Genome assembly of nine wild species and two domesticated accessions of tomato generated a super-pangenome for the tomato clade. Comparative analyses revealed the landscape of structural variations in wild and cultivated tomatoes and led to the discovery of a wild tomato gene that has the potential...
Although pangenomes for cultivated tomato and its close wild relatives have been reported13, the gene pool ofLycopersicon, which contains wild and cultivated tomato species, remains largely inaccessible. Here, we extended the tomato pangenome that integrates genomes from threeSolanumspecies13to a super...
Li, N. et al. Super-pangenome analyses highlight genomic diversity and structural variation across wild and cultivated tomato species.Nat. Genet.55, 852–860 (2023). CASPubMedPubMed CentralGoogle Scholar Abberton, M. et al. Global agricultural intensification during climate change: a role for...
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 r...
Genome to Pangenome: A Paradigm Shift SVs Drive the Dispensable Genome Pangenome Development: Approaches and Critical Factors Walking on the Wild Side by Exploiting CWRs Current Status of the Pangenome in Crop Plants Super-Pangenome: A Way Forward Concluding Remarks Acknowledgments Supplemental Informat...
Finally, we developed a user-friendly web-based tool encompassing the multi-omics resources associated with the Populus super-pangenome (http://www.populus-superpangenome.com). Together, the present pioneering super-pangenome resource in forest trees not only aids in the advancement of breeding ...
As plants lack a CTCF homolog, transcription factors are suspected to function as potential mediators or regulators of the plant 3D genome. Recent studies provided support to this hypothesis in plants with TCP1 inMarchantiaand HSFA1a in tomato [22,38]. However, their impact on 3D genome struct...
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The observed variations in genome size can be primarily explained by the number of TEs (Fig. 1d; Supplementary information, Fig. S1k, l), particularly by long terminal repeats (LTRs) (Fig. 1e–g; Supplementary information, Table S1d). A super pan-genome of cultivated rice and wild rice...
To decipher the genetic diversity within the cucurbit genus Citrullus, we generated telomere-to-telomere (T2T) assemblies of 27 distinct genotypes, encompassing all seven Citrullus species. This T2T super-pangenome has expanded the previously published r