Plant Presentations - pacb.com · You are encouraged to check the PAG website for any presentation you are interested in attending as times ... The Apple Genome and Methylome :

You are encouraged to check the PAG website for any presentation you are interested in attending as times

and room locations are subject to change.

Plant Presentations

Saturday, January 13

8:30 AM Town and Country

Development of Genetic and Genomic Resources to Evaluate Wheat Organellar Genome Variants and their Functional Implications Katie L. Liberatore, USDA-ARS and University of Minnesota

9:20 AM Pacific Salon 3

Citrus Genomes and Excavation of Apomixis Genes Qiang Xu, Huazhong Agricultural University


Chromosome-Scale Genomic Resources for High Resolution Genetic Analysis in Pistachio William J. Palmer, University of California Davis

9:40 AM Pacific Salon 4-5 (2nd floor)

Development of the Alfalfa Breeder's Toolbox: Integration of Genomic, Genetic and Germplasm Resources for Alfalfa Improvement Maria J. Monteros, Noble Research Institute


The Apple Genome and Methylome : New Gene Regulatory Roles for DNA Methylation? Nicolas Daccord, IRHS, INRA

12:00 PM Pacific Salon 3

Towards Developing a Chromosome Scale Reference Genome Sequence of Blueberry Massimo Iorizzo, North Carolina State University

2:30 PM Pacific Salon 6-7 (2nd floor)

Resolving the Diploid Genome of Fairchild Mandarin with Single Molecule Sequencing Technologies Jinfeng Chen, University of California

4:00 PM Towne-Meeting House

Diatom Evolution through the Lens of the Largest Diatom Genome Sequenced to Date, Psammoneis japonica Matthew Parks, Chicago Botanic Garden


Map-Based Cloning of Pc2/Vb: A Doubled-Edge Sword of Immunity Matthew J. Moscou


The Funaria Genome: A Chromosome-Scale Assembly. Peter Szovenyi, University of Zurich

Sunday, January 14

8:00 AM Royal Palm Salon 1-2

A Reference Sequence of the Monoploid Genome of Sugarcane Angelique D'Hont, CIRA, UMR AGAP


Genomic Analysis of Saccharum spontaneum Haploid AP85-441 Ray Ming, University of Illinois at Urbana-Champagne

10:30 AM Esquire- Meeting House

An Updated Chromosome-Scale Assembly of Quinoa using Hi-C David E. Jarvis, Brigham Young University


Rpi-amr1, a Novel Class of Solanum Resistance Genes against Phytophthora infestans Kamil Witek, The Sainsbury Laboratory


Cowpea: Navigating the Genome of a Climate Resilient Legume Timothy J. Close, University of California Riverside

12:00 PM Esquire- Meeting House

A PacBio and Hi-C Based Proximity-Guided Assembly of Chenopodium pallidicaule Hayley Hansen, Brigham Young University


Comparative Genome of Repeat Elements among Selected Species under Caryophyllales Shubham Dixit, Institute of Bioinformatics and Applied Biotechnology


Insights into the Evolution of Vitis vinifera Brandon S. Gaut, University of California Irvine

1:50 PM Royal Palm Salon 1-2

Assembling a Hybrid Sugarcane Genome Jeremy Shearman, National Center for Genetic Engineering and Biotechnology


Unraveling the Genome of a High Yielding Colombian Sugarcane Hybrid John Riascos, CENICANA


A Phased, Chromosome-Scale, Diploid Genome Reference for the Wine Grape Cultivar Cabernet Sauvignon Dario Cantu, University of California Davis


Chromosome Scale Scaffolding of the High-Quality Genome Assemblies of the Allotetraploid Coffea arabica and its Maternal Ancestor C. eugenioides and Validation using Genetic and Physical Mapping Data Aleksey Zimin, University of Marlyland and Johns Hopkins University

4:40 PM Golden Ballroom

The Coconut Genome: Providing a Reference Sequence Towards Coconut Varietal Improvement Darlon V. Lantican, University of the Philippines Los Banos


Coconut Genetics and Genomics for Host Insect Resistance Hayde F. Galvez, University of Philippines Los Banos


The Evolution from Autosome to X and Y Chromosomes in Asparagus Alex Harkess, Donald Danforth Plant Science Center


A Near-Finished Reference Genome for the Wheat Blast Fungus Provides Insight on Pathogenicity and Adaptation Sanzhen Liu, Kansas State University

5:50 PM Sunset- Meeting House

Single-Molecule Sequencing of G. arboreum Genome and GWAS Analysis of Chinese G. arboreum Accessions Xiongming Du, Chinese Academy of Agricultural Science

