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

Abstract

Brazil's tropical soybean germplasm still has few genomic resources: only one assembly of a Brazilian cultivar is available at NCBI. Here we describe chromosome-level de novo assemblies of two contrasting cultivars: IAC-100, described as resistant to phytophagous stink bugs, and CD-215, susceptible. We sequenced high molecular weight DNA using 10x Genomics linked reads, assembled the reads with Supernova, anchored the assembly to the Williams 82 reference with RaGOO and corrected structural errors with REAPR. The assemblies span 1.057 and 1.061 Gb, with scaffold N50 values of 53.6 and 54.2 Mb (48.0 and 47.7 Mb excluding gaps), and recover more than 97% of conserved plant genes assessed by BUSCO. Homology-based projection of the reference protein-coding genes generated 46,774 and 46,620 gene models. Comparing the proteomes of the two cultivars, we identified 2,002 divergent isoforms in 1,427 loci, classified by sequence divergence, length variation, combined divergence and non-conserved homology. These data expand the genomic resources for tropical soybean germplasm, still underrepresented in public databases, and for studies of insect resistance.