Independent assessment and improvement of wheat genome sequence assemblies using Fosill jumping libraries

GigaScience
Fu-Hao LuMichael W Bevan

Abstract

The accurate sequencing and assembly of very large, often polyploid, genomes remains a challenging task, limiting long-range sequence information and phased sequence variation for applications such as plant breeding. The 15-Gb hexaploid bread wheat (Triticum aestivum) 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 are 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 Bacterial Artificial Chromosome (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 use...Continue Reading

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Datasets Mentioned

BETA
PRJEB23322
PRJEB23893
PRJEB23358

Methods Mentioned

BETA
Illumina sequencing
PCR

Key Resources (RRID) Mentioned

SCR_016165
SCR_016166
SCR_005476
SCR_006525

Software Mentioned

FLASH
DenovoMAGIC
NGSimple
SciCrunch
ProgramRoot
bowtie
Linux
samtools
Fosill
DevoMAGIC

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