Pangenomics in Microbial and Crop Research: Progress, Applications, and Perspectives

Abstract

Advances in sequencing technologies and bioinformatics tools have fueled a renewed interest in whole genome sequencing efforts in many organisms. The growing availability of multiple genome sequences has advanced our understanding of the within-species diversity, in the form of a pangenome. Pangenomics has opened new avenues for future research such as allowing dissection of complex molecular mechanisms and increased confidence in genome mapping. To comprehensively capture the genetic diversity for improving plant performance, the pangenome concept is further extended from species to genus level by the inclusion of wild species, constituting a super-pangenome. Characterization of pangenome has implications for both basic and applied research. The concept of pangenome has transformed the way biological questions are addressed. From understanding evolution and adaptation to elucidating host-pathogen interactions, finding novel genes or breeding targets to aid crop improvement to design effective vaccines for human prophylaxis, the increasing availability of the pangenome has revolutionized several aspects of biological research. The future availability of high-resolution pangenomes based on reference-level near-complete genome assemblies would greatly improve our ability to address complex biological problems.

Keywords: NGS; biological research; evolution; genome sequence; germplasm; novel genes; pangenome.

Figure 1

Organization of a pangenome composed of core and dispensable components of the genome.

Figure 2

Different forms of a reference genome. The horizontal bars represent the DNA sequence of a genome. represents a disabling mutation that disrupts the gene function. , , and depict various sequence polymorphisms.

Figure 3

Genomic variation in terms of proportion (a) and distribution (b) of PAVs and CNVs in the genome of major crops for agriculturally important traits (Interpreted from Tao et al. [21].

Figure 4

A basic approach for pangenome construction. Genome sequences of different strains represented schematically as A (blue), B (red), C (green), D (light blue), and E (yellow) are aligned to identify the core and accessory components of the pangenome.

Figure 5

A model of heterosis proposed by Swanson-Wagner et al. [105]. Bars represent genes. Three genes are considered in each hypothetical gene family, situated on different chromosomes. represents “functional block” leading to null or altered protein function. In a real scenario, accumulation of a similar effect with many gene families leads to reduced vigor in inbreeds and heterosis in hybrid. Pangenomics can help to unravel heterosis in a phenotypic trait by discovering new gene variants.