Biodiversity solutions
PacBio sequencing delivers the data that empowers biodiversity and conservation initiatives with exceptional multiomic insights. Our state-of-the-art technologies enable you to more comprehensively document and delve into the hidden wonders of the biosphere and launch campaigns to safeguard them for future generations.
Plant + animal biology
Efficiently assemble, phase, and capture genomic diversity from single-nucleotide polymorphisms to complex structural variants.
Fungi + invertebrates
Overcome DNA input barriers to sequence small-bodied organisms with workflows requiring little DNA input. Identify host-symbiont adaptations using transcriptomes sequenced with the Iso-Seq method.
Marine + avian biodiversity
Study evolution, obtain insights into developmental biology, and address the challenges of climate change faced by marine and terrestrial ecosystems with sequencing data of exceptional quality.
Protect species, populations, and ecosystems
Climate change, pollution, and habitat loss impact a concerning majority of species and ecosystems on our planet. To preserve and protect the biosphere against such threats, it is vital to document, catalog, and expand our understanding of the intricate biology of organisms across the full scale of complexity, from cells to entire ecosystems. Our sequencing tools offer powerful multiomic solutions that are applicable across disciplines, from entomology and botany to evo-devo, plant and animal genetics, marine biology, and more.
- Decipher complex structural variants and single nucleotide polymorphisms
across phased reference-quality genomes that are easy to assemble, allowing you to better capture genetic diversity. - Explore phenotypic plasticity in populations and survey the epigenome
with HiFi 5mC methylation detection without any changes to library prep or sequencing workflows. - Glimpse environmental responses and better understand physiological adaptations
like hibernation in bears with high-quality transcriptomes using the Iso-Seq method.
White paper
Transforming plant + animal research with full-length and single-cell isoform sequencing
In this whitepaper, you’ll discover how full-length and single-cell isoform sequencing with the Iso-Seq method can enhance your plant and animal research. Learn how combining Iso-Seq with Kinnex kits boosts throughput, making PacBio long reads a cost-effective RNA sequencing solution for your projects.
Common questions about biodiversity
Biodiversity in action
Plant + animal biology brochure
Bring your team up to speed on the advantages of HiFi sequencing for multiomics applications, from interpreting cryptic insect metabolisms to mapping the gargantuan 27 Gb genome of the coastal redwood (Sequoia sempervirens).
Introducing the Vega system – HiFi sequencing within reach
Bring the power of HiFi to every corner of the globe with the first benchtop PacBio long-read sequencing platform.
Whole genome sequencing best practices
Look at recommended workflows for assembling reference-quality genomes of everything from insects and big cats to giant coastal redwoods, de novo.
Metabarcoding of fungi and other eukaryotes
Explore how HiFi sequencing is being used to help researchers peer deep into the evolutionary tree of life to better understand when and how eukaryotic lineages colonized different habitats.
Plant + animal biology
Embark on a new voyage of discovery with long, high quality genomic reads to better document and understand diverse organisms. From the genome of the semi-mangrove plant that sheds light on adaptation to coastal stress, to assemblies of the entire sea turtle clade that reveal evolutionary patterns across ancient marine vertebrates, HiFi is helping unlock species uniqueness with unprecedented resolution.
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- Build reference quality, haplotype resolved genomes and pangenomes to better understand individuals, populations, and species.
- Reveal SNPs, indels, and structural variants that can be imputed to traits of interest using high accuracy long-read sequencing.
- Capture genomic variation at a genome wide scale across outbred, inbred, and population level studies.
Insect + fungal biology
Confidently explore some of the smallest and most difficult-to-sequence organisms with dedicated HiFi workflows requiring only 1 ng of DNA input†
- Assemble, phase, and capture genomic diversity from single-nucleotide polymorphisms to complex structural variants.
- Examine host-symbiont interactions and adaptations with isoform level annotations using the Iso-Seq method.
- Deconvolute insect microbiomes with HiFi shotgun metagenomics workflows that allow you to profile taxonomy and function at the same time.
Marine + avian biodiversity
Use HiFi sequencing to generate high quality genomes and transcriptomes for marine and avian species that represent diverse evolutionary lineages and ecological roles. Highly accurate genomic data supports investigation of genome organization, gene family evolution, and adaptation in species that come from the earth’s waters or skies.
- Assemble reference quality genomes to resolve complex genome architectures and lineage specific gene expansions.
- Characterize transcriptional complexity and regulatory features using full length transcriptome sequencing with the Iso-Seq method.
- Identify, sequence, and multiplex genomic regions of interest while preserving long amplicon integrity across individuals and populations.
Biodiversity
A grand challenge with a grand vision: the Earth Biogenome Project
PacBio has partnered with the Earth BioGenome Project (EBP) to deploy the power of HiFi sequencing to catapult humanity into a new era of biodiversity conservation and comprehension. With the goal of sequencing and assembling genomes for all known eukaryotic species on the planet within ten years, the pursuit is challenging but the benefits are immeasurable.
Applications to fuel biodiversity research and discovery
Whole genome sequencing
Quickly and affordably create more complete, contiguous, and correct de novo assemblies of even the most complex genomes like the 27 Gb coastal redwood.
Structural variant calling
Acquire high-sensitivity variant calls with low false discovery rates to gain actionable insights across populations.
RNA sequencing
Leverage the isoform sequence (Iso-Seq) method using the Kinnex RNA kit to obtain full-length cDNA sequences — from 5’ to the poly-A tail — to confidently characterize the full transcriptome.
Metagenomics
Uncover hidden microbiome functions and confidently capture microbial species richness and diversity with the highest quality metagenomic data available — only with HiFi metagenomic sequencing.
| Application | Samples per Vega SMRT Cell | Samples per Revio SMRT Cell |
| Whole genome sequencing | ||
| De novo assembly (2 Gbs genome) | 1 | 2 |
| Variant detection (2 Gbs genome) | Structural varients: 3 All variants: 1 | Structural varients: 6 All variants: 2 |
| Microbial de novo assembly (2 Gb total) | 384 | 384 |
| RNA sequencing | ||
| Kinnex single-cell RNA sequencing | 1 (3,000-6,000 cells) | 1 (6,000-10,000 cells) |
| Kinnex full-length RNA sequencing | ||
| 5M reads | 6 | 12 |
| 10M reads | 3 | 6 |
| Targeted sequencing | ||
| Amplicon sequencing | >1,000 | >1,000 |
| Microbial sequencing | ||
| Shotgun metagenomic profiling | 64 communities | 128 communities |
| Shotgun metagenomic assembly | 8 communities | 16 communities |
| Kinnex 16S rRNA | 1,024 communities | 1,536 communities |
| All sample throughputs are estimates for either the Vega system with 1 SMRT Cell or the Revio system using SPRQ-Nx chemistry with 1 SMRT Cell. Coverage may vary based on sample quality, library quality, and fragment lengths. Currently available SMRTbell adapter index plates 96A-96D contain a total of 384 SMRTbell barcoded adapters. Microbial de novo assembly assumes microbes with 2 Gb of total genome size at 30x per sample. Single-cell transcriptomics assumes ≥80 million reads per library on the Revio system and ~50-60 million reads per library on the Vega system. Full-length RNA sequencing assumes a total of 60M reads for Revio SPRQ-Nx and 30M reads for Vega, regardless of plexity. Amplicon sequencing assumes a 12-hour movie time for 1–5 kb, 24-hour movie time for 5+ kb, and >50× per sample. Target enrichment assumes >50× per sample. | ||
