Supporting data for "Independent assessment and improvement of wheat genome sequence assemblies using Fosill jumping libraries."

Dataset type: Software, Genomic
Data released on May 08, 2018

Lu F; McKenzie N; Kettleborough G; Heavens D; Clark MD; Bevan MW (2018): Supporting data for "Independent assessment and improvement of wheat genome sequence assemblies using Fosill jumping libraries." GigaScience Database. http://dx.doi.org/10.5524/100446

DOI10.5524/100446

The accurate sequencing and assembly of very large, often polyploid, genomes remain a challenging task, limiting long-range sequence information and phased sequence variation for applications such as plant breeding. The 15 Gb hexaploid bread wheat genome has been particularly challenging to sequence, and several different approaches have recently generated long-range assemblies. Mapping and understanding the types of assembly errors is important for optimising future sequencing and assembly approaches and for comparative genomics.
Here we use a Fosill 38 Kb jumping library to assess medium and longer–range order of different publicly available wheat genome assemblies. Modifications to the Fosill protocol generated longer Illumina sequences and enabled comprehensive genome coverage. Analyses of two independent BAC-based chromosome-scale assemblies, two independent Illumina whole genome shotgun assemblies, and a hybrid Single Molecule Real Time (SMRT-PacBio) and short read (Illumina) assembly were carried out. We revealed a surprising scale and variety of discrepancies using Fosill mate-pair mapping and validated several of each class. In addition, Fosill mate-pairs were used to scaffold a whole genome Illumina assembly, leading to a three-fold increase in N50 values.
Our analyses, using an independent means to validate different wheat genome assemblies, show that whole genome shotgun assemblies based solely on Illumina sequences are significantly more accurate by all measures compared to BAC-based chromosome-scale assemblies and hybrid SMRT-Illumina approaches. Although current whole genome assemblies are reasonably accurate and useful, additional improvements will be needed to generate complete assemblies of wheat genomes using open-source, computationally efficient and cost-effective methods.

Additional details

Read the peer-reviewed publication(s):

Lu, F.-H., McKenzie, N., Kettleborough, G., Heavens, D., Clark, M. D., & Bevan, M. W. (2018). Independent assessment and improvement of wheat genome sequence assemblies using Fosill jumping libraries. GigaScience, 7(5). doi:10.1093/gigascience/giy053

Additional information:

https://github.com/lufuhao/NGSimple

https://github.com/lufuhao/ReadCleaner4Scaffolding

Accessions (data included in GigaDB):

BioProject: PRJEB23322
ENA: OEIT01000000





Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
Chinese Spring 424565Canadian hard winter wheatbread wheatTriticum aestivum Description:A single-seed-descent line of Triticum...
Genotype:Chinese Spring 42
Alternative accession-BioProject:PRJEB23322
...
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Displaying 1-1 of 1 Sample(s).




File NameSample IDData TypeFile FormatSizeRelease Date 
GitHub archivearchive38.96 KB2018-05-02
GitHub archivearchive44.98 MB2018-05-02
Genome sequenceFASTA4.04 MB2018-05-02
Genome sequenceFASTA3.36 MB2018-05-02
External linkFASTA226 MB2018-05-02
Genome sequenceFASTA3.55 MB2018-05-02
ReadmeTEXT4.09 KB2018-05-02
External linkUNKNOWN0 KB2018-05-02
External linkUNKNOWN0 KB2018-05-02
External linkUNKNOWN3.6 GB2018-05-02
Displaying 1-10 of 13 File(s).
Funding body Awardee Award ID Comments
Biological and Biotechnological Sciences Research Council (BBSRC) MWB BB/J00328X/1 strategic LOLA award
Biological and Biotechnological Sciences Research Council (BBSRC) MDC BB/J003743/1 strategic LOLA
European Commission MWB FP7 Triticeae Genome Project
Biological and Biotechnological Sciences Research Council (BBSRC) MWB BB/P013511/1 Institute Strategic Programme Grant
Biological and Biotechnological Sciences Research Council (BBSRC) BB/J004669/1
Biological and Biotechnological Sciences Research Council (BBSRC) BB/CSP17270/1 Core Strategic Programme Grant
Biological and Biotechnological Sciences Research Council (BBSRC) BB/J010375/1 National Capability in Genomics
Date Action
May 8, 2018 Dataset publish
July 9, 2018 Manuscript Link added : 10.1093/gigascience/giy053