Optical mapping in plant comparative genomics.

Haibao Tang,Christopher D Town,Eric Lyons

doi:10.1186/s13742-015-0044-y

Haibao Tang, Christopher D Town + Show 1 more

Open Access

https://doi.org/10.1186/s13742-015-0044-y

Copy DOI

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.

Highlights

Optical mapping is a molecular technique that produces fingerprints of DNA sequences in order to construct genome-wide maps [1]
* Correspondence: tanghaibao@gmail.com 1Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, People’s Republic of China 2School of Plant Sciences, iPlant Collaborative, University of Arizona, Tucson, AZ 85721, USA Full list of author information is available at the end of the article optical mapping is readily available across a wide range of organisms including bacterial, fungi, plant and mammalian genomes [5-9], this review focuses on the applications and of optical mapping in the field of plant comparative genomics
Comparisons of different approaches to identify structural variations Despite recent progress in genome assembly methodologies, a significant portion of many genomes remains inaccessible to assembly by short sequencing reads [10]

Summary

Introduction

Optical mapping is a molecular technique that produces fingerprints of DNA sequences in order to construct genome-wide maps [1]. Optical map guided genome assemblies A hierarchical approach is typically adopted for building a high quality genome assembly for most organisms – starting with identifying read overlaps to build contigs, adding read pairs to build scaffolds, and ordering scaffolds to assemble large chromosomal regions using various sources of long distance mapping information [10]. There are several ways in the assembly process that optical mapping can assist in building high quality reference genomes.

Results

Conclusion