TRITEX

TRITEX assembles chromosome-scale genome sequences for Triticeae crops such as wheat and barley by integrating paired-end reads, mate-pair reads, 10X Genomics linked-reads and chromosome conformation capture (Hi-C) data to produce ordered chromosomal pseudomolecules for pan-genomic analyses.

Key Features:

• Integration of multiple sequencing technologies: Combines paired-end reads, mate-pair reads, 10X Genomics linked-reads and chromosome conformation capture (Hi-C) sequencing data to generate sequence scaffolds with megabase-scale contiguity.
• Chromosomal pseudomolecule construction: Orders and orients large contigs and scaffolds into chromosomal pseudomolecules suitable for downstream annotation and comparative analyses.

Scientific Applications:

• Pan-genomic research: Produces chromosome-scale assemblies to support pan-genome analyses across Triticeae species including wheat and barley.
• Genome annotation: Improves contiguity of assemblies to enhance accuracy of gene and feature annotation.
• Comparative genomics: Enables detailed comparisons within the Triticeae family to investigate evolutionary relationships and functional genomics.
• Breeding and marker discovery: Facilitates identification of genetic markers and structural variation relevant to breeding programs.

Methodology:

Leverages multiple sequencing technologies to produce high-contiguity sequence scaffolds and to order these into chromosomal pseudomolecules; the workflow was evaluated using publicly available sequence data from tetraploid wild emmer and hexaploid bread wheat and was used to construct an improved annotated reference genome assembly for the barley cultivar Morex.