Pangenome – its Aspect and Prospect

Abstract

Pangenome is a very new discipline showing a collection of unique and variable genomes of any species in one model. This discipline is a combination of three subjects of Biology like Computer Science and Applied Mathematics. All genes from all species or strains are called Pangenomes. Pangenome was first discovered during the preparation of protein-based vaccine of the G group of Streptococcus sp. which is the main cause of neonatal life-threatening disease by a team of scientists led by Tettelin. Conventional method of Vaccine preparation was not successful due to the existence of five different serotypes in this organism. Then Tettelin with groups of scientists tried to use the genome sequence information for preparing protein- based vaccine in G group of Streptococcus. During their studies, two gap free genomes were found in this G group of bacteria. After sequencing studies of many strains, they found several regions of diversity (genomic diversity) among different isolates of same strain. After sequencing a large number of genomes, they realized that genes belong to isolates present in the species but not present in genomes. Then the Pangenome concept came to their mind and genes were classified into Core genome, Accessory or Dispensable genome and Species-specific genomes. Bacteria genomes have a distinct number of genes but there are differences in the genomes of different strains of a single species that is mainly due to horizontal gene transfer of genes from other bacteria. The Pangenome concept and its discovery was discussed. Plant genomes are dynamic with whole genome duplication, tandem duplication, transposable element duplication, chromosomal rearrangements or structural variations like deletion, inversion, translocation and recombination between species. Several methods have already been tried for the improvement of crop plants like Marker Assisted Selection (MAS), QTL mapping, Single Nucleotide Polymorphisms (SNP), Copy number variations and Genome Wide Association Studies (GWAS) by comparing with Reference Genome Assemblies representing the genome sequence of the genome of an individual or organism. But the Reference genome is not able to locate all genetic variations of a species. To overcome this limitation the concept of Pangenomes may help in the crop improvement which has been discussed. Pangenomic studies have already been done in many crop plants like Rice, Wheat, Maize, Brassica, Soybean etc. Some of all these aspects have been discussed.