6.10.18.
17. Haas, B.J., Delcher, A.L., Wortman, J.R. and Salzberg, S.L. (2004) DAGchainer: a tool for mining segmental genome duplications and synteny. Bioinformatics, 20, 3643-3646. (Pubitemid 40136803)
18. Wang, X., Shi, X., Li, Z., Zhu, Q., Kong, L., Tang, W., Ge, S. and Luo, J. (2006) Statistical inference of chromosomal homology based on gene colinearity and applications to Arabidopsis and rice. BMC Bioinformatics, 7, 447.
19. Tang, H., Wang, X., Bowers, J.E., Ming, R., Alam, M. and Paterson, A.H. (2008) Unraveling ancient hexaploidy through multiply-aligned angiosperm gene maps. Genome Res., 18, 1944-1954.
20. Soderlund, C., Nelson, W., Shoemaker, A. and Paterson, A. (2006) SyMAP: a system for discovering and viewing syntenic regions of FPC maps. Genome Res., 16, 1159-1168. (Pubitemid 44320403)
21. Calabrese, P.P., Chakravarty, S. and Vision, T.J. (2003) Fast identification and statistical evaluation of segmental homologies in comparative maps. Bioinformatics, 19(Suppl. 1), i74-i80. (Pubitemid 41185602)
22. Rodelsperger, C. and Dieterich, C. (2010) CYNTENATOR: progressive gene order alignment of 17 vertebrate genomes. PLoS One, 5, e8861.
23. Tang, H., Bowers, J.E., Wang, X., Ming, R., Alam, M. and Paterson, A.H. (2008) Synteny and collinearity in plant genomes. Science, 320, 486-488. (Pubitemid 351590631)
24. Abrouk, M., Murat, F., Pont, C., Messing, J., Jackson, S., Faraut, T., Tannier, E., Plomion, C., Cooke, R., Feuillet, C. et al. (2010) Palaeogenomics of plants: synteny-based modelling of extinct ancestors. Trends Plant Sci., 15, 479-487.
25. Jun, J., Mandoiu, I.I. and Nelson, C.E. (2009) Identification of mammalian orthologs using local synteny. BMC Genomics, 10, 630.
26. Casneuf, T., De Bodt, S., Raes, J., Maere, S. and Van de Peer, Y. (2006) Nonrandom divergence of gene expression following gene and genome duplications in the flowering plant Arabidopsis thaliana. Genome Biol., 7, R13.
27. 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.
28. Cai, B., Yang, X., Tuskan, G.A. and Cheng, Z.M. (2011) MicroSyn: a user friendly tool for detection of microsynteny in a gene family. BMC Bioinformatics, 12, 79.
29. Wang, X., Tang, H. and Paterson, A.H. (2011) Seventy million years of concerted evolution of a homoeologous chromosome pair, in parallel, in major Poaceae lineages. Plant Cell, 23, 27-37.
30. Wang, X., Tang, H., Bowers, J.E. and Paterson, A.H. (2009) Comparative inference of illegitimate recombination between rice and sorghum duplicated genes produced by polyploidization. Genome Res., 19, 1026-1032.
31. Lyons, E., Pedersen, B., Kane, J., Alam, M., Ming, R., Tang, H., Wang, X., Bowers, J., Paterson, A., Lisch, D. et al. (2008) Finding and comparing syntenic regions among Arabidopsis and the outgroups papaya, poplar, and grape: CoGe with rosids. Plant Physiol., 148, 1772-1781. (Pubitemid 352847452)
32. Charles, M., Tang, H.B., Belcram, H., Paterson, A., Gornicki, P. and Chalhoub, B. (2009) Sixty million years in evolution of soft grain trait in grasses: emergence of the softness locus in the common ancestor of Pooideae and Ehrhartoideae, after their divergence from Panicoideae. Mol. Biol. Evol., 26, 1651-1661.
33. Lin, L., Pierce, G.J., Bowers, J.E., Estill, J.C., Compton, R.O., Rainville, L.K., Kim, C., Lemke, C., Rong, J., Tang, H. et al. (2010) A draft physical map of a D-genome cotton species (Gossypium raimondii). BMC Genomics, 11, 395.
34. Lin, L., Tang, H., Compton, R.O., Lemke, C., Rainville, L.K., Wang, X., Rong, J., Rana, M.K. and Paterson, A.H. (2011) Comparative analysis of Gossypium and Vitis genomes indicates genome duplication specific to the Gossypium lineage. Genomics, 97, 313-320.
35. Tang, H., Bowers, J.E., Wang, X. and Paterson, A.H. (2010) Angiosperm genome comparisons reveal early polyploidy in the monocot lineage. Proc. Natl Acad. Sci. USA, 107, 472-477.
