BioProject

The aims of this project were to generate a chromosome-scale genome assembly of Glycine max cv EMBRAPA BRS 537 for genomic studies of cultivars well adapted to tropical climate. More...

The aims of this project were to generate a chromosome-scale genome assembly of Glycine max cv EMBRAPA BRS 537 for genomic studies of cultivars well adapted to tropical climate. Large-scale shotgun sequencing and assembly of BRS 537 has been made available pre-publication for advancing research. Discrepancies between the genome assembly and independently genetic and physical maps have not been reviewed yet, so there should be errors in the large-scale structure of the genome. BRS 537 is a non GMO soybean developed by the team of the Soybean Improvement Program of the Brazilian Agricultural Research Corporation (EMBRAPA) through traditional genetic breeding. The cultivar presents good productive stability across the Southeastern, Southern and Central-West regions of Brazil (21 to 25 degrees south latitude), with high level of resistance to rot infections caused by Phytophthora diseases. The cultivar is early cycle MG 6.0 (average time from emergence to flowering and maturity are 36 days and 116 days, respectively), which allows its insertion in the succession and rotation systems with other crops such as maize. The assembly incorporates subreads and Hi-C (Proximo Plant Kit from Phase Genomics) data from PACBIO Sequel I and Illumina HiSeq4000 PE 101bp, respectively. De novo assembly of subreads to form contigs was performed using Falcon pipeline. Pseudomolecule anchoring of scaffolds was accomplished using Hi-C contact maps following Phase Genomics Proximo scaffolding method. The relationship between contigs, scaffolds and chromosomes was defined based on evidence obtained from a single proximity-ligation assay using a restriction enzyme to digest chromatin, followed by paired-end sequencing. Additional evidence of linkage of these components to form chromosomes was achieved by inferring synteny in comparisons with Glycine max assembly for cultivar Williams 82 (JGI Glyma.Wm82.a2) with minor manual intervention to correct the results of homology assessment. Less...