Assembly, comparative analysis, and utilization of a single haplotype reference genome for soybean.

Area of Science:

• Plant genomics and genetics
• Bioinformatics and computational biology
• Crop science and breeding

Background:

• The Williams 82 soybean cultivar has been the standard reference genome since 2008.
• Existing reference genomes exhibit genomic heterogeneity across different sub-lines.
• Accurate and contiguous genome assemblies are crucial for advancing soybean research.

Purpose of the Study:

• To provide an updated, high-quality reference genome assembly for soybean (Williams 82, version Wm82.a6).
• To characterize genomic heterogeneity and introgression within the Williams 82 genome.
• To generate a high-quality genome assembly for the abiotic stress-resistant cultivar Fiskeby III.

Main Methods:

• Genome assembly using Pacific Biosciences HiFi long reads.
• Chromosomal integration utilizing HiC technology.
• Genome annotation and comparative analysis with existing assemblies and the Fiskeby III genome.

Main Results:

• A 1.01 Gb genome assembly (Wm82.a6) comprising 36 contigs across 20 soybean chromosomes, with 48,387 gene models.
• Identification of extensive genomic heterogeneity in Wm82.a6, including introgression from the Kingwa cultivar on chromosomes 03 and 07.
• Discovery of a novel heterogeneous region (>20 Mb) on chromosome 12 and characterization of polymorphisms between Wm82.a6 and Fiskeby III, particularly within an iron deficiency chlorosis resistance QTL.

Conclusions:

• The Wm82.a6 assembly offers a more contiguous and accurate representation of the Williams 82 genome, resolving previous heterogeneity.
• The identified genomic variations highlight the complexity of the Williams 82 genome and provide insights into its evolutionary history.
• The Wm82.a6 and Fiskeby III genome assemblies significantly enhance soybean comparative and functional genomics capabilities.