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  • Introduction
  • Avian Phylogenetics Consortium
  • B10K project
  • G10K project
  • Setting up new vertebrate genome lab @ Rockefeller University
  • Quality of genome contiguity makes a big difference in outcomes of scientific accuracy & labor required for analyses
  • Dopamine receptor family in avian genomes
  • Decide to test different genome technologies to generate reference genomes for G10K/B10K for < $10,000/species
  • Comparison of genome assembly stats
  • Hummingbird contigs – NG50*
  • Hummingbird scaffolds – NG50*
  • Checking assembly internal quality
  • Base QV*
  • Ranking of scaffold structural qualities*
  • BUSCO vertebrate genes
  • Phasing anecdotes
  • What about own species gene representation? Brain RNASeq reads from vocal learning finch brain regions mapped to finch assemblies
  • Brain HK327ac ChipSeq reads from vocal learning finch brain regions mapped to finch assemblies
  • Hybrid Pacbio + Bionano assembly: chromosome size scaffolds
  • Pacbio + Phase Genomics Hi-C; 43 hummingbird chromosomes
  • Pacbio + Arima Genomics phasing Hi-C; 38 finch chromosomes, 1/3 phased, but 40-50%
  • Dovetail Hi-C Hummingbird vs. zebra finch and chicken
  • Dovetail hummingbird assembly
  • What are the brain mechanisms of this difference?
  • Four genes of interest
  • EGR1 : Pacbio long reads fill in missing GC promoter & more
  • DUSP1: Pacbio long reads filled and corrected microsattelites found in vocal learners
  • SLIT1: Pacbio long reads filled & corrected all gaps in ~60Kb gene, allowed discovery of 2 missing exon supported by RNASeq
  • FOXP2 : Pacbio long reads filled & corrected all gaps in ~400Kb gene
  • Problems long reads have resolved
  • Problems that need resolution
  • Summary
  • Company Acknoweldgements
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  • Speaker: Erich Jarvis, Professor, The Rockefeller University
  • Speaker: Erich Jarvis, Professor, The Rockefeller University
  • Speaker: Erich Jarvis, Professor, The Rockefeller University
  • Speaker: Erich Jarvis, Professor, The Rockefeller University
  • Speaker: Erich Jarvis, Professor, The Rockefeller University
  • Speaker: Erich Jarvis, Professor, The Rockefeller University
  • Speaker: Erich Jarvis, Professor, The Rockefeller University
  • Speaker: Erich Jarvis, Professor, The Rockefeller University
  • Speaker: Erich Jarvis, Professor, The Rockefeller University
  • Speaker: Erich Jarvis, Professor, The Rockefeller University
  • Speaker: Erich Jarvis, Professor, The Rockefeller University
  • Speaker: Erich Jarvis, Professor, The Rockefeller University
  • Speaker: Erich Jarvis, Professor, The Rockefeller University
  • Speaker: Erich Jarvis, Professor, The Rockefeller University
  • Speaker: Erich Jarvis, Professor, The Rockefeller University
  • Speaker: Erich Jarvis, Professor, The Rockefeller University
  • Speaker: Erich Jarvis, Professor, The Rockefeller University
  • Speaker: Erich Jarvis, Professor, The Rockefeller University
  • Speaker: Erich Jarvis, Professor, The Rockefeller University
  • Speaker: Erich Jarvis, Professor, The Rockefeller University
  • Speaker: Erich Jarvis, Professor, The Rockefeller University
  • Speaker: Erich Jarvis, Professor, The Rockefeller University
  • Speaker: Erich Jarvis, Professor, The Rockefeller University
  • Speaker: Erich Jarvis, Professor, The Rockefeller University
  • Speaker: Erich Jarvis, Professor, The Rockefeller University
  • Speaker: Erich Jarvis, Professor, The Rockefeller University
  • Speaker: Erich Jarvis, Professor, The Rockefeller University
  • Speaker: Erich Jarvis, Professor, The Rockefeller University
  • Speaker: Erich Jarvis, Professor, The Rockefeller University
  • Speaker: Erich Jarvis, Professor, The Rockefeller University
  • Speaker: Erich Jarvis, Professor, The Rockefeller University
  • Speaker: Erich Jarvis, Professor, The Rockefeller University
  • Speaker: Erich Jarvis, Professor, The Rockefeller University