Viana, J. P. G. | Search bioRxiv

bioRxiv2026

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

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.

genomics↗

bioRxiv2021

Selective signatures and high genome-wide diversity in traditional Brazilian manioc (Manihot esculenta Crantz) varieties

Knowledge about crops genetic diversity is essential to promote effective use and conservation of their genetic resources, because genetic diversity enables farmers to adapt their crops to specific needs and is the raw material for breeding efforts. Currently, manioc (Manihot esculenta ssp. esculenta) is one of the most important food crops in the world and has the potential to help achieve food security in the context of on-going climate changes. In this study we assessed the patterns of genome-wide diversity of traditional Brazilian manioc varieties conserved in the gene bank of the Luiz de Queiroz College of Agriculture, University of Sao Paulo. We used single nucleotide polymorphisms to evaluate the organization of genetic diversity and to identify selective signatures contrasting varieties from different biomes with samples of maniocs wild relative M. esculenta ssp. flabellifolia. We identified signatures of selection putatively associated with resistance genes, plant development and response to abiotic stresses. This presumed adaptive variation might have been important for the initial domestication and for the crops diversification in response to cultivation in different environments. The neutral variation revealed high levels of genetic diversity within groups of varieties from different biomes and low to moderate genetic divergence among biomes. These results reflect the complexity of maniocs biology and its evolutionary dynamics under traditional cultivation. Our results exemplify how the smallholder practices contribute to the conservation of maniocs genetic resources, maintaining variation of potential adaptive significance and high levels of neutral genetic diversity.

genetics↗