We've put together a whole genome multiple alignment workflow for plants, showing that parameter tuning can boost alignment rate of non-coding functional regions. Work with Lynn Johnson, Cinta Romay, Yaoyao Wu Baoxing Song Michelle Stitzer Adam Siepel Ed Buckler biorxiv.org/content/10.110…

Yuxuan Yuan et al. review the current status of structural variations (SV) studies in plants, examine the roles that SVs play in phenotypic traits, compare current technologies and assess future challenges for SV studies. #OpenAccess link: bit.ly/2UOJ6Le

Telomere-to-telomere assembly of a fish Y chromosome reveals the origin of a young sex chromosome pair  doi.org/10.1186/s13059…

Happy to share our latest tool to help view pangenome graphs using an rGFA file or a VCF file. A desktop-based version and a web browser-based version are provided. Please check if there are any bugs. github.com/TF-Chan-Lab/pa…

High-quality genome assembly and resequencing of modern cotton cultivars provide resources for crop improvement nature.com/articles/s4158…

In a new The Plant Cell paper with Felix Wolter and others in the Puchta lab, we show how repair of single-strand breaks (SSBs) differs from double-strand break repair. Understanding SSB repair could help us induce short tandem duplications, e.g. of TFBSs academic.oup.com/plcell/advance…

Resequencing 250 Soybean Accessions: New Insights into Genes Associate... sciencedirect.com/science/articl…

GAPIT Version 3: Boosting Power and Accuracy for Genomic Association and Prediction doi.org/10.1016/j.gpb.…

Genomic insights into the origin, domestication and diversification of Brassica juncea nature.com/articles/s4158…

Gramtools enables multiscale variation analysis with genome graphs doi.org/10.1186/s13059…

Here we report chromosome-length genome assemblies of not just ONE but SIX different legumes (#chickpea, #pigeonpea, #subterraneanclover, #soybean, and two wild progenitors of cultivated #peanut)- in Jour Adv Res Journal of Advanced Research (JAR)- #openaccess article bit.ly/3bNUUCq

Nanopore sequencing technology, bioinformatics and applications doi.org/10.1038/s41587…

Excited to share our most awaited nature article on 3366 chickpea genomes- nature.com/articles/s4158…. Great work and excellent outputs from a massive collaboration of 57 researchers from 41 organizations across 10 countries. #PressRelease from ICRISAT nature.com/articles/s4158…

Nice collabration with Armin Scheben and Dave. Towards haplotype studies in polyploid plants to assist breeding doi.org/10.1016/j.molp…

Towards haplotype studies in polyploid plants to assist breeding #opinion #MolecularPlant cell.com/molecular-plan…

Graph-based pan-genome reveals structural and sequence variations related to agronomic traits and domestication in cucumber doi.org/10.1038/s41467…

Hello, I have developed a new tool to speed up variant identification from whole genome alignment. It was fully written in rust. Here is a beta version. Feel free to test and let me know if you have any questions. Thank you. github.com/yuxuanyuan/WGA…

Pan-genomes of tomato and potato. Back-to-back papers in Nature by Sanwen’s group. nature.com/articles/s4158… nature.com/articles/s4158…