🧬 Pan-genome Construction Strategies
1. What are the strategies for constructing a pan-genome?
If a reference genome is available, one can map sequencing reads from individual accessions to the reference and assemble the unmapped reads, constructing the pan-genome through an iterative "mapping-assembly" process. Alternatively, one can perform de novo genome assembly for all accessions and construct the pan-genome by comparing these assemblies. A third approach involves constructing a pan-genome based on a variation graph.
🌿 Material Selection for Pan-genomics
2. How should materials be selected for pan-genome studies?
First, the selected materials must capture broad genetic diversity; priority should be given to individuals from diverse geographical regions, ecological types, subpopulations, or domestication backgrounds. Second, closely related individuals should be avoided, as they can lead to an underestimation of the pan-genome size. Finally, it is crucial to include both wild and domesticated (or cultivated) materials, as wild species typically harbor more dispensable genes, aiding in the discovery of functional genes lost during domestication.
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