36. Wang, Y., Wang, X., Tang, H., Tan, X., Ficklin, S.P., Feltus, F.A. and Paterson, A.H. (2011) Modes of gene duplication contribute differently to genetic novelty and redundancy, but show parallels across divergent angiosperms. PLoS One, 6, e28150.
37. Paterson, A.H., Bowers, J.E., Bruggmann, R., Dubchak, I., Grimwood, J., Gundlach, H., Haberer, G., Hellsten, U., Mitros, T., Poliakov, A. et al. (2009) The Sorghum bicolor genome and the diversification of grasses. Nature, 457, 551-556.
38. Causier, B., Castillo, R., Xue, Y.B., Schwarz-Sommer, Z. and Davies, B. (2010) Tracing the evolution of the floral homeotic B-and C-function genes through genome synteny. Mol. Biol. Evol., 27, 2651-2664.
39. Knoller, A.S., Blakeslee, J.J., Richards, E.L., Peer, W.A. and Murphy, A.S. (2010) Brachytic2/ZmABCB1 functions in IAA export from intercalary meristems. J. Exp. Bot., 61, 3689-3696.
40. Watanabe, M., Mochida, K., Kato, T., Tabata, S., Yoshimoto, N., Noji, M. and Saito, K. (2008) Comparative genomics and reverse genetics analysis reveal indispensable functions of the serine acetyltransferase gene family in Arabidopsis. Plant Cell, 20, 2484-2496. (Pubitemid 352844613)
41. Okazaki, Y., Shimojima, M., Sawada, Y., Toyooka, K., Narisawa, T., Mochida, K., Tanaka, H., Matsuda, F., Hirai, A., Hirai, M.Y. et al. (2009) A chloroplastic UDP-glucose pyrophosphorylase from Arabidopsis is the committed enzyme for the first step of sulfolipid biosynthesis. Plant Cell, 21, 892-909.
42. Hyun, T.K., Kim, J.S., Kwon, S.Y. and Kim, S.H. (2010) Comparative genomic analysis of mitogen activated protein kinase gene family in grapevine. Genes Genom., 32, 275-281.
43. Li, C. and Zhang, Y.M. (2011) Molecular evolution of glycinin and beta-conglycinin gene families in soybean (Glycine max L. Merr.). Heredity, 106, 633-641.
44. Li, W., Liu, B., Yu, L., Feng, D., Wang, H. and Wang, J. (2009) Phylogenetic analysis, structural evolution and functional divergence of the 12-oxo-phytodienoate acid reductase gene family in plants. BMC Evol. Biol., 9, 90.
45. Kopriva, S., Mugford, S.G., Matthewman, C. and Koprivova, A. (2009) Plant sulfate assimilation genes: redundancy versus specialization. Plant Cell Rep., 28, 1769-1780.
46. Palmieri, F., Pierri, C.L., De Grassi, A., Nunes-Nesi, A. and Fernie, A.R. (2011) Evolution, structure and function of mitochondrial carriers: a review with new insights. Plant J., 66, 161-181.
47. Higgins, J.A., Bailey, P.C. and Laurie, D.A. (2010) Comparative genomics of flowering time pathways using Brachypodium distachyon as a model for the temperate grasses. PLoS One, 5, e10065.
48. Wang, X., Gowik, U., Tang, H., Bowers, J.E., Westhoff, P. and Paterson, A.H. (2009) Comparative genomic analysis of C4 photosynthetic pathway evolution in grasses. Genome Biol., 10, R68.
49. Altschul, S.F., Gish, W., Miller, W., Myers, E.W. and Lipman, D.J. (1990) Basic local alignment search tool. J. Mol. Biol., 215, 403-410.
50. Li, L., Stoeckert, C.J. Jr and Roos, D.S. (2003) OrthoMCL: identification of ortholog groups for eukaryotic genomes. Genome Res., 13, 2178-2189. (Pubitemid 37161775)
51. Nei, M. and Gojobori, T. (1986) Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Mol. Biol. Evol., 3, 418-426. (Pubitemid 16010523)
52. 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)
53. Zhao, X.P., Si, Y., Hanson, R.E., Crane, C.F., Price, H.J., Stelly, D.M., Wendel, J.F. and Paterson, A.H. (1998) Dispersed repetitive DNA has spread to new genomes since polyploid formation in cotton. Genome Res., 8, 479-492. (Pubitemid 28256797)
54. Ganko, E.W., Meyers, B.C. and Vision, T.J. (2007) Divergence in expression between duplicated genes in Arabidopsis. Mol. Biol. Evol., 24, 2298-2309. (Pubitemid 47574728)
55. Jiang, N., Bao, Z., Zhang, X., Eddy, S.R. and Wessler, S.R. (2004) Pack-MULE transposable elements mediate gene evolution in plants. Nature, 431, 569-573. (Pubitemid 39336337)
56. Yang, L. and Bennetzen, J.L. (2009) Distribution, diversity, evolution, and survival of Helitrons in the maize genome. Proc. Natl Acad. Sci. USA, 106, 19922-19927.
