Optical maps refine the bread wheat Triticum aestivum cv. Chinese Spring genome assembly.

Area of Science:

• Genomics
• Plant Biology
• Bioinformatics

Background:

• Achieving a reference-quality genome sequence for bread wheat (Triticum aestivum) was challenging due to its large size and high repetitive content.
• The International Wheat Genome Sequencing Consortium (IWGSC) RefSeq v1.0 assembly was a significant milestone, providing a chromosome-scale sequence.

Purpose of the Study:

• To refine the IWGSC RefSeq v1.0 bread wheat genome assembly.
• To improve contiguity, accuracy, and gene model mapping for enhanced utility in wheat research.

Main Methods:

• Utilized direct label and stain (DLS) and nick, label, repair and stain (NLRS) optical maps.
• Integrated optical maps with Pacific Biosciences long-read sequence contigs.
• Developed a dedicated approach within the MAGAAT pipeline for gene model mapping.

Main Results:

• Reconciled inconsistencies and closed gaps, increasing pseudomolecule length by 168 Mb.
• Corrected positions and orientations for numerous scaffolds, validating 90% of the assembly.
• Increased contiguity led to higher counts of transposable elements (TEs) and mapped 98% of v1.0 gene models, with a slight increase in high-confidence genes.

Conclusions:

• The refined IWGSC RefSeq v2.1 assembly significantly enhances the utility of the bread wheat genome sequence.
• This improved assembly facilitates advancements in genetic mapping, comparative genomics, gene annotation, and wheat biology studies.