Genome assembly and characterization of two Brazilian soybean cultivars contrasting for stink bug resistance

The tropical soybean germplasm in Brazil remains underexplored in genomic terms, with only one assembly of a Brazilian cultivar currently available at NCBI. To address this gap, researchers have now described chromosome-level de novo assemblies of two contrasting Brazilian soybean cultivars: IAC-100, known for stink bug resistance, and CD-215, which is susceptible to these pests.

Using high molecular weight DNA and 10x Genomics linked reads, they constructed the assemblies with Supernova, then anchored them to the Williams 82 reference genome using RaGOO. Structural errors were refined through the REAPR tool. The final assemblies encompass 1.057 and 1.061 gigabases, boasting scaffold N50 values of 53.6 and 54.2 megabases (excluding gaps), and successfully recovered over 97% of essential plant genes as identified by BUSCO.

By aligning the reference protein-coding genes, the study generated gene models for both cultivars, totaling 46,774 and 46,620 respectively. A comparative proteomics analysis revealed 2,002 divergent isoforms across 1,427 loci, which were classified based on sequence divergence, length variation, and combined divergence factors.

These findings significantly bolster the genomic resources available for tropical soybean germplasm, which remains underrepresented in public databases, and pave the way for further investigations into insect resistance mechanisms.