Conserved syntenic regions among publicly available cotton genomes were analyzed by CottonGen and made available using the Tripal Synteny Viewer developed by the Fei Bioinformatics Lab from the Boyce Thomson Institute at Cornell University. Analysis was done using MCScanX (Wang et al. 2012) with default settings and blast files were made using blastp with an expectation value cutoff < 1e-10, maximum alignment of 5, and maximum scores of 5.
The synteny viewer displays all the conserved syntenic blocks between a selected chromosome of a genome and another genome in a circular and tabular layout. Once a block is chosen in the circular or tabular layout, all the genes in the block are shown in a graphic and tabular format. The gene names have hyperlinks to gene pages where detailed information of the gene can be accessed. The ‘synteny’ section of the gene page displays all the orthologs and the paralogs with link to the corresponding syntenic blocks or gene pages.
SyntenyViewer can be accessed from multiple locations including the Tools header menu (Fig. 38A) and in the Tools section (Fig. 38C) of Species Overview pages (Fig. 38B)
From the SyntenyViewer main page, clicking Select and View Synteny Among Cotton Genome Sequences will bring up Syntenic Blocks Search Page (Fig. 39). There are two ways to search and view Syntenic Blocks: One is searching by a genome (Fig. 39A) and a chromosome/scaffold of it (Fig. 39B), and (a) genome(s) for the comparison (Fig. 39C); The other way is to view a block by search its ID (Fig. 39D)
Fig. 40 gives an example as the chromosome Dt 12 of AD1-UTX-JGI genome is selected and compared by the D5-JGI genome. A. the the syntenic blocks in circle plot; B. Information table of pair-wised collinear blocks; C. Gene names involved in a specific block ID and display; D. Gene names are linked to CottonGen