Sequencing

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11th Annual Sequencing, Finishing, and Analysis in the Future Meeting THE OIL PALM GENOME IN OUR PALMS: THE IMMEDIATE IMPACT OF THE GENOME SEQUENCE OF THE WORLD’S MOST IMPORTANT OIL CROP Friday, 3rd June 11:10 La Fonda Ballroom Invited Speaker (IS‐3) Nathan Lakey Orion Genomics, LLC Nathan Lakey, Rajinder Singh, Meilina Ong‐Abdullah, Eng‐Ti Leslie Low, Rajanaidu Nookiah, Steven W Smith, Jared M Ordway, Robert A Martienssen and Ravigadevi Sambanthamurthi. We recently reported 1.535 Gb of assembled sequence and transcriptome data from the African oil palm, Elaeis guineensis, and the interfertile S. American oil palm, Elaeis oleifera, which diverged in the new world. The oil palm sequence has already led to the discoveries of the VIR gene, the SHELL gene and the epigenetic cause of the mantled somaclonal abnormality. VIR is responsible for oil palm fruit color, and the identification of VIR mutations associated with the virescens fruit color phenotype will facilitate the development of elite breeding lines with a natural color indicator for fruit ripening. SHELL is responsible for increased oil yields in tenera hybrids through single gene heterosis. Statistical sampling of palms in independent planting sites throughout Malaysia suggests that a novel molecular precision agriculture approach involving SHELL gene testing and culling of non‐tenera (lowperforming) palms at the nursery stage before field planting will enable the exclusive planting of high yielding tenera pal This will result in a significant increase in oil yield from existing planted area and increasing wealth creation among the nation’s poorest farmers. The genome sequence also enabled epigenome‐wide association studies, which were used to find Karma, a transposon inserted into the MANTLED gene, whose methylation protects clonal planting materials from floral abnormalities. These discoveries, and more to come, are already helping to achieve sustainability for the most important oil crop worldwide. Speaker’s biographical sketch Nathan D. Lakey, MBA, is Founding Principal, President & Chief Executive Officer of Orion Genomics, LLC. Lakey received a BA in Biochemistry from the University of Texas at Austin and an MBA from Washington University St. Louis. Lakey was regionally recognized with the top 40 under 40 award (2004 St. Louis), presented with the governor's top technology award (2005 Missouri) and currently serves as chairman of the Investment Advisory Committee, Biogenerator, and Chairman of Orion Biosains SDN BHD, and serves on the boards of Orion Genomics LLC, Missouri Baptist Hospital, Apse LLC, EpigenTX, INC, and YourBevCo LLC. Lakey has more than 25 years of experience in genomics, he was Director of DNA Sequencing at Millennium Pharmaceuticals, Inc., helped form Millennium Predictive Medicine, Millennium Biotherapeutics and Cereon Inc. Before joining Millennium, Lakey held various positions with Molecular Dynamics, Ambion Inc., and Harvard Medical School, Department of Genetics, in the laboratory of next generation sequencing pioneer, Professor George M. Church. Lakey holds numerous issued and pending patents in the US and around the world. 137
11th Annual Sequencing, Finishing, and Analysis in the Future Meeting PACBIO, DOVETAIL, AND BIONANO TECHNOLOGIES ENABLE QUALITY PLANT GENOME ASSEMBLIES. Friday, 3rd June 11:40 La Fonda Ballroom Talk (OS‐8.01) Thiruvarangan Ramaraj 1 , Diego Fajardo 1 , Karen Moll 1 , Peng Zhou 2 , Peter Tiffin 2 , Jason Miller 3 , Kevin Silverstein 2 , Nevin Young 4 , Joann Mudge 1 1 National Center for Genome Resources (NCGR), 2 University of Minnesota, 3 J. Craig Venter Institute, 4 University of New Mexico Next generation sequencing and physical/optical mapping technologies have enabled interrogation of rapidly evolving genomic regions that generate a high frequency of tandem duplications. In plants, these regions are important because they control interactions with microbes. For Medicago truncatula, a nitrogen‐fixing legume, interactions with microbial partners include not only plant defense, but symbiotic interactions with both nitrogen‐fixing bacteria and fungal mycorrhizae, neither of which is present in the model plant, Arabidopsis thaliana. Here, we have used long reads (PacBio) to generate a de novo genome assembly of R108, an important Medicago truncatula accession because of its ability to be transformed. We have also generated a BioNano map and a Dovetail library for scaffolding. We’ve used the BioNano and Dovetail data to improve the continuity of the assembly, generating five different assemblies with different combinations and orderings of these long‐range technologies. On these data, assembly connectivity increased with applications of BioNano or Dovetail and even further with their combination. The largest increase was produced having the Dovetail step precede the BioNano step. 138
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Sequencing

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