pan-genomesoybeande novo assemblyGmHapMapgenic PAVlong-read sequencingStudies on structural variation in plants have revealed the inadequacy of a single reference genome for an entire species and suggest that it is necessary to build a species-representative genome called a pan-genome to better ...
In addition, they also explored the selection process of 3D genome in wild soybean, landraces and cultivars during domestication and improvement. They found that the selection of 3D genome mainly occurred during domestication, rather than during improvement. This selection reshaped the gene regulation ...
Here, we perform the pan-3D genome analysis using Hi-C sequencing data from 27 soybean accessions and comprehensively investigate the relationships between 3D genomic variations and structural variations (SVs) as well as gene expression. We find that intersection regions between A/B compartments largel...
PanSoy uncovers 108Mb (11%) of novel nonreference sequences encompassing 3621 protein-coding genes (including 1659 novel genes) absent from the soybean 'Williams 82' reference genome. Nonetheless, the core genome represents an exceptionally large proportion of the genome, with >90.6% of genes ...
A map of rice genome variation reveals the origin of cultivated rice. Nature 490, 497–501 (2012). Article CAS PubMed PubMed Central Google Scholar Zhou, Z. et al. Resequencing 302 wild and cultivated accessions identifies genes related to domestication and improvement in soybean. Nat. ...
To capture the entire genomic diversity, it is needed to construct a complete high-quality pan-genome from diverse soybean accessions. In this study, we performed individual de novo genome assemblies for 26 representative soybeans that were selected from 2,898 deeply sequenced accessions. Using ...
Here, we describe a reference-unbiased super-pangenome of North American wild grapes in the genusVitiswith as a main objective to identify and analyze the interspecific genetic variability. To build the super-pangenome, we first sequenced and assembled diploid, chromosome-scaled genomes from nine ...
To capture the entire genomic diversity, it is needed to construct a complete high-quality pan-genome from diverse soybean accessions. In this study, we performed individual de novo genome assemblies for 26 representative soybeans that were selected from 2,898 deeply sequenced accessions. Using ...
Polyploidy is common in angiosperm plants and proved to be tremendous source of raw material for gene genesis (Jaillon et al., 2007;Huang et al., 2013;Salman-Minkov et al., 2016). A soybean pan-genome showed that the nucleotide diversity in the WGD regions was significantly lower than th...
Modern tomatoes have narrow genetic diversity limiting their improvement potential. We present a tomato pan-genome constructed using genome sequences of 725 phylogenetically and geographically representative accessions, revealing 4,873 genes absent from