Wheat RCC1 Gene Collinearity Analysis

The RCC1 gene loci of wheat and its related genome donors were extracted from the corresponding annotated gff3 file (downloaded from Ensembl Plants, http://plants.ensembl.org/index.html) using a perl script. The Multiple Collinearity Scan toolkit (MCScanX) was used to analyze the gene collinearity among wheat, emmer wheat, and Aegilops tauschii with the default parameters (Kozlov et al., 2019 (link)
).
Homolog analysis of RCC1 genes among the A, B, and D genomes of wheat was performed based on the aligned result. The chromosomal distribution and collinearity of RCC1 genes among the wheat and its donors and of the homoeologous RCC1 genes among A, B, and D genomes were visualized by the circle package in R (Gu et al., 2014 (link)
).