Short-read sequencing techniques have made it affordable to study the genetics and the genomes of various species . However, the short sequence lengths obtained using these techniques make it difficult to assemble sequencing reads of the most complex and repetitive regions of the genome, resulting in collapsed and fragmented genome assemblies . Therefore, assemblies based on short-read sequencing are limited in the accuracy of downstream analyses such as the identification of genomic variations . Several methodologies, such as next generation sequencing (NGS) and recently developed algorithms, have been developed to overcome this problem, it has been difficult to completely eliminate the shortcomings of short-read length sequencing . The power of NGS lies in its capacity to generate a huge volume of reads. However, because these reads are rather short, it is impossible to resolve the assembly of many families of repetitive DNA elements that populate fungal genomes. Moreover, fungal genome sequencing is also hampered by the wrong orientation of assembled contigs.
The recent development of long-read sequencing methods, such as optical mapping, have enabled the spanning of most repeats and the generation more complete and correct genome assemblies . Optical mapping techniques have been performed extensively in genomic studies on human diseases, animals, plants, and microorganisms . In the original version of the method, high molecular weight DNA molecules were cleaved on an open glass surfaces and then imaged on fluorescence microscopy . The image from the fluorescence microscopy help to order the partially digested molecules, which is called optical map. The genomic sequence of an organism from de novo sequencing is align on to image and therefore sequence information is placed in correct order of optical map . Using these techniques, it is possible to detect errors in the arrangement and structure of contigs, even if the organism’s genome contains distinct repetitive regions . Therefore, optical maps are an ideal means of finishing fungal sequence assembly because in most cases, the restriction regions cover repetitive regions  such as retrotransposons . Relying on the currently published complete genome sequences that are stored at NCBI may be risky because such sequences likely contain assembly errors . In current study, BNG technology was used to generate an optical map of FOMG and verify contigs. We demonstrated that short-read sequencing assembly could generate some assembly errors within the FOMG genome (Table 1, Fig. (1)). Thus, by utilizing more uniform linearization, BNG technology highly improves the throughput and accuracy of genome length prediction. Moreover, by using nicking enzymes to generate only single-strand breaks, this approach preserves the contiguity of molecules more than other optical mapping technologies .
Dong et al.  reported that the size of the FOMG reference genome is 53.9 Mb, with an N50 value of 0.56 Mb. However, optical mapping indicates a genome size of 57.7 Mb with an N50 value of 0.85 Mb (Table 1). The difference in sequence length may be due to errors in the assembly of the draft genome, which was produced by the Genome Québec (Montreal, Canada) platform . These errors were corrected by BNG mapping to ensure the efficient use of the data. Support of our results, previous studies have indicated that the length of the optical map of FOMG is slightly different from that of the assembled genome [23, 34]. Although the length differences is often attributed to repetitive regions of the genome, they may also result from poor the quality of the assemblies using both sides of the comparison . The supercontig BNG map was obtained from a few genomic sequences that were aligned onto the supercontig. This is likely because previously sequenced FOMG DNA was not derived from high molecular weight DNA (Fig. (1)).
We obtained a high N50 value of 0.85 Mb, indicating that a high percentage of the BNG optical map aligned with the reference map. The N50 value defines how much of an assembly is consists of segments larger than a given size where "N" is the size of the scaffold or contig and "50" is the assembly length percentage . Solely genome assemblies with mega-base scale N50s can be verified performing optical mapping technology because contigs/scaffolds smaller than 100 kb usually do not have sufficient nick knowledge to be securely aligned .
In the current study, each DNA sequence was converted into a restriction map format to match the sequence with the BNG map contigs. As seen in Fig. (1), correct matches between the nick patterns of the BNG map contigs and the reference DNA sequence confirms the base pair distances between nick sites in the DNA sequence. Mismatched regions of the genome may be due to the poor quality of the assemblies of the reference genome.