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.