Detection of colinear blocks and synteny and evolutionary analyses based on utilization of MCScanX

Yupeng Wang, Haibao Tang, Xiyin Wang, Ying Sun, Paule V. Joseph, Andrew H. Paterson

Published: 2024-03-15 DOI: 10.1038/s41596-024-00968-2

MCScanX

colinear blocks

synteny

evolutionary analysis

genome reorganization

AI 解读

Supplementary information

Supplementary Table 1

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Supplementary information

Guo, H. et al. Gene duplication and genetic innovation in cereal genomes. Genome Res. 29, 261–269 (2019).
Tang, H. et al. Synteny and collinearity in plant genomes. Science 320, 486–488 (2008).
Tang, H. B. et al. Unraveling ancient hexaploidy through multiply-aligned angiosperm gene maps. Genome Res. 18, 1944–1954 (2008).
Wang, X. Y. et al. Statistical inference of chromosomal homology based on gene colinearity and applications to Arabidopsis and rice. BMC Bioinforma. 7, 447 (2006).
Myers, P. Z. Synteny: inferring ancestral genomes. Nat. Educ. 1, 47 (2008).
Darling, A. C., Mau, B., Blattner, F. R. & Perna, N. T. Mauve: multiple alignment of conserved genomic sequence with rearrangements. Genome Res. 14, 1394–1403 (2004).
Bowers, J. E., Chapman, B. A., Rong, J. K. & Paterson, A. H. Unravelling angiosperm genome evolution by phylogenetic analysis of chromosomal duplication events. Nature 422, 433–438 (2003).
Tang, H. B., Bowers, J. E., Wang, X. Y. & Paterson, A. H. Angiosperm genome comparisons reveal early polyploidy in the monocot lineage. Proc. Natl Acad. Sci. USA 107, 472–477 (2010).
Freeling, M. et al. Many or most genes in Arabidopsis transposed after the origin of the order Brassicales. Genome Res. 18, 1924–1937 (2008).
Pevzner, P. & Tesler, G. Genome rearrangements in mammalian evolution: lessons from human and mouse genomes. Genome Res. 13, 37–45 (2003).
Jun, J., Mandoiu, I. I. & Nelson, C. E. Identification of mammalian orthologs using local synteny. BMC Genomics 10, 630 (2009).
Tekaia, F. Inferring orthologs: open questions and perspectives. Genomics Insights 9, 17–28 (2016).
Zheng, X. H., Lu, F., Wang, Z. Y., Hoover, J. & Mural, R. Using shared genomic synteny and shared protein functions to enhance the identification of orthologous gene pairs. Bioinformatics 21, 703–710 (2005).
Freeling, M. Bias in plant gene content following different sorts of duplication: tandem, whole-genome, segmental, or by transposition. Annu. Rev. f. Plant Biol. 60, 433–453 (2009).
Hakes, L., Pinney, J. W., Lovell, S. C., Oliver, S. G. & Robertson, D. L. All duplicates are not equal: the difference between small-scale and genome duplication. Genome Biol. 8, R209 (2007).
Li, Z. et al. Multiple large-scale gene and genome duplications during the evolution of hexapods. Proc. Natl Acad. Sci. USA 115, 4713–4718 (2018).
Liu, C. et al. Illegitimate recombination between homeologous genes in wheat genome. Front. Plant Sci. 11, 1076 (2020).
Wang, X. Y., Tang, H. B., Bowers, J. E. & Paterson, A. H. Comparative inference of illegitimate recombination between rice and sorghum duplicated genes produced by polyploidization. Genome Res. 19, 1026–1032 (2009).
Wang, Y., Ficklin, S. P., Wang, X., Feltus, F. A. & Paterson, A. H. Large-scale gene relocations following an ancient genome triplication associated with the diversification of core eudicots. PLoS One 11, e0155637 (2016).
Wang, Y., Li, J. & Paterson, A. H. MCScanX-transposed: detecting transposed gene duplications based on multiple colinearity scans. Bioinformatics 29, 1458–1460 (2013).
Qiao, X. et al. Gene duplication and evolution in recurring polyploidization-diploidization cycles in plants. Genome Biol. 20, 38 (2019).
Wang, Y. P. et al. Modes of gene duplication contribute differently to genetic novelty and redundancy, but show parallels across divergent angiosperms. Plos One 6, e28150 (2011).
Wang, Y. et al. MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity. Nucleic Acids Res. 40, e49 (2012).
Krzywinski, M. et al. Circos: an information aesthetic for comparative genomics. Genome Res. 19, 1639–1645 (2009).
Bandi, V., Gutwin, C. Interactive exploration of genomic conservation. In Proceedings of the 46th Graphics Interface Conference 2020 (Waterloo, 2020).
Chen, C. et al. TBtools: an integrative toolkit developed for interactive analyses of big biological data. Mol. Plant 13, 1194–1202 (2020).
Altschul, S. F. et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25, 3389–3402 (1997).
Haas, B. J., Delcher, A. L., Wortman, J. R. & Salzberg, S. L. DAGchainer: a tool for mining segmental genome duplications and synteny. Bioinformatics 20, 3643–3646 (2004).
Lallemand, T., Leduc, M., Landes, C., Rizzon, C. & Lerat, E. An overview of duplicated gene detection methods: why the duplication mechanism has to be accounted for in their choice. Genes (Basel) 11, 1046 (2020).
Drillon, G., Carbone, A. & Fischer, G. SynChro: a fast and easy tool to reconstruct and visualize synteny blocks along eukaryotic chromosomes. PLoS One 9, e92621 (2014).
Xu, Y. et al. VGSC: a web-based vector graph toolkit of genome synteny and collinearity. Biomed. Res. Int. 2016, 7823429 (2016).
Kolishovski, G. et al. The JAX Synteny Browser for mouse-human comparative genomics. Mamm. Genome 30, 353–361 (2019).
Lovell, J. T. et al. The genomic landscape of molecular responses to natural drought stress in Panicum hallii. Nat. Commun. 9, 5213 (2018).
Marchant, D. B. et al. Dynamic genome evolution in a model fern. Nat. Plants 8, 1038–1051 (2021).
Lovell, J. T. et al. Four chromosome scale genomes and a pan-genome annotation to accelerate pecan tree breeding. Nat. Commun. 12, 4125 (2021).
Song, J. M. et al. Eight high-quality genomes reveal pan-genome architecture and ecotype differentiation of Brassica napus. Nat. Plants 6, 34–45 (2020).
Yang, T. et al. Improved pea reference genome and pan-genome highlight genomic features and evolutionary characteristics. Nat. Genet. 54, 1553–1563 (2022).
Tao, Y. et al. Extensive variation within the pan-genome of cultivated and wild sorghum. Nat. Plants 7, 766–773 (2021).
Tamura, K., Stecher, G. & Kumar, S. MEGA11: molecular evolutionary genetics analysis version 11. Mol. Biol. Evol. 38, 3022–3027 (2021).

Detection of colinear blocks and synteny and evolutionary analyses based on utilization of MCScanX

Supplementary information

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