Uploaded January 2026 | Updated September 2026, 1 hour ago
Get chromosome-scale phased assemblies, tissue-specific gene expression, and regulatory element maps—all from 15 milligrams of tissue. In this presentation from the PacBio workshop at PAG 33, learn how the "holistic genome" approach maximizes data from minimal input.
The melon fly is a major specialty crop pest kept out of mainland US through sterile insect technique programs. Sheina Sim, PhD and team at USDA-ARS Hawaii needed comprehensive genomic resources to study insecticide resistance. From a single fly, they generated Fiber-seq (for HiFi assembly), CiFi (for phasing), and Kinnex Iso-Seq (for annotation)—achieving chromosome-scale contigs with no manual curation. Using EGAPx with Iso-Seq only, they detected 50% more mRNA isoforms and 3x more non-coding RNAs than short-read annotation, enabling discovery of regulatory elements controlling resistance genes.
*What you'll learn*
- Generate three complementary library types from a single small insect
- Achieve chromosome-scale phased assemblies using CiFi with minimal curation
- Annotate genomes with Iso-Seq only using EGAPx (no RNA-seq required)
- Map tissue-specific gene expression and chromatin accessibility simultaneously
*Featured speakers*
- Sheina Sim, Research Biologist, USDA Agricultural Research Service (Hawaii)
*Chapters*
00:00 Introduction
00:58 USDA fruit fly research mission
02:04 Ag100Pest and Beenome100 initiatives
02:36 Genome assembly pipeline overview
03:21 The holistic genome concept
03:50 One fly, three library types
05:10 Kinnex Iso-Seq for annotation
05:45 Melon fly biology and importance
06:45 Sterile insect technique
07:54 Genetic sexing strain
08:26 Fiber-seq + CiFi phased assembly results
09:13 CiFi contact maps and scaffolding
10:30 Centromere-spanning contigs
11:03 Sex chromosome phasing
11:47 EGAPx annotation with Iso-Seq
12:26 Long-read vs short-read annotation comparison
13:45 Tissue-specific expression: ORCO and OBPs
14:37 Insecticide resistance GWAS application
16:07 Key takeaways
16:56 Acknowledgments
*Resources*
- Fiber-seq application note: pacb.com/wp-content/uploads/Application-note-Fiber-seq-high-resolution-long-read-chromatin-fiber-sequencing-in-a-single-multiomic-assay.pdf
- CiFi application note: pacb.com/wp-content/uploads/Application-note-CiFi-Long-read-multi-contact-3C-for-chromosome-scale-assemblies-using-PacBio-HiFi-reads.pdf
- Kinnex full-length RNA kit: pacb.com/technology/kinnex
What insect would you want to build a holistic genome for? *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
#HolisticGenome #InsectGenomics #HiFiSequencing
Get chromosome-scale phased assemblies, tissue-specific gene expression, and regulatory element maps—all from 15 milligrams of tissue. In this presentation from the PacBio workshop at PAG 33, learn how the "holistic genome" approach maximizes data from minimal input.
The melon fly is a major specialty crop pest kept out of mainland US through sterile insect technique programs. Sheina Sim, PhD and team at USDA-ARS Hawaii needed comprehensive genomic resources to study insecticide resistance. From a single fly, they generated Fiber-seq (for HiFi assembly), CiFi (for phasing), and Kinnex Iso-Seq (for annotation)—achieving chromosome-scale contigs with no manual curation. Using EGAPx with Iso-Seq only, they detected 50% more mRNA isoforms and 3x more non-coding RNAs than short-read annotation, enabling discovery of regulatory elements controlling resistance genes.
*What you'll learn*
- Generate three complementary library types from a single small insect
- Achieve chromosome-scale phased assemblies using CiFi with minimal curation
- Annotate genomes with Iso-Seq only using EGAPx (no RNA-seq required)
- Map tissue-specific gene expression and chromatin accessibility simultaneously
*Featured speakers*
- Sheina Sim, Research Biologist, USDA Agricultural Research Service (Hawaii)
*Chapters*
00:00 Introduction
00:58 USDA fruit fly research mission
02:04 Ag100Pest and Beenome100 initiatives
02:36 Genome assembly pipeline overview
03:21 The holistic genome concept
03:50 One fly, three library types
05:10 Kinnex Iso-Seq for annotation
05:45 Melon fly biology and importance
06:45 Sterile insect technique
07:54 Genetic sexing strain
08:26 Fiber-seq + CiFi phased assembly results
09:13 CiFi contact maps and scaffolding
10:30 Centromere-spanning contigs
11:03 Sex chromosome phasing
11:47 EGAPx annotation with Iso-Seq
12:26 Long-read vs short-read annotation comparison
13:45 Tissue-specific expression: ORCO and OBPs
14:37 Insecticide resistance GWAS application
16:07 Key takeaways
16:56 Acknowledgments
*Resources*
- Fiber-seq application note: pacb.com/wp-content/uploads/Application-note-Fiber-seq-high-resolution-long-read-chromatin-fiber-sequencing-in-a-single-multiomic-assay.pdf
- CiFi application note: pacb.com/wp-content/uploads/Application-note-CiFi-Long-read-multi-contact-3C-for-chromosome-scale-assemblies-using-PacBio-HiFi-reads.pdf
- Kinnex full-length RNA kit: pacb.com/technology/kinnex
What insect would you want to build a holistic genome for? *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
#HolisticGenome #InsectGenomics #HiFiSequencing
