A Single Molecule Scaffold for the Maize Genome

Abstract

About 85% of the maize genome consists of highly repetitive sequences that are interspersed by low-copy, gene-coding sequences. The maize community has dealt with this genomic complexity by the construction of an integrated genetic and physical map (iMap), but this resource alone was not sufficient for ensuring the quality of the current sequence build. For this purpose, we constructed a genome-wide, high-resolution optical map of the maize inbred line B73 genome containing >91,000 restriction sites (averaging 1 site/∼23 kb) accrued from mapping genomic DNA molecules. Our optical map comprises 66 contigs, averaging 31.88 Mb in size and spanning 91.5% (2,103.93 Mb/∼2,300 Mb) of the maize genome. A new algorithm was created that considered both optical map and unfinished BAC sequence data for placing 60/66 (2,032.42 Mb) optical map contigs onto the maize iMap. The alignment of optical maps against numerous data sources yielded comprehensive results that proved revealing and productive. For example, gaps were uncovered and characterized within the iMap, the FPC (fingerprinted contigs) map, and the chromosome-wide pseudomolecules. Such alignments also suggested amended placements of FPC contigs on the maize genetic map and proactively guided the assembly of chromosome-wide pseudomolecules, especially within complex genomic regions. Lastly, we think that the full integration of B73 optical maps with the maize iMap would greatly facilitate maize sequence finishing efforts that would make it a valuable reference for comparative studies among cereals, or other maize inbred lines and cultivars.

Genome sequence of foxtail millet (Setaria italica) provides insights into grass evolution and biofuel potential

“…3). We also used optical mapping 30 to validate our genome assembly. We mapped 99.8% of the optical fragments to the assembly ( Supplementary Fig.…”

Sequencing and automated whole-genome optical mapping of the genome of a domestic goat (Capra hircus)

“…Optical mapping has been used to compare the structures of bacterial genomes [6][7][8] , complete bacterial genome assembly 9,10 , assist in bacterial artificial chromosome (BAC) assembly 11 and correct genome assembly errors 12 . Two plant genomes 13,14 have recently been sequenced using BACs assembled through such optical mapping. However, the traditional process for generating optical mapping data involves mostly manual steps, and as a result the primary applications of optical mapping have been in the assembly of bacterial genomes, integration of BAC end sequencing and BAC clone assembly, and iterative correction of assemblies.…”

A Sequence-Ready Physical Map of Barley Anchored Genetically by Two Million Single-Nucleotide Polymorphisms

“…Apart from recombination-based mapping, radiation hybrid panels similar to those implemented in wheat (Kalavacharla et al, 2006) or obtained for barley by the activity of gametocidal chromosomes (Masoudi-Nejad et al, 2005) may be of value. Similarly, fluorescent in situ hybridization mapping (Cheng et al, 2001) and optical mapping (Zhou et al, 2009) hold some promise and may be used to order markers in recombinogenically inert regions. More importantly, once the MTP has been sequenced, overlapping adjacent physical contigs can be merged using sequence information and result in an improved linear order in the same genetic bin.…”