… The plant genomes are generally redundant and associated with high gene similarity.
Current homology analysis tools that are generally based on sequence similarity ( …

… continue to improve Evol2Circos’s functionality by including annotation of the syntenic
blocks, synteny between multiple genomes, SSR/repeat mapping onto the syntenic blocks, etc. …

… To illustrate the usage of MCScanX-transposed.pl, we apply it to the cacao (ie, target)
genome by using two other plant genomes as possible outgroups: yam and American chestnut. …

… all genes from all species. We then treat each pair of genes along every collinear block as
… Tandem duplicates represent a specific case of syntenic orthology, and where present, are …

… Currently, most visualization toolkits of synteny and collinearity do … genome synteny and
collinearity analysis. The updated version enables four types of plots for synteny and collinearity, …

… in the plant genomic landscape but also highlight a potentially meaningful genomic contrast
… other vascular plants, we assessed synteny between flowering plants Amborella trichopoda (…

… As an example, we highlight a synteny context of 15 genes where 8 genes (highlighted red)
… 29), we obtained orthogroups for the 123 plant genomes using OrthoFinder 106 (version 2.4.…

… In addition, comparative analyses of deep and shallowly divergent seed plant genomes
provided detailed insights into genome evolution and dynamics both at longer and shorter …

… genes for species tree reconstruction. Our syntenic gene sets comprised a large number of
genes … many plant genomes and also among our selected species, the use of orthologous …

… best material for genome synteny analyses, but some plant genome assemblies currently …
) genome, only one ARF gene was clustered in the synteny network because the genome …