Uploaded January 2026 | Updated September 2026, 1 hour ago
Discover how HiFi long-read sequencing is enabling reference-quality pan genomes across plant species and improving diagnostic rates for rare human diseases.
Jeremy Schmutz shares results from the JGI and HudsonAlpha at PAG 33, including a 30-genome sorghum pan genome, chromosome-scale gymnosperms 63x larger than poplar, and the first look at SPRQ-Nx chemistry performance for genome assembly. He also demonstrates how full-length Kinnex 16S sequencing resolves microbial species that short V4 amplicons cannot distinguish.
*What you'll learn*
- Build haplotype-resolved pan genomes for complex polyploid crops like sugarcane and sorghum
- Apply HiFi sequencing to identify structural variants missed by exome capture in rare disease cases
- Use the panJGC annotation pipeline to reduce gene proliferation artifacts across pan genome members
- Resolve microbial community composition with full-length 16S using Kinnex
- Evaluate SPRQ-Nx chemistry yield, accuracy, and multi-use SMRT Cell performance
*Featured speaker*
- Jeremy Schmutz, Faculty Investigator (HudsonAlpha Institute for Biotechnology / JGI)
*Chapters*
00:00 Introduction
00:58 Looking back: PacBio in 2010
02:00 Why HiFi changed plant and human genomics
02:54 Sugarcane R570 genome
03:28 What we're doing with PacBio
03:55 Rare disease discovery with HiFi
04:55 Plant pan genomes overview
06:01 Sorghum dhurrin biosynthetic cluster
06:57 From one genome to a pan genome
07:34 Wild sorghum diversity in Australia
08:19 Pan genome annotation challenges
10:54 Eucalyptus grandis tandem duplications
11:32 Dirty, devious microbes: root microbiome
13:56 Full-length 16S with Kinnex
14:33 SPRQ-Nx chemistry: a new chemistry?
15:49 Yield and base pair accuracy
17:51 Yield loss and carryover between runs
19:22 SNP and SV calling performance
19:53 Building contig assemblies
21:33 Current thoughts on SPRQ-Nx
22:00 Downsides and considerations
22:48 JGI Community Science Program
23:17 Phytozome and HudsonAlpha resources
23:59 Acknowledgments
*Resources*
- HiFi sequencing for plant genomics: pacb.com/research-focus/plant-and-animal-sciences
- Phytozome comparative genomics portal: phytozome-next.jgi.doe.gov
- Kinnex full-length RNA kits: pacb.com/products-and-services/consumables/kinnex-kits
- Revio system overview: pacb.com/revio
What species would benefit most from a pan genome approach in your research? *Comment below.*
*Subscribe for more PacBio genomics content:*
youtube.com/@PacificBiosciences?sub_confirmation=1
Learn more about PacBio at pacb.com
Legal & Trademarks: pacb.com/legal-and-trademarks
#PlantGenomics #PanGenome #HiFiSequencing
Discover how HiFi long-read sequencing is enabling reference-quality pan genomes across plant species and improving diagnostic rates for rare human diseases.
Jeremy Schmutz shares results from the JGI and HudsonAlpha at PAG 33, including a 30-genome sorghum pan genome, chromosome-scale gymnosperms 63x larger than poplar, and the first look at SPRQ-Nx chemistry performance for genome assembly. He also demonstrates how full-length Kinnex 16S sequencing resolves microbial species that short V4 amplicons cannot distinguish.
*What you'll learn*
- Build haplotype-resolved pan genomes for complex polyploid crops like sugarcane and sorghum
- Apply HiFi sequencing to identify structural variants missed by exome capture in rare disease cases
- Use the panJGC annotation pipeline to reduce gene proliferation artifacts across pan genome members
- Resolve microbial community composition with full-length 16S using Kinnex
- Evaluate SPRQ-Nx chemistry yield, accuracy, and multi-use SMRT Cell performance
*Featured speaker*
- Jeremy Schmutz, Faculty Investigator (HudsonAlpha Institute for Biotechnology / JGI)
*Chapters*
00:00 Introduction
00:58 Looking back: PacBio in 2010
02:00 Why HiFi changed plant and human genomics
02:54 Sugarcane R570 genome
03:28 What we're doing with PacBio
03:55 Rare disease discovery with HiFi
04:55 Plant pan genomes overview
06:01 Sorghum dhurrin biosynthetic cluster
06:57 From one genome to a pan genome
07:34 Wild sorghum diversity in Australia
08:19 Pan genome annotation challenges
10:54 Eucalyptus grandis tandem duplications
11:32 Dirty, devious microbes: root microbiome
13:56 Full-length 16S with Kinnex
14:33 SPRQ-Nx chemistry: a new chemistry?
15:49 Yield and base pair accuracy
17:51 Yield loss and carryover between runs
19:22 SNP and SV calling performance
19:53 Building contig assemblies
21:33 Current thoughts on SPRQ-Nx
22:00 Downsides and considerations
22:48 JGI Community Science Program
23:17 Phytozome and HudsonAlpha resources
23:59 Acknowledgments
*Resources*
- HiFi sequencing for plant genomics: pacb.com/research-focus/plant-and-animal-sciences
- Phytozome comparative genomics portal: phytozome-next.jgi.doe.gov
- Kinnex full-length RNA kits: pacb.com/products-and-services/consumables/kinnex-kits
- Revio system overview: pacb.com/revio
What species would benefit most from a pan genome approach in your research? *Comment below.*
*Subscribe for more PacBio genomics content:*
youtube.com/@PacificBiosciences?sub_confirmation=1
Learn more about PacBio at pacb.com
Legal & Trademarks: pacb.com/legal-and-trademarks
#PlantGenomics #PanGenome #HiFiSequencing
