MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity
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Open Access
- 4 January 2012
- journal article
- research article
- Published by Oxford University Press (OUP) in Nucleic Acids Research
- Vol. 40 (7), e49
- https://doi.org/10.1093/nar/gkr1293
Abstract
MCScan is an algorithm able to scan multiple genomes or subgenomes in order to identify putative homologous chromosomal regions, and align these regions using genes as anchors. The MCScanX toolkit implements an adjusted MCScan algorithm for detection of synteny and collinearity that extends the original software by incorporating 14 utility programs for visualization of results and additional downstream analyses. Applications of MCScanX to several sequenced plant genomes and gene families are shown as examples. MCScanX can be used to effectively analyze chromosome structural changes, and reveal the history of gene family expansions that might contribute to the adaptation of lineages and taxa. An integrated view of various modes of gene duplication can supplement the traditional gene tree analysis in specific families. The source code and documentation of MCScanX are freely available at http://chibba.pgml.uga.edu/mcscan2/.This publication has 74 references indexed in Scilit:
- Ancestral polyploidy in seed plants and angiospermsNature, 2011
- Molecular evolution of glycinin and β-conglycinin gene families in soybean (Glycine max L. Merr.)Heredity, 2010
- Angiosperm genome comparisons reveal early polyploidy in the monocot lineageProceedings of the National Academy of Sciences of the United States of America, 2009
- Distribution, diversity, evolution, and survival of Helitrons in the maize genomeProceedings of the National Academy of Sciences of the United States of America, 2009
- Reconstruction of monocotelydoneous proto-chromosomes reveals faster evolution in plants than in animalsProceedings of the National Academy of Sciences of the United States of America, 2009
- The Sorghum bicolor genome and the diversification of grassesNature, 2009
- The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phylaNature, 2007
- Genome evolution in yeastsNature, 2004
- OrthoMCL: Identification of Ortholog Groups for Eukaryotic GenomesGenome Research, 2003
- Basic Local Alignment Search ToolJournal of Molecular Biology, 1990