Product introduction

The pan-genome encompasses all genes within a population, consisting of core genes (present in all samples), dispensable genes (found in some samples), and unique genes (exclusive to specific samples). Core genes indicate species stability and are typically linked to species' biological functions and key traits; dispensable and unique genes reflect species-specific biological attributes and adaptability to particular environments. Pan-genome sequencing not only offers a comprehensive genetic overview of the species but also enables genome comparisons among individuals through sequencing, identifying genomic variations in each sample, such as SNPs, InDels, SVs, and PAVs. This wealth of variation information facilitates in-depth exploration of species trait mechanisms.

Published pan-genome species statistics：

Technology roadmap：

Sequencing strategy:

Option 1: Choose a core sample for T2T genome assembly, with the rest undergoing high-quality chromosome-level genome assembly. The high-quality T2T genome acts as the reference genome, aligning the genomes of other samples and identifying variations, which establishes the basis for creating a high-quality pan-genome of the species.

Option 2: Haplotype-resolved genome construction for all samples.

Research case：

Pan gene family Research:

A gene family comprises genes that stem from a common ancestor, resulting from gene duplication or amplification to generate two or more copies, displaying notable similarities in both structure and function, and encoding similar protein products. Gene families are frequently employed in comparative genomics research. By comparing the specific gene members, structures, and functions within gene families among diverse species, it aids in further understanding the biological distinctions among species, encompassing traits like stress resistance, developmental regulation, and tissue specificity. Pan-genomic studies, leveraging the genomes of numerous closely related varieties or species within the same genus, offer avenues for exploring disparities in gene family structure and functional evolution, laying the groundwork for in-depth analyses of the biological characteristics of closely related species. Shang et al. (2022) utilized the rice pan-genome to establish the rice pan-NLRome, establishing the collinearity among pan-NLR gene families, thereby establishing a basis for investigating the functionality and evolutionary patterns of disease-resistant genes and introducing novel perspectives for studying intricate gene families within populations or chromosomal regions.

Characterization of NLRs in super pan-genome（Shang et al., 2022）

SV-GWAS Research:

Structural variation (SV) stands out as the primary source of genetic variability. While the detection capacity of SV using a single reference genome is finite, leveraging genetic variations from pangenomes can enhance the estimation of genetic influences, thereby fully realizing the research impact of SV. Gui et al. (2022) conducted an SV-GWAS study based on the maize pangenome and observed that, in contrast to common genetic variations such as SNPs and insertions/deletions (InDels), structural variations can account for a greater proportion of phenotypic variability and are more likely to represent functional loci. Notably, 37% of structural variations cannot be substituted by previously utilized high-density SNP or InDel markers. Similarly, Li et al. (2023) reached a similar conclusion in their SV-GWAS study using the tomato pangenome, where 21.3% of QTLs can only be pinpointed through SV analysis. The integration of pangenomes with SV-GWAS facilitates a comprehensive exploitation of graphic pangenomes, significantly boosting the detection capabilities of GWAS.

SV-based GWAS identify additional association signals for tomato fruit flavor（Li et al., 2023）

Reference:

1. Shang, Lianguang, et al. "A super pan-genomic landscape of rice." Cell Research 32.10 (2022): 878-896.

2. Li, Ning, et al. "Super-pangenome analyses highlight genomic diversity and structural variation across wild and cultivated tomato species." Nature Genetics 55.5 (2023): 852-860.

3. Gui, Songtao, et al. "A pan-Zea genome map for enhancing maize improvement." Genome biology 23.1 (2022): 178.