Monday, January 15


A Whole Genome Association Study in Bailinggu (Pleurotus tuoliensis) Yongping Fu, Jilin Agricultural University


Genome Sequencing and Comparative Analysis of the Early Flowering Rice Variety Kitaake Rashmi Jain, University of California Davis

Tuesday, January 16


Analysis of Variations in Genes Controlling Fruit Colors of Capsicum using SMRT Sequencing Byoung-Cheorl Kang, Seoul National University

11:35 AM Towne- Meeting House

Updates to the Tomato Reference Genome and ITAG Annotation Surya Saha, Boyce Thompson Institute


High-Quality de novo Genome Assembly of the Tomato Genome using Combination of PacBio, BioNano and Chromium 10x Long Molecules Sequencing Technologies Mohamed Zouine, INPT-ENSAT


Draft Tragopogon dubius (Asteraceae) Genome Assembly using Linked-Read Sequencing and a Survey of Alternative Splicing Xiaoxian Liu, University of Florida

3:10 PM Pacific Salon 4-5

Towards More Durable Resistance to Lettuce Downy Mildew Kyle Fletcher, University of California Davis


Insights into Virulence Evolution from 31 Phytophthora Plant Pathogen Genomes produced by Illumina and PacBio Sequencing Brent Kronmiller, Oregon State University

4:20 PM Esquire-Meeting House

A Genomic Approach to Study Apomixis using Eragrostis curvula as a Model Species Viviana Echenique, CERZOS CCT_CONICET Bahia Blanca


Comparative Genomics of the Perennial Model Grass Brachypodium sylvaticum and its Annual Relative B. distachyon Sean Gordon, DOE JGI


Low Number of Fixed Somatic Mutations in a Long-Lived Oak Tree Emanuel Schmid-Siegert, Swiss Institute of Bioinformatics

Wednesday, January 17


The Wolffia australiana Genome Todd Michael, JCVI

Animal Presentations

Friday, January 12

4:41 PM Sunrise- Meeting House

Developing the Functional Annotation of the Sheep Genome Brenda M. Murdoch, University of Idaho



Assembly and Computational Use of Aquatic Genome Models Wesley Warren, Washington University


A de novo Hybrid Assembly of a Dromedary Camel Heather M. Holl, University of Florida


Chromosome Level Assembly of the Water Buffalo Genome Lloyd Low, Davies Research Center


Ensembl Sscrofa11.1 Genome Annotation Thibaut Hourlier, European Molecular Biology Laboratory- EBI


Additional Annotation of the Pig Transcriptome Using Integrated Iso-Seq and Illumina RNA-Seq Analysis Hamid Beiki, Iowa State University

1:55 PM San Diego

Two New Cattle Reference Genomes for the Price of One Arang Rhie, NHGRI-NIH


Deciphering the Genome of the Insect Vector Diaphorina citri to Develop Solutions for the Citrus Greening Disease Surya Saha, Boyce Thompson Institute


EquCab3: Assembly Complete Edward S. Rice, University of California Santa Cruz

3:00 PM San Diego

Impact of the New Reference Genome on Genotype Imputation Accuracy Robert D. Schnabel, Informatics Institute

3:25 PM San Diego

Rambouillet Sheep Genome and Annotation Resources Kim C. Worley, Baylor College of Medicine

4:00 PM Sunrise- Meeting House

High-Resolution Comparative Analysis of Great Ape Genomes Zev Kronenberg, University of Washington and Phase Genomics

4:05 PM San Diego

Long-Read Sequencing Enables the Accurate Annotation of Immune Gene Clusters in Goat Derek M. Bickhart, USDA-ARS


A Strategy to Assemble High-Quality Reference Genomes for All Vertebrate Orders Adam M. Phillippy, NHGRI-NIH

Sunday, January 14

8:00 AM San Diego

Oxford Nanopore and PacBio Shotgun Sequencing and Analysis of the Cattle Rumen Metagenome Sergey Koren, NHGRI-NIH

8:50 AM San Diego

Holstein Reference Genome: Long Read Sequencing, de novo Assembly and Annotation Gonzalo Rincon, Zoetis

9:15 AM San Diego

Cattle CNVs - the Long and Short (sequence) of It All Christine Couldrey


Variant Discovery for Feline Precision Medicine Wesley Warren, Washington University

Monday, January 15


The Ovine FAANG Project Brenda M. Murdoch, University of Idaho

12:05 PM Towne- Meeting House

Rambouillet Sheep Reference Genome and Initial Analysis of FAANG Sample RNA Sequencing Kim C. Worley, Baylor College of Medicine

