Visualization of Conserved Syntenic Blocks Among Six Cotton Genomes in CottonGen

Assessment of synteny between related genome sequences, coupled with software to visualize these relationships, has become a powerful tool in facilitating our understanding of genome and gene family evolution. As a resource for genomics, genetics and breeding research, the CottonGen research team has developed new synteny resources in the database using publicly available genome sequences, analysis software and graphical visualization tools. Synteny between Gossypium raimondii D5_BGI, Gossypium raimondii D5_JGI, Gossypium arboreum A2_BGI, Gossypium hirsutum AD1_BGI, Gossypium hirsutum AD1_NBI and Gossypium barbadense AD2_HAU was identified using MCScanX v1.0. Results are displayed using the Tripal Syntenic Viewer at the Cotton Genome website (https://www.cottongen.org/) with various highlighted features. The overall pattern of synteny and collinearity between chromosomes is displayed in a circular layout and the homologous gene pairs in each block are also displayed both in graphics and tables with hyperlinks to gene pages.