Tang Haibao, Lyons Eric, Town Christopher D
Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian People's Republic of China ; School of Plant Sciences, iPlant Collaborative, University of Arizona, Tucson, AZ 85721 USA.
School of Plant Sciences, iPlant Collaborative, University of Arizona, Tucson, AZ 85721 USA.
Gigascience. 2015 Feb 10;4:3. doi: 10.1186/s13742-015-0044-y. eCollection 2015.
Optical mapping has been widely used to improve de novo plant genome assemblies, including rice, maize, Medicago, Amborella, tomato and wheat, with more genomes in the pipeline. Optical mapping provides long-range information of the genome and can more easily identify large structural variations. The ability of optical mapping to assay long single DNA molecules nicely complements short-read sequencing which is more suitable for the identification of small and short-range variants. Direct use of optical mapping to study population-level genetic diversity is currently limited to microbial strain typing and human diversity studies. Nonetheless, optical mapping shows great promise in the study of plant trait development, domestication and polyploid evolution. Here we review the current applications and future prospects of optical mapping in the field of plant comparative genomics.
光学图谱已被广泛用于改进从头开始的植物基因组组装，包括水稻、玉米、苜蓿、无油樟、番茄和小麦，还有更多基因组正在进行组装。光学图谱提供基因组的长程信息，并且能够更轻松地识别大的结构变异。光学图谱分析长单链DNA分子的能力很好地补充了短读长测序，短读长测序更适合于识别小的和短程变异。目前，直接利用光学图谱研究群体水平的遗传多样性仅限于微生物菌株分型和人类多样性研究。尽管如此，光学图谱在植物性状发育、驯化和多倍体进化研究中显示出巨大潜力。在此，我们综述了光学图谱在植物比较基因组学领域的当前应用和未来前景。
