Optical mapping in plant comparative genomics

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• 作者：Haibao Tang (1) (2)
  Eric Lyons (2)
  Christopher D Town (3)
  
  1. Center for Genomics and Biotechnology ; Fujian Agriculture and Forestry University ; Fuzhou ; 350002 ; Fujian ; People鈥檚 Republic of China
  2. School of Plant Sciences ; iPlant Collaborative ; University of Arizona ; Tucson ; AZ ; 85721 ; USA
  3. J. Craig Venter Institute ; Rockville ; MD ; 20850 ; USA
  
• 关键词：Optical mapping ; Comparative genomics ; De novo assembly ; Structural variation
• 刊名：GigaScience
• 出版年：2015
• 出版时间：December 2015
• 年：2015
• 卷：4
• 期：1
• 全文大小：829 KB
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• 刊物主题：Bioinformatics; Computational Biology/Bioinformatics; Computer Appl. in Life Sciences; Proteomics; Data Mining and Knowledge Discovery;
• 出版者：BioMed Central
• ISSN：2047-217X

文摘

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.