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Synteny and dot plot generation for the analysis of chromosome evolution

YL Ying Li
PS Pengchuan Sun
ZL Zhiqiang Lu
JC Jinyuan Chen
ZW Zhenyue Wang
XD Xin Du
ZZ Zeyu Zheng
YW Ying Wu
HH Hongyin Hu
JY Jiao Yang
JM Jianxiang Ma
JL Jianquan Liu
YY Yongzhi Yang
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For genomes with pseudochromosomes, syntenic blocks between pairs of genomes, defined as a region containing more than five collinear genes, were searched for by the MCScanX79 package. The results were represented visually in combination with the phylogenetic tree. Ks of the collinear orthologous gene pairs was determined using the Perl script “add_ka_and_ks_to_collinearity.pl” implemented in MCScanX79. CDS anchors between every possible pair of chromosomes in multiple genomes were searched for using BLASTP69 (E-value < 1 × 10−5). The best matches were displayed in red, and other matches were displayed in blue to help distinguish orthology from paralogy. All dot plots were drawn by WGDI (https://pypi.org/project/WGDI/).

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