The multiple Arabidopsis genome regions with synteny to overlapping Prunus regions, which we observed, may represent the duplicated regions that subsequently went through gene loss.
The syntenic blocks usually contained only several loci, however, and each linkage group of the crop genetic maps matched to multiple Arabidopsis genome regions.
The proposed methodologies can be used to entertain a wide variety of hypotheses, including those that engage, for example, the contribution of a particular chromosome, genome-wide heterozygosity, and multiple genomic regions, to phenotypic expression.
Easyfig has been designed to enable any biologist to visualize comparisons between multiple genomes or genomic regions and produce clear, publication quality images quickly and easily.
Here, we describe Easyfig, a Python application for plotting comparison figures of multiple genomes or genomic regions from annotation files (e.g. GenBank and EMBL) and tabular comparison files [e.g. BLAST (Altschul et al., 1990)].
CARs: Contiguous ancestral regions; MGRA: Multiple genome rearrangements and ancestors; OR: Orthologous region; PID: Percentage identity; RosCOS: Rosaceous conserved orthologous sequences; SSR: Simple sequence repeat; WGD: Whole genome duplication.
Furthermore, the CRM regions may be shuffled in evolution and cannot be aligned with their true orthologous CRM regions in multiple genome alignments.
Further shotgun sequencing would be ineffective due to the significant overrepresentation of certain genome regions in multiple displacement amplification (MDA) products (Fig. S5A).
They will also enable marker-assisted selection for multiple traits or for specific genome regions.
Attenuated vaccine viruses are thought to be safe because multiple mutations are required to make them pathogenic, however, if the strains contained in a multivalent vaccine are attenuated via different suites of mutations, then recombination could produce pathogenic viruses by combining mutation-free genome regions from multiple strains.
