Exploring Pan-Genomes: An Overview of Resources and Tools for Unraveling Structure, Function, and Evolution of Crop Genes and Genomes

Abstract

The availability of multiple sequenced genomes from a single species made it possible to explore intra- and inter-specific genomic comparisons at higher resolution and build clade-specific pan-genomes of several crops. The pan-genomes of crops constructed from various cultivars, accessions, landraces, and wild ancestral species represent a compendium of genes and structural variations and allow researchers to search for the novel genes and alleles that were inadvertently lost in domesticated crops during the historical process of crop domestication or in the process of extensive plant breeding. Fortunately, many valuable genes and alleles associated with desirable traits like disease resistance, abiotic stress tolerance, plant architecture, and nutrition qualities exist in landraces, ancestral species, and crop wild relatives. The novel genes from the wild ancestors and landraces can be introduced back to high-yielding varieties of modern crops by implementing classical plant breeding, genomic selection, and transgenic/gene editing approaches. Thus, pan-genomic represents a great leap in plant research and offers new avenues for targeted breeding to mitigate the impact of global climate change. Here, we summarize the tools used for pan-genome assembly and annotations, web-portals hosting plant pan-genomes, etc. Furthermore, we highlight a few discoveries made in crops using the pan-genomic approach and future potential of this emerging field of study.

Exploring intra- and intergenomic variation in haplotype-resolved pangenomes

“…In the past decade, we have seen a rise of many pangenomic software toolkits [47]. PanTools distinguishes itself through its hierarchical pangenome graph and by providing an extensive set of comparative genomics functionalities, partially through a connection to existing tools.…”

Climate Change—The Rise of Climate-Resilient Crops

“…Additionally, the superpangenomic approach is being developed, referring not only to the species but to the entire genus. By constructing more genome sequences representative of a species or genus, it will be possible to capture a holistic picture of genetic diversity spanning the entire gene pool of crops [ 58 , 68 , 72 , 73 ]. Long-read sequencing, in combination with improved haplotype resolution for complete genome assemblies, helps to create platinum standard reference genome sequences (PSRefSeq).…”

Role of Genome Sequences of Major and Minor Millets in Strengthening Food and Nutritional Security for Future Generations

“…The available genomic resources for millets have been developed from a single germplasm line/genotype of millets, which provides genetic information on a single genotype. Pan-genome studies will enable the simultaneous generation of genome resources for different cultivars, landraces, and wild species [55]. This will allow researchers to search for novel genes and alleles that may have been inadvertently lost in domesticated crops during the historical process of crop breeding or extensive plant breeding.…”