Tuesday, January 16


High-Quality Assembly of European House Dust Mite Genome, Transcriptome and Proteome Reveal a Wide Range of Novel Allergens Ming-Qiang Wang, The Chinese University of Hong Kong

Methods Presentations


10:30 AM Town and Country

Assembly of Large Plant Genomes from Hybrid Long and Short Read Data. Aleksey Zimin, University of Maryland

Sunday, January 14


A Novel and Efficient Approach for Phasing Highly Heterozygous Plant Genomes Tingting Zhu, University of California Davis


Targeted Sequencing in Allopolyploids: Comparison of BAC-by-BAC and Whole Genome Approaches using Third Generation Sequencing Carlos Ernesto Maldonado, CENICAFE

Tuesday, January 16

10:30 AM Golden West

Towards Haplotype-Resolved Genomes with Canu Sergey Koren, NHGRI-NIH

11:10 AM Golden West

In Pursuit of Perfect Genome Sequencing: Accurate Identification and Phasing of Structural Variations using Short, Long, and Linked Reads Michael C. Schatz, Johns Hopkins University

Wednesday, January 17

11:45 AM California

Dot: An Interactive Dot Plot Viewer for Comparative Genomics Maria Nattestad, DNAnexus

Plant Posters

Presentations of even numbered posters are scheduled for Monday, January 15 from 10:00 – 11:30 AM.

Presentations of odd numbered posters are scheduled for Monday, January 15 from 3:00 – 4:30 PM. You are

encouraged to check the PAG website for any poster presentation you are interested in attending, as times

and poster numbers are subject to change.

P0160 Development and Characterization of Microsatellite Markers on Linkage Group 6 of European Hazelnut Golnaz Komaei Koma, Oregon State University

P0178 Recombination Generates Mitochondrial Genome Diversity in Wild and Domesticated Lettuce Beth Rowan, University of California Davis

P0196 Optical Maps Combined with Recent NGS Reach High Quality Genome Assembly in Plants Sandrine Arribat, CNRGV-INRA

P0203 Differential Gene Expression during Flower and Fruit Development of the Blueberry Cv. O'neal Rishi Aryal, North Caorlina State University

P0601 Single-Molecule Sequencing of G. arboreum Genome and GWAS Analysis of Chinese G. arboreum Accessions Xiongming Du, Chinese Academy of Agricultural Science

P0622 Full Length Isoform Sequencing and Profiling of Expressed Genes in Cambial Zone and Needle Leaf of Japanese Larch (Larix kaempferi) Kentaro Mishima, FFPRI

P0676 A High Quality Draft Assembly of the Diploid ‘Regina’ Sweet Cherry Genome Mathieu Fouche, INRA

P0702 Genomic Analyses of Primitive, Wild, and Cultivated Citrus Provide Insights into Citrus Polyembryony Xia Wang, Key Laboratory of Horticultural Plant Biology

P0729 Molecular Mechanisms Regulating Nut Weight in Castanea crenata Eung-Jun Park, National Institute of Forest Science

P0733 Coconut Genetics and Genomics for Host Insect Resistance Hayde F. Galvez, University of the Philippines Los Banos

P0735 The Coconut Genome: Providing a Reference Sequence Towards Coconut Varietal Improvement Darlon V. Lantican, University of the Philippines Los Banos

P0743 A High-Quality Wild Soybean Reference Genome Min Xie, The Chinese University of Hong Kong

P0815 Expanding Cowpea Genetic and Genomic Resources Maria Munos-Amatriain, University of California Riverside

P0843 Building Maize High Quality, Chromosome-Scale, de novo Genome Assemblies by Scaffolding Next-Generation Sequencing Assemblies with Bionano Maps Generated with the New Direct Labeling Enzyme Yang Zhang, BioNano Genomics

P0911 High-Quality Genome Sequences of Cultivated (Linum usitatissimum) and Wild (L. bienne) Flax Khalid Rashid, Agriculture and Agri-Food Canada

P0956 Sequencing and de novo Assembly of the Genome of Jaltomata sinuosa, a Species in the Sister Clade to Solanum and Capsicum, Allows New Comparative Genomic Analyses in the Solanaceae Meng Wu, Indiana University Bloomington

P0975 Rpi-amr1, a Novel Class of Solanum Resistance Genes against Phytophthora infestans Kamil Witek, The Sainsbury Laboratory

P0999 The Genome of Triticum urartu, a Progenitor of Wheat a Genome Hong-Qing Ling, CAS

P1120 Assembly and Annotation of the Hexaploid Oat Genome Rachel N. Walstead, University of North Carolina at Charlotte

P1166 The Complete Genome Sequence of the Parasitic Weed Orobanche cumana (Sunflower Broomrape) Nicolas Pouilly

