W465Strategy Developments for Wheat Chromosome MTP Sequencing
Strategy Developments for Wheat Chromosome MTP Sequencing
Date: Tuesday, January 14, 2014
Time: 2:10 PM
Time: 2:10 PM
Room: Pacific Salon 3
As the main source of calories, wheat is the most important crop worldwide before maize and rice. However, despite its socio-economic importance, wheat is the last major crop for which no reference genome sequence is available. Beside its importance for humankind, wheat is also a model to study the impact of genome structure on its organization, function, regulation and evolution.
Bread wheat is an allohexaploid (AABBDD) species whose genome size is estimated to be 17 000 Mb, i.e. 40 times the rice genome and 7 times the maize genome (Gill et al., Genetics 2004). Approx. 90% of the genome is composed of transposable element-derived sequences (Choulet et al. Plant Cell 2010; Brenchley et al., Nature 2012). The BAC-by-BAC approach based on chromosome-specificity reduces the size and complexity of the genome by dissecting it into smaller pieces corresponding to chromosome or chromosome arms.
The sequencing and assembly strategy proposed is a cost efficient improved version of the strategy that was established to produce a reference sequence of the 1Gb chromosome 3B (Choulet et al., submitted). While improving the sequencing strategy to exploit new technological development, the final objective is to maintain high quality and the capacity to assemble pseudomolecules. To date, this is the only strategy that has proven to deliver a high quality product. This sequencing strategy, based on sequencing BACs from the MTP established for each individual chromosome or chromosome arm, relies on a combination of long overlapping paired end reads for contig assembly and mate pair reads for scaffolding, produced by Illumina technology on MiSeq. Details of this strategy will be presented.
Bread wheat is an allohexaploid (AABBDD) species whose genome size is estimated to be 17 000 Mb, i.e. 40 times the rice genome and 7 times the maize genome (Gill et al., Genetics 2004). Approx. 90% of the genome is composed of transposable element-derived sequences (Choulet et al. Plant Cell 2010; Brenchley et al., Nature 2012). The BAC-by-BAC approach based on chromosome-specificity reduces the size and complexity of the genome by dissecting it into smaller pieces corresponding to chromosome or chromosome arms.
The sequencing and assembly strategy proposed is a cost efficient improved version of the strategy that was established to produce a reference sequence of the 1Gb chromosome 3B (Choulet et al., submitted). While improving the sequencing strategy to exploit new technological development, the final objective is to maintain high quality and the capacity to assemble pseudomolecules. To date, this is the only strategy that has proven to deliver a high quality product. This sequencing strategy, based on sequencing BACs from the MTP established for each individual chromosome or chromosome arm, relies on a combination of long overlapping paired end reads for contig assembly and mate pair reads for scaffolding, produced by Illumina technology on MiSeq. Details of this strategy will be presented.