Analysing complex Triticeae genomes - concepts and strategies

Area of Science:

• Genomics
• Bioinformatics
• Plant Science

Background:

• Triticeae crop genomes (e.g., barley, wheat) are large, polyploid, and repeat-rich, complicating genomic assembly and analysis.
• Recent advances in next-generation sequencing (NGS) have enabled draft genome sequencing of barley and bread wheat.
• High repeat content hinders direct sequence read assembly and gene content access.

Purpose of the Study:

• To develop novel analytical strategies for structuring massive NGS data from complex grass genomes.
• To enable access and analysis of the gene repertoire in allo-hexaploid bread wheat.
• To pave the way for structured, ordered sequence data and gene order determination.

Main Methods:

• GenomeZipper: A synteny-driven approach to order and structure NGS survey sequences for grass genomes lacking physical maps.
• Reference-guided approach: Utilizing representative genes from related species (rice, Brachypodium distachyon, sorghum, barley) for sub-assembly in bread wheat.
• Machine learning algorithms: Applied to wheat sub-genome progenitor sequences to differentiate between A, B, and D sub-assemblies.

Main Results:

• Successfully structured massive NGS data, enabling ordered sequence data and gene order insights.
• Prevented collapsing of homeologous wheat genes during sub-assembly, allowing estimation of gene retention rates and family sizes.
• Enabled discrimination of wheat sub-assemblies (A, B, D genomes) using machine learning.

Conclusions:

• Developed effective analytical strategies (GenomeZipper, reference-guided sub-assembly, ML) for complex Triticeae genomes.
• These methods provide access to gene repertoires and facilitate genome structuring for large, polyploid species.
• The outlined concepts are applicable to other complex plant and non-plant genomes.