P1200 Improvement of a Rubber Tree Hevea brasiliensis Genome Sequence Takako Mochizuki, National Institute of Genetics, ROIS

P1208 Developmental Dynamics of Crassulacean Acid Metabolism (CAM) in Opuntia ficus-indica Nicholas A. Niechayev, University of Nevada Reno

Animal Posters

P0175 Updates to Farm Animals Annotation in Ensembl Thibaut Hourlier

P0208 High-Quality Assembly of European House Dust Mite Genome, Transcriptome and Proteome Reveal a Wide Range of Novel Allergens Ming-Qiang Wang, The Chinese University of Hong Kong

P0271 Genome Assembly and Annotation for Almaco Jack (Seriola rivoliana) Arun Seetharam, Iowa State University

P0280 The Eastern Oyster Genome: A Resource for Comparative Genomics in Shellfish Aquaculture Species Marta Gomez-Chiarri, University of Rhode Island

P0286 The Red Abalone Genome and the Consequences of Inbreeding in White Abalone Aquaculture Rick Masonbrink, Iowa State University

P0287 Draft Genome Sequence of the Pearl Millet Downy Mildew Pathogen Rakesh K. Srivastava, ICRISAT

P0303 Genome Sequencing of Thecaphora frezii (Peanut Smut) and Comparative Genomics to Ustilago maydis Renee S. Arias, USDA-ARS

P0309 Genome Assembly and Comparison of Macrophomina phaseolina Isolates on Strawberry and Alfalfa Alyssa Burkhardt, USDA-ARS

P0321 Intra-Specific Comparison of Mitochondrial Genome in Tremella fuciformis Suggests a Model of Host Gene Fragment Exchange via Intron Mobility Youjin Deng, Fujian Agriculture and Forestry University

P0333 EquCab3: A New Horse Reference Genome Assembled Using First-, Second-, and Third-Generation Sequencing Data Edward Stallknecht Rice, UC Santa Cruz

P0371 Chromosome Level Assembly of the Water Buffalo Genome Lloyd Low, Davies Research Center

P0374 A de novo Hybrid Assembly of a Dromedary Camel Heather M. Holl, University of Florida

P0380 Chromosomal Evolution of Muntjac Deer Revisited By High Quality Reference Genomes Yuan Yin, Northwestern Polytechnical University

P0384 De novo Assembly of the Tube-Snout Genome and Comparative Genomics Study Qiushi Li, University of Calgary and China Academy of Chinese Medical Sciences

P0391 A Whole Genome Association Study in Bailinggu (Pleurotus tuoliensis) Yongping Fu, Jilin Agricultural University

P0419 Rambouillet Sheep Genome and Annotation Resources Kim C. Worley, Baylor College of Medicine

P0439 Additional Annotation of the Pig Transcriptome using Integrated Iso-Seq and Illumina RNA-Seq Analysis Hamid Beiki, Iowa State University

P0450 Genome Sequences for African Suidae Species Lel Eory, The Roslin Institute and R(D)SVS

P0795 A Trio of Evolutionary Mechanisms Give Rise to a Diversity of Parasitic Effector Genes in the Soybean Cyst Nematode Rick Masonbrink, Iowa State University

P1070 Draft Genome Sequence of Karnal Bunt Pathogen (Tilletia indica) of Wheat Soma Marla, ICAR.NBPGR

Methods Posters

P0078 Evaluating the Haplotype Phasing of de novo Assemblies using FALCON Unzip Brett Hannigan, DNAnexus

P0079 Using a Combination of Sequencing Methods for Improved de novo Genome Assembly Alana J Firl, University of California Davis

P0127 Functional and Comparative Genomics of the Water-Use Efficient Crassulacean Acid Metabolism Adaptation of Photosynthetic CO2 Fixation in the Genus Kalanchoë James Hartwell, University of Liverpool

P0174 Optimized Methods for High Molecular Weight Genomic DNA Isolation Erwan Denis, CEA-Genoscope

P0177 Benchmarking High-Molecular-Weight DNA and Tissue Preservation Protocols at the Vertebrate Genome Lab Jacquelyn Mountcastle, The Rockefeller University

P0190 State of the Art and Comparison of Long Reads Technologies Celine Vandesasteele, INRA

P0193 A Novel and Efficient Approach for Phasing Highly Heterozygous Plant Genomes Tingting Zhu, University of California Davis

P0204 Generating High Quality Reference Genomes at the Vertebrate Genome Lab Olivier Fedrigo, The Rockefeller University

Documents

Plant Presentations - pacb.com · You are encouraged to check the PAG website for any presentation you are interested in attending as times ... The Apple Genome and Methylome :