Optical mapping in plant comparative genomics

Haibao Tang, Eric H Lyons, Christopher D. Town

Research output: Contribution to journalArticle

19 Citations (Scopus)

Abstract

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.

Original languageEnglish (US)
Article number3
JournalGigaScience
Volume4
Issue number1
DOIs
StatePublished - Feb 10 2015

Fingerprint

Genomics
Genome
Plant Genome
Medicago
Polyploidy
Plant Development
Population Genetics
Lycopersicon esculentum
Triticum
Zea mays
Genes
DNA
Assays
Pipelines
Molecules
Oryza
Domestication

Keywords

  • Comparative genomics
  • De novo assembly
  • Optical mapping
  • Structural variation

ASJC Scopus subject areas

  • Health Informatics
  • Computer Science Applications

Cite this

Optical mapping in plant comparative genomics. / Tang, Haibao; Lyons, Eric H; Town, Christopher D.

In: GigaScience, Vol. 4, No. 1, 3, 10.02.2015.

Research output: Contribution to journalArticle

Tang, Haibao ; Lyons, Eric H ; Town, Christopher D. / Optical mapping in plant comparative genomics. In: GigaScience. 2015 ; Vol. 4, No. 1.
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