The seeds for genomics were sown with the development of DNA sequencing(Sanger et al.,1977),cultivated with each advance in molecular biology,and have since grown into one of the most important aspects of the life sciences.With the sequencing of the first draft human genome(Venter et al.,2001),the era of post-genomics began.Once one genome has been sequenced,it can be used as the reference for a certain species,and sequences from individuals can be mapped onto it to compare genetic variations among different lines.This allows further population studies,such as whole genome genotyping,molecular evolution,and identification of trait-conferring loci.Construction of a reference genome has become a prerequisite for deeper functional analyses.How-ever,the increasing number of genomics and genetics studies have shown us that a reference genome cannot fully re-present the entire genetic variation of a species.Instead,we must consider to what extent a reference genome is re-presentative(Ballouz et al.,2019;Yang et al.,2019).In this insight,we discuss the trends and challenges of constructing reference genomes(Figure 1).