57. Wang, W., Zheng, H., Fan, C., Li, J., Shi, J., Cai, Z., Zhang, G., Liu, D., Zhang, J., Vang, S. et al. (2006) High rate of chimeric gene origination by retroposition in plant genomes. Plant Cell, 18, 1791-1802. (Pubitemid 44260178)
58. Vergara, I.A. and Chen, N. (2010) Large synteny blocks revealed between Caenorhabditis elegans and Caenorhabditis briggsae genomes using OrthoCluster. BMC Genomics, 11, 516.
59. Jiao, Y., Wickett, N.J., Ayyampalayam, S., Chanderbali, A.S., Landherr, L., Ralph, P.E., Tomsho, L.P., Hu, Y., Liang, H., Soltis, P.S. et al. (2011) Ancestral polyploidy in seed plants and angiosperms. Nature, 473, 97-100.
60. Jaillon, O., Aury, J.M., Noel, B., Policriti, A., Clepet, C., Casagrande, A., Choisne, N., Aubourg, S., Vitulo, N., Jubin, C. et al. (2007) The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla. Nature, 449, 463-467. (Pubitemid 47509545)
61. Schmutz, J., Cannon, S.B., Schlueter, J., Ma, J., Mitros, T., Nelson, W., Hyten, D.L., Song, Q., Thelen, J.J., Cheng, J. et al. (2010) Genome sequence of the palaeopolyploid soybean. Nature, 463, 178-183.
62. Wei, F., Coe, E., Nelson, W., Bharti, A.K., Engler, F., Butler, E., Kim, H., Goicoechea, J.L., Chen, M., Lee, S. et al. (2007) Physical and genetic structure of the maize genome reflects its complex evolutionary history. PLoS Genet., 3, e123.
63. Salse, J., Bolot, S., Throude, M., Jouffe, V., Piegu, B., Quraishi, U.M., Calcagno, T., Cooke, R., Delseny, M. and Feuillet, C. (2008) Identification and characterization of shared duplications between rice and wheat provide new insight into grass genome evolution. Plant Cell, 20, 11-24. (Pubitemid 352844030)
64. Rizzon, C., Ponger, L. and Gaut, B.S. (2006) Striking similarities in the genomic distribution of tandemly arrayed genes in Arabidopsis and rice. PLoS Comput. Biol., 2, e115.
65. Sampedro, J., Lee, Y., Carey, R.E., dePamphilis, C. and Cosgrove, D.J. (2005) Use of genomic history to improve phylogeny and understanding of births and deaths in a gene family. Plant J., 44, 409-419.
66. Guindon, S., Dufayard, J.F., Lefort, V., Anisimova, M., Hordijk, W. and Gascuel, O. (2010) New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst. Biol., 59, 307-321.
67. Becker, A. and Theissen, G. (2003) The major clades of MADS-box genes and their role in the development and evolution of flowering plants. Mol. Phylogenet. Evol., 29, 464-489. (Pubitemid 37491891)
68. Freeling, M., Lyons, E., Pedersen, B., Alam, M., Ming, R. and Lisch, D. (2008) Many or most genes in Arabidopsis transposed after the origin of the order Brassicales. Genome Res., 18, 1924-1937.
69. Cannon, S.B., Kozik, A., Chan, B., Michelmore, R. and Young, N.D. (2003) DiagHunter and GenoPix2D: programs for genomic comparisons, large-scale homology discovery and visualization. Genome Biol., 4, R68.
70. Sinha, A.U. and Meller, J. (2007) Cinteny: flexible analysis and visualization of synteny and genome rearrangements in multiple organisms. BMC Bioinformatics, 8, 82.
71. Ng, M.P., Vergara, I.A., Frech, C., Chen, Q., Zeng, X., Pei, J. and Chen, N. (2009) OrthoClusterDB: an online platform for synteny blocks. BMC Bioinformatics, 10, 192.
72. Fostier, J., Proost, S., Dhoedt, B., Saeys, Y., Demeester, P., Van de Peer, Y. and Vandepoele, K. (2011) A greedy, graph-based algorithm for the alignment of multiple homologous gene lists. Bioinformatics, 27, 749-756.
73. Soderlund, C., Bomhoff, M. and Nelson, W.M. (2011) SyMAP v3.4: a turnkey synteny system with application to plant genomes. Nucleic Acids Res., 39, e68.