Can different species within the same genus be used as reference genomes?

Plants of the same genus but different species can be used as a reference genome. When a reference genome for the target species is not available, the genome of a closely related species is often chosen as a reference. This is because they have similar genetic backgrounds and evolutionary histories, and their genome structures may be similar to that of the target species. However, the accuracy of this method can be affected by genetic differences between species. Ideally, the reference genome of the target species should be used.

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