Construction of a new chromosome-scale, long-read reference genome assembly of the Syrian hamster, Mesocricetus auratus

Harris, R. A.; Raveendran, M.; Lyfoung, D. T.; Sedlazeck, F. J.; Mahmoud, M.; Prall, T.; Karl, J.; Doddapaneni, H.; Meng, Q.; Han, Y.; Muzny, D.; Wiseman, R. W.; O'Connor, D. H.; Rogers, J.

doi:10.1101/2021.07.05.451071

bioRxiv · 10.1101/2021.07.05.451071

Construction of a new chromosome-scale, long-read reference genome assembly of the Syrian hamster, Mesocricetus auratus

Harris, R. A.·Raveendran, M.·Lyfoung, D. T.·Sedlazeck, F. J.·Mahmoud, M.·Prall, T.·Karl, J.·Doddapaneni, H.·Meng, Q.·Han, Y.·Muzny, D.·Wiseman, R. W.·O'Connor, D. H.·Rogers, J.

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Abstract

BackgroundThe Syrian hamster (Mesocricetus auratus) has been suggested as a useful mammalian model for a variety of diseases and infections, including infection with respiratory viruses such as SARS-CoV-2. The MesAur1.0 genome assembly was generated in 2013 using whole-genome shotgun sequencing with short-read sequence data. Current more advanced sequencing technologies and assembly methods now permit the generation of near-complete genome assemblies with higher quality and greater continuity. FindingsHere, we report an improved assembly of the M. auratus genome (BCM_Maur_2.0) using Oxford Nanopore Technologies long-read sequencing to produce a chromosome-scale assembly. The total length of the new assembly is 2.46 Gbp, similar to the 2.50 Gbp length of a previous assembly of this genome, MesAur1.0. BCM_Maur_2.0 exhibits significantly improved continuity with a scaffold N50 that is 6.7 times greater than MesAur1.0. Furthermore, 21,616 protein coding genes and 10,459 noncoding genes are annotated in BCM_Maur_2.0 compared to 20,495 protein coding genes and 4,168 noncoding genes in MesAur1.0. This new assembly also improves the unresolved regions as measured by nucleotide ambiguities, where approximately 17.11% of bases in MesAur1.0 were unresolved compared to BCM_Maur_2.0 in which the number of unresolved bases is reduced to 3.00%. ConclusionsAccess to a more complete reference genome with improved accuracy and continuity will facilitate more detailed, comprehensive, and meaningful research results for a wide variety of future studies using Syrian hamsters as models.

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Harris, R. A., Raveendran, M., Lyfoung, D. T., Sedlazeck, F. J., Mahmoud, M., Prall, T., Karl, J., Doddapaneni, H., Meng, Q., Han, Y., Muzny, D., Wiseman, R. W., O'Connor, D. H., Rogers, J.. 2021-07-05. Construction of a new chromosome-scale, long-read reference genome assembly of the Syrian hamster, Mesocricetus auratus. https://doi.org/10.1101/2021.07.05.451071

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