A review of the pangenome: how it affects our understanding of genomic variation, selection and breeding in domestic animals?

Abstract

As large-scale genomic studies have progressed, it has been revealed that a single reference genome pattern cannot represent genetic diversity at the species level. While domestic animals tend to have complex routes of origin and migration, suggesting a possible omission of some population-specific sequences in the current reference genome. Conversely, the pangenome is a collection of all DNA sequences of a species that contains sequences shared by all individuals (core genome) and is also able to display sequence information unique to each individual (variable genome). The progress of pangenome research in humans, plants and domestic animals has proved that the missing genetic components and the identification of large structural variants (SVs) can be explored through pangenomic studies. Many individual specific sequences have been shown to be related to biological adaptability, phenotype and important economic traits. The maturity of technologies and methods such as third-generation sequencing, Telomere-to-telomere genomes, graphic genomes, and reference-free assembly will further promote the development of pangenome. In the future, pangenome combined with long-read data and multi-omics will help to resolve large SVs and their relationship with the main economic traits of interest in domesticated animals, providing better insights into animal domestication, evolution and breeding. In this review, we mainly discuss how pangenome analysis reveals genetic variations in domestic animals (sheep, cattle, pigs, chickens) and their impacts on phenotypes and how this can contribute to the understanding of species diversity. Additionally, we also go through potential issues and the future perspectives of pangenome research in livestock and poultry.

How structural variants shape avian phenotypes: Lessons from model systems

“…Traditional reference‐based genome studies have predominantly focused on a single reference genome, leading to the underrepresentation of SVs, as sequences from individuals which possess the SV may not map against reference genomes which lack them. Pangenomes integrate information from multiple genomes within a species or a group of related organisms, thus revealing a more comprehensive landscape of genetic variation, including SVs (Gong et al., 2023). Pangenomes aim to uncover the full spectrum of genetic variation, including both small and large‐scale SVs, capturing the core genome shared among all individuals from that species and the accessory or variable genome containing non‐reference sequences.…”

“…While it is possible to construct pangenomes from short‐read genome assemblies, the best resolution is achieved by generating pangenomes from high‐quality reference genomes derived from long reads, ideally telomere‐to‐telomere, because short‐read assemblies may not capture important variants such as long repeats. Pangenomics is an emerging research field, and its adoption in eukaryotes has been slow, primarily attributed to the challenges of transitioning the approach from the simpler and shorter bacterial genomes (where they were first developed) to effectively capture the genomic complexity of eukaryotes (see review by Gong et al., 2023). Other major challenges include the computationally demanding analytical and storage requirements.…”

“…Pangenomes remain most prevalent in bacteria and plants, but there is an increasing effort to generate pangenomes in other organisms (Gong et al., 2023). Currently, the chicken (Rice et al., 2023; Wang et al., 2021) and the domestic duck (Wang et al., 2023) are the only avian model species with an available pangenome.…”

RepeatOBserver: tandem repeat visualization and centromere detection

“…The increasing availability of chromosome-scale genome assemblies for a wide range of non-model species, as well as fully haplotype-resolved assemblies and pangenomes for wellstudied species (e.g. Homo sapiens, Solanum spp., Sorghum bicolor, Gallus gallus domesticus) (Li et al, 2022;Gong et al, 2023;Liao et al, 2023;Li et al, 2023;Ruperao et al, 2021; Wang genome assemblies. Another proposed method uses patterns in HiC maps to predict centromere locations (Varoquaux et al, 2015).…”

“…The increasing availability of chromosome-scale genome assemblies for a wide range of non-model species, as well as fully haplotype-resolved assemblies and pangenomes for well-studied species (e.g. Homo sapiens, Solanum spp., Sorghum bicolor, Gallus gallus domesticus ) (Li et al ., 2022; Gong et al ., 2023; Liao et al ., 2023; Li et al ., 2023; Ruperao et al ., 2021; Wang et al ., 2021, Wlodzimierz, Rabanal, et al ., 2023), is opening a world of possibilities for looking at non-genic regions (including tandem repeats, centromeres) and genome structural evolution. Along with improving long read and phasing sequencing technologies, bioinformatics tools are needed to better visualize genome-wide patterns of sequence and structural variation in these genome assemblies (Miga, 2020).…”