@article {112, title = {Major Impacts of Widespread Structural Variation on Gene Expression and Crop Improvement in Tomato.}, journal = {Cell}, volume = {182}, year = {2020}, month = {2020 07 09}, pages = {145-161.e23}, abstract = {

Structural variants (SVs) underlie important crop improvement and domestication traits. However, resolving the extent, diversity, and quantitative impact of SVs has been challenging. We used long-read nanopore sequencing to capture 238,490 SVs in 100 diverse tomato lines. This panSV genome, along with 14 new reference assemblies, revealed large-scale intermixing of diverse genotypes, as well as thousands of SVs intersecting genes and cis-regulatory regions. Hundreds of SV-gene pairs exhibit subtle and significant expression changes, which could broadly influence quantitative trait variation. By combining quantitative genetics with genome editing, we show how multiple SVs that changed gene dosage and expression levels modified fruit flavor, size, and production. In the last example, higher order epistasis among four SVs affecting three related transcription factors allowed introduction of an important harvesting trait in modern tomato. Our findings highlight the underexplored role of SVs in genotype-to-phenotype relationships and their widespread importance and utility in crop improvement.

}, keywords = {Alleles, Crops, Agricultural, Cytochrome P-450 Enzyme System, Ecotype, Epistasis, Genetic, Fruit, Gene Duplication, Gene Expression Regulation, Plant, Genome, Plant, Genomic Structural Variation, Genotype, Inbreeding, Lycopersicon esculentum, Molecular Sequence Annotation, Phenotype, Plant Breeding, Quantitative Trait Loci}, issn = {1097-4172}, doi = {10.1016/j.cell.2020.05.021}, author = {Alonge, Michael and Wang, Xingang and Benoit, Matthias and Soyk, Sebastian and Pereira, Lara and Zhang, Lei and Suresh, Hamsini and Ramakrishnan, Srividya and Maumus, Florian and Ciren, Danielle and Levy, Yuval and Harel, Tom Hai and Shalev-Schlosser, Gili and Amsellem, Ziva and Razifard, Hamid and Caicedo, Ana L and Tieman, Denise M and Klee, Harry and Kirsche, Melanie and Aganezov, Sergey and Ranallo-Benavidez, T Rhyker and Lemmon, Zachary H and Kim, Jennifer and Robitaille, Gina and Kramer, Melissa and Goodwin, Sara and McCombie, W Richard and Hutton, Samuel and Van Eck, Joyce and Gillis, Jesse and Eshed, Yuval and Sedlazeck, Fritz J and van der Knaap, Esther and Schatz, Michael C and Lippman, Zachary B} } @article {82, title = {RaGOO: fast and accurate reference-guided scaffolding of draft genomes.}, journal = {Genome Biol}, volume = {20}, year = {2019}, month = {2019 Oct 28}, pages = {224}, abstract = {

We present RaGOO, a reference-guided contig ordering and orienting tool that leverages the speed and sensitivity of Minimap2 to accurately achieve chromosome-scale assemblies in minutes. After the pseudomolecules are constructed, RaGOO identifies structural variants, including those spanning sequencing gaps. We show that RaGOO accurately orders and orients 3 de novo tomato genome assemblies, including the widely used M82 reference cultivar. We then demonstrate the scalability and utility of RaGOO with a pan-genome analysis of 103 Arabidopsis thaliana accessions by examining the structural variants detected in the newly assembled pseudomolecules. RaGOO is available open source at https://github.com/malonge/RaGOO .

}, issn = {1474-760X}, doi = {10.1186/s13059-019-1829-6}, author = {Alonge, Michael and Soyk, Sebastian and Ramakrishnan, Srividya and Wang, Xingang and Goodwin, Sara and Sedlazeck, Fritz J and Lippman, Zachary B and Schatz, Michael C} }