Статья

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

Yupeng WangUniversity of GeorgiaHaibao TangPlant Genome Mapping Laboratory, 2Institute of Bioinformatics, 3Department of Plant Biology, University of Georgia, Athens, GA 30602, 4J. Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD 20850, 5Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, GA 30602, USA, 6Center for Genomics and Computational Biology, School of Life Sciences and School of Sciences, Hebei United University, Tangshan, Hebei 063009, China, 7Department of Genetics and 8Department of Crop and Soil Sciences, University of Georgia, Athens, GA 30602, USAJeremy D. DeBarryCenter for Tropical and Emerging Global Diseases, University of Georgia, Athens, GA 30602, USA,Xu TanDepartment of Plant Biology, University of Georgia, Athens, GA 30602,Jun LiInstitute of Bioinformatics,Xuewen WangCenter for Genomics and Computational Biology, School of Life Sciences and School of Sciences, Hebei United University, Tangshan, Hebei 063009, China,Taeyoung LeePlant Genome Mapping Laboratory,H. JinInstitute of Bioinformatics,Barry S. MarlerPlant Genome Mapping Laboratory,Hui GuoDepartment of Plant Biology, University of Georgia, Athens, GA 30602,Jessica C. KissingerUniversity of GeorgiaA. H. PatersonPlant Genome Mapping Laboratory, 2Institute of Bioinformatics, 3Department of Plant Biology, University of Georgia, Athens, GA 30602, 4J. Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD 20850, 5Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, GA 30602, USA, 6Center for Genomics and Computational Biology, School of Life Sciences and School of Sciences, Hebei United University, Tangshan, Hebei 063009, China, 7Department of Genetics and 8Department of Crop and Soil Sciences, University of Georgia, Athens, GA 30602, USA

2012en

ABI

Аннотация

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/.

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Идентификаторы

DOI: 10.1093/nar/gkr1293

Цитирования и источники

Цитирований: 7Использованных источников: 0

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