5 | CONCLUSION
It is crucial that the in silico mate-pair method be used to assemble genomes from samples with only short fragment DNA, especially in the case of ancient DNA samples. Multiple reference genomes were used to select conserved mate-pair reads prior to assembling the genome. The contiguity and accuracy of genome assemblies were significantly improved. We suggest the following: (i) the closer the reference, the better the in silico mate-pair method; (ii) the optimizedin silico mate-pair method should be used if two closely related references are available; and (iii) of the two reference genomes, the one with higher quality must be used as the first reference. This study provides guidelines for genome assembly using references and may benefit future genomic studies.