**5.2. Chromosome level aquatic genome assembly**

Accurate chromosome assemblies require correctly ordered contigs in scaffolds for gene functional interpretation. During chromosome construction, the placement and order of scaffolds on chromosomes relies on a genetic map, which is based on meiotic recombination. Among the aquatic genome models created in the past few years, the *Xiphophorus* genome assembly has been aligned to chromosomes using a Rad-Tag approach to generate a meiotic gene map having over 16,000 markers ([21] and unpublished data). The RAD-tag markers and microsatellite makers from older studies were used to guide the placement of scaffolds into the *Xiphophorus* chromosomes (for RAD-tag method, see [38]). However, the RAD-tag map method is resource and labor intensive, for examples, 267 backcross *Xiphophorus* hybrids were used for genetic mapping and sequence alignment [21].

Recently, new optical mapping technology has been provided by BioNano (http://www.bion‐ anogenomics.com). The optical mapping improves the process of constructing whole genome physical map. In this process, high molecular weight genomic DNA is immobilized onto the positively charged glass surface of a chip-like device having engraved nano-channels that are only wide enough to stretch a single DNA molecule. Buffer fluid that flows though the channel stretches a single DNA molecule to maintain its orientation and integrity. The DNA molecules are subsequently sheared by a restriction enzyme into fragments that are stained with florescent dye. An imaging system then measures the florescent light intensity that represents the length of each DNA fragment. Accompanied with the restriction enzyme site sequence, the length of each fragment is linked to form a single-molecule optical restriction map.

During chromosome assembly, the scaffold sequences can be converted to *in silico* restriction map. The location of the restriction enzyme digestion sequence and the distance between these sequences can then be used to assign scaffolds into chromosomes [39]. Using this approach, incorrect joining errors of contigs may be corrected to improve the current reference genome continuity concurrent with scaffolds alignment into chromosomes.

**Figure 4.** Illustration of optic mapping technology. Genomic DNA is obtained from lysed cells and is loaded onto a chip-like channel-forming device. DNA molecules are stretched onto a positively changed glass surface by buffer fluid that flows through the channels. This step maintains the integrity and orientation of the DNA molecule for subsequent steps. The stretched and immobilized DNA molecules are digested with a restriction enzyme and subsequently stained with florescent dye. The florescent light intensity of each DNA fragment was imaged, and the images are analyzed to measure the size of DNA fragments. Using the restriction enzyme digestion site sequence and the distance between digestion sites, a single-molecule restriction map can be generated to guide scaffold assignment.
