Abstract
As different taxa evolve, gene order often changes slowly enough that chromosomal ‘blocks’ with conserved gene orders (synteny) are discernible. The MCScanX toolkit (https://github.com/wyp1125/MCScanX) was published in 2012 as freely available software for the detection of such ‘colinear blocks’ and subsequent synteny and evolutionary analyses based on genome-wide gene location and protein sequence information. Owing to its simplicity and high efficiency for colinear block detection, MCScanX provides a powerful tool for conducting diverse synteny and evolutionary analyses. Moreover, the detection of colinear blocks has been embraced as an integral step for pangenome graph construction. Here, new application trends of MCScanX are explored, striving to better connect this increasingly used tool to other tools and accelerate insight generation from exponentially growing sequence data. We provide a detailed protocol that covers how to install MCScanX on diverse platforms, tune parameters, prepare input files from data from the National Center for Biotechnology Information, run MCScanX and its visualization and evolutionary analysis tools, and connect MCScanX with external tools, including MCScanX-transposed, Circos and SynVisio. This protocol is easily implemented by users with minimal computational background and is adaptable to new data of interest to them. The data and utility programs for this protocol can be obtained from http://bdx-consulting.com/mcscanx-protocol.
Key points
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During evolution, chromosomes are dynamically reorganized by duplication, inversion and translocation. Comparative analysis of genomes is empowered by identifying homologous genes that remain in their ancestral positions (colinearity). The MCScanX software package aids evolutionary studies by facilitating the detection of colinearity blocks, in particular, enabling alignments of multiple chromosomes (or segments).
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MCScanX generates easy-to-read output files and has built-in visualization tools for easy representation of evolutionary insights.
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Data availability
Users can download the reference genome sequences and gene annotations of this study from Phytozome 13 (https://phytozome-next.jgi.doe.gov) and NCBI genome (https://www.ncbi.nlm.nih.gov/datasets/genome). Small-scale testing data for MCScanX are available under the ‘data’ folder of the MCScanX package. The data and programs for this protocol are wrapped as a ZIP file named ‘MCScanX_protocol.zip’, which is available at http://bdx-consulting.com/mcscanx-protocol.
Code availability
MCScanX is available at https://github.com/wyp1125/MCScanX. MCScanX-transposed is available at https://github.com/wyp1125/MCScanX-transposed. Programs especially for this protocol are available within the ‘MCScanX_protocol.zip’ file, which is available at http://bdx-consulting.com/mcscanx-protocol.
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Acknowledgements
A.H.P. appreciates funding from the National Science Foundation (NSF: DBI 0849896, MCB 0821096 and MCB 1021718) and from a Regents Professorship from the University System of Georgia. H.T. is supported by funding from the National Key Research and Development Program (2021YFF1000104). X.W. is supported by funding from the China Natural Science Foundation program (32070669). P.V.J. is supported by the National Institute on Alcohol Abuse and Alcoholism under award number Z01AA000135, the National Institute of Nursing Research and the Rockefeller University Heilbrunn Nurse Scholar Award. P.V.J. is supported by the Office of Workforce Diversity and the Office of Workforce Diversity, National Institutes of Health Distinguished Scholar Program.
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A.H.P. conceived the project. A.H.P. and P.V.J. guided the project. X.W. and H.T. developed early versions of the genome alignment algorithms. Y.W. improved on algorithms and developed the MCScanX protocol. Y.S. performed the experiments. Y.W., P.V.J. and A.H.P. drafted the manuscript. All authors contributed to the final writing and editing of the manuscript.
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Nature Protocols thanks Ingo Ebersberger and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.
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Key references using this protocol
Tang, H. B. et al. Genome Res. 18, 1944–1954 (2008): https://doi.org/10.1101/gr.080978.108
Wang, Y. et al. Nucleic Acids Res. 40, e49 (2012): https://doi.org/10.1093/nar/gkr1293
Wang, Y. et al. PLoS One 11, e0155637 (2016): https://doi.org/10.1371/journal.pone.0155637
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Supplementary Table 1
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Wang, Y., Tang, H., Wang, X. et al. Detection of colinear blocks and synteny and evolutionary analyses based on utilization of MCScanX. Nat Protoc (2024). https://doi.org/10.1038/s41596-024-00968-2
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DOI: https://doi.org/10.1038/s41596-024-00968-2
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