We selected two genetically diverse subspecies of the Trifolium model species, subterranean clover cvs. Daliak and Yarloop. The structural variations (SVs) discovered by Bionano optical mapping (BOM) were validated using Illumina short reads. In the analysis, BOM identified 12 large-scale regions containing deletions and 19 regions containing insertions in Yarloop. The 12 large-scale regions contained 71 small deletions when validated by Illumina short reads. The results suggest that BOM could detect the total size of deletions and insertions, but it could not precisely report the location and actual quantity of SVs in the genome. Nucleotide-level validation is crucial to confirm and characterize SVs reported by optical mapping. The accuracy of SV detection by BOM is highly dependent on the quality of reference genomes and the density of selected nickases.

Centre for Plant Genetics and Breeding School of Agriculture and Environment The University of Western Australia Perth WA Australia

Institute of Agriculture The University of Western Australia Perth WA Australia

Institute of Experimental Botany Centre of the Region Haná for Biotechnological and Agricultural Research Olomouc Czechia

School of Biological Sciences The University of Western Australia Perth WA Australia

Telethon Kids Institute Perth WA Australia

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Chiang C., Layer R. M., Faust G. G., Lindberg M. R., Rose D. B., Garrison E. P., et al. (2015). SpeedSeq: ultra-fast personal genome analysis and interpretation. Nat. Methods 12 966–968. 10.1038/nmeth.3505 PubMed DOI PMC

Escaramis G., Docampo E., Rabionet R. (2015). A decade of structural variants: description, history and methods to detect structural variation. Brief. Funct. Genomics 14 305–314. 10.1093/bfgp/elv014 PubMed DOI

Feuk L., Carson A. R., Scherer S. W. (2006). Structural variation in the human genome. Nat. Rev. Genet. 7 85–97. 10.1038/nrg1767 PubMed DOI

Francis C., Devitt A. (1969). The effect of waterlogging on the growth and isoflavone concentration of Trifolium subterraneum L. Aust. J. Agric. Res. 20 819–825. 10.1071/AR9690819 DOI

Hastie A. R., Dong L., Smith A., Finklestein J., Lam E. T., Huo N., et al. (2013). Rapid genome mapping in nanochannel arrays for highly complete and accurate de novo sequence assembly of the complex Aegilops tauschii genome. PLoS One 8:e55864. 10.1371/journal.pone.0055864 PubMed DOI PMC

Katznelson J., Morley F. H. W. (1965a). A taxonomic revision of sect calycomorphum of the genus Trifolium. 1. The geocarpic species. Isr. J. Bot. 14 112–134.

Katznelson J., Morley F. H. W. (1965b). Speciation processes in Trifolium subterraneum L. Isr. J. Bot. 14 15–35.

Kaur P., Bayer P. E., Milec Z., Vrana J., Yuan Y., Appels R., et al. (2017). An advanced reference genome of Trifolium subterraneum L. reveals genes related to agronomic performance. Plant Biotechnol. J. 15 1034–1046. 10.1111/pbi.12697 PubMed DOI PMC

Layer R. M., Chiang C., Quinlan A. R., Hall I. M. (2014). LUMPY: a probabilistic framework for structural variant discovery. Genome Biol. 15:R84. 10.1186/gb-2014-15-6-r84 PubMed DOI PMC

Li L., Leung A. K., Kwok T. P., Lai Y. Y. Y., Pang I. K., Chung G. T., et al. (2017). OMSV enables accurate and comprehensive identification of large structural variations from nanochannel-based single-molecule optical maps. Genome Biol. 18:230. 10.1186/s13059-017-1356-2 PubMed DOI PMC

Li Y., Zheng H., Luo R., Wu H., Zhu H., Li R., et al. (2011). Structural variation in two human genomes mapped at single-nucleotide resolution by whole genome de novo assembly. Nat. Biotechnol. 29 723–730. 10.1038/nbt.1904 PubMed DOI

Nichols P. G. H., Foster K. J., Piano E., Pecetti L., Kaur P., Ghamkhar K., et al. (2013). Genetic improvement of subterranean clover (Trifolium subterraneum L.). 1. Germplasm, traits and future prospects. Crop Pasture Sci. 64 312–346. 10.1071/CP13118 DOI

Robinson J. T., Thorvaldsdottir H., Winckler W., Guttman M., Lander E. S., Getz G., et al. (2011). Integrative genomics viewer. Nat. Biotechnol. 29 24–26. 10.1038/nbt.1754 PubMed DOI PMC

Shelton J. M., Coleman M. C., Herndon N., Lu N., Lam E. T., Anantharaman T., et al. (2015). Tools and pipelines for BioNano data: molecule assembly pipeline and FASTA super scaffolding tool. BMC Genomics 16:734. 10.1186/s12864-015-1911-8 PubMed DOI PMC

Šimková H., Číhalíková J., Vrána J., Lysák M. A., Doležel J. (2003). Preparation of HMW DNA from plant nuclei and chromosomes isolated from root tips. Biol. Plant. 46 369–373. 10.1186/s12864-015-1911-8 PubMed DOI PMC

Vrána J., Cápal P., Číhalíková J., Kubaláková M., Doležel J. (2016). Flow sorting plant chromosomes. Methods Mol. Biol. 1429 119–134. 10.1023/A:1024322001786 PubMed DOI

Xia L. C., Sakshuwong S., Hopmans E. S., Bell J. M., Grimes S. M., Siegmund D. O., et al. (2016). A genome-wide approach for detecting novel insertion-deletion variants of mid-range size. Nucleic Acids Res. 44:e126. 10.1007/978-1-4939-3622-9_10 PubMed DOI PMC

Yuan Y., Bayer P. E., Batley J., Edwards D. (2017a). Improvements in genomic technologies: application to crop genomics. Trends Biotechnol. 35 547–558. 10.1093/nar/gkw481 PubMed DOI

Yuan Y., Bayer P. E., Lee H. T., Edwards D. (2017b). runBNG: a software package for BioNano genomic analysis on the command line. Bioinformatics 33 3107–3109. 10.1016/j.tibtech.2017.02.009 PubMed DOI

Flow Sorting-Assisted Optical Mapping