An improved assembly and annotation of the allohexaploid wheat genome identifies complete families of agronomic genes and provides genomic evidence for chromosomal translocations

Abstract

Advances in genome sequencing and assembly technologies are generating many high-quality genome sequences, but assemblies of large, repeat-rich polyploid genomes, such as that of bread wheat, remain fragmented and incomplete. We have generated a new wheat whole-genome shotgun sequence assembly using a combination of optimized data types and an assembly algorithm designed to deal with large and complex genomes. The new assembly represents >78% of the genome with a scaffold N50 of 88.8 kb that has a high fidelity to the input data. Our new annotation combines strand-specific Illumina RNA-seq and Pacific Biosciences (PacBio) full-length cDNAs to identify 104,091 high-confidence protein-coding genes and 10,156 noncoding RNA genes. We confirmed three known and identified one novel genome rearrangements. Our approach enables the rapid and scalable assembly of wheat genomes, the identification of structural variants, and the definition of complete gene models, all powerful resources for trait analysis and breeding of this key global crop.

Domestication and crop evolution of wheat and barley: Genes, genomics, and future directions

“…Baking quality in wheat is controlled by genes known as prolamins (gliadins and glutenins) (Payne 1987). A recent assembly of the bread wheat genome (Clavijo et al 2017) identified all previously known gluten genes, corrected 21 of these genes and identified an additional 33 genes. Thus, sequencing is useful for characterizing gluten genes to improve baking quality.…”

“…The International Wheat Genome Sequencing Consortium (IWGSC) released an initial draft of the bread wheat genome in 2014 (IWGSC 2014) and will soon release an updated version (https://wheat-urgi.versai lles.inra.fr/Seq-Repository/Assemblies). Clavijo et al (2017) published a version of the hexaploid genome and a small research team released their version prior to the upcoming IWGSC release (Zimin et al 2017a). The fact that an individual research team has been able to take on a genome such as wheat is an indication that we have arrived at a time when the availability of reference genomes will no longer be the rate-limiting step.…”

TaZIM‐A1 negatively regulates flowering time in common wheat (Triticum aestivum L.)

“…Cloning and gene structural analysis of TaZIM-1 homoeologs Based on the Chinese Spring draft genome sequence (Clavijo et al 2017), we identified three contigs of TaZIM-1 genomic sequences, including TaZIM-A1 on chromosome 7A (TGACv1_scaffold_559305_7AL), TaZIM-B1 on chromosome 7B (TGACv1_scaf-fold_576994_7BL) and TaZIM-D1 on chromosome 7D (TGACv1_scaffold_603797_7DL). Using specific primers (Table S2), we cloned the coding sequences (CDS) and genomic sequence of the three TaZIM-1 homoeologs using Chinese Spring mixed cDNA and genomic DNA, respectively.…”

“…Cloning and sequence analysis of TaZIM-1 According to the database of predicted proteins encoded by Triticum aestivum genes (TGACV1), three contigs of the TaZIM-1 genomic sequence were identified based on the Chinese Spring draft genome sequence (Clavijo et al 2017). Specific primers (Table S2) were designed to obtain the TaZIM-1 coding sequences from Chinese Spring cDNA.…”

Review and in silico analysis of fermentation, bioenergy, fiber, and biopolymer genes of biotechnological interest in Agave L. for genetic improvement and biocatalysis

“…It is therefore urgently needed to form a collaborative research consortium focused in understanding the information coded in the genome of Agave, as it has been implemented for other economically important crops. 197…”