Pangenomics Comes of Age: From Bacteria to Plant and Animal Applications

The pangenome is composed of core genes/sequences found in all individuals and accessory genes/sequences found in some individuals only. While introduced in prokaryotic research, the pangenome concept has been shown to be applicable across tree of life, including protists, fungi, plants, and animals. Studies of bacterial, fungal, plant, and animal pangenomes allowed identification of a large number of accessory genes/sequences that were missing from reference genomes. The accessory genes are often over-represented in functions related to signaling and virulence/defense response. Moving from using a single genome to a pangenome as a reference will improve variant calling and identification of genes associated with key traits. The pangenome refers to a collection of genomic sequence found in the entire species or population rather than in a single individual; the sequence can be core, present in all individuals, or accessory (variable or dispensable), found in a subset of individuals only. While pangenomic studies were first undertaken in bacterial species, developments in genome sequencing and assembly approaches have allowed construction of pangenomes for eukaryotic organisms, fungi, plants, and animals, including two large-scale human pangenome projects. Analysis of the these pangenomes revealed key differences, most likely stemming from divergent evolutionary histories, but also surprising similarities. The pangenome refers to a collection of genomic sequence found in the entire species or population rather than in a single individual; the sequence can be core, present in all individuals, or accessory (variable or dispensable), found in a subset of individuals only. While pangenomic studies were first undertaken in bacterial species, developments in genome sequencing and assembly approaches have allowed construction of pangenomes for eukaryotic organisms, fungi, plants, and animals, including two large-scale human pangenome projects. Analysis of the these pangenomes revealed key differences, most likely stemming from divergent evolutionary histories, but also surprising similarities. allopatric bacteria live isolated from other microorganisms (e.g., obligate intracellular bacteria). a section of noncoding DNA, which regulates transcription of neighboring genes. CREs can be proximal (promoters) or distal (enhancers/silencers). genes/DNA sequence found in all the individuals under study. genes/DNA sequence found in some individuals but not others. The term has increasingly been replaced by ‘accessory genome’ or ‘variable genome’, as sequence that is dispensable for one individual may be important for another due to differences in total gene/sequence content (genetic background) and environment. death within the embryonic period of development. a process in which additional copies of the entire genomes are generated. The resulting cells are polyploid (contain more than two copies of chromosomes). a conformation capture method used to study spatial organization of chromatin within a cell. Can be used to identify promoter–enhancer interactions. movement of genetic material by means other than descent (not from parent to offspring). HGT allows sharing of genetic material between unrelated organisms and is especially prevalent in prokaryotes. (homologous gene cluster); clusters of genes in different species that are related by descent, originating from a single ancestral gene. reproductive practice which requires crossing of two unrelated individuals to produce progeny. Outcrossing increases genetic diversity. sympatric bacteria interact with many other bacteria, often belonging to different phyla, allowing them to exchange genes. conservation of gene order across chromosomes, reflecting ancestral gene order.