Biodiversity genomics

01Overview and value chain#

Markers EC: Convention on Biological Diversity | OECD: genomics-bioinformatics | Regulator: USDA-APHIS, EFSA, MOA

Biodiversity genomics aims to decode the genetic blueprints of the planet’s entire eukaryotic biodiversity. The Earth BioGenome Project (EBP) — often called biology’s Moon program — is the central effort: a 10-year consortium target to sequence, catalogue and openly publish chromosome-level reference genomes for all of the roughly 1.5-1.8 million eukaryotic species (plants, animals, fungi and protists). This archive underpins three application domains: bioprospecting (mining secondary-metabolite pathways to port into synthetic-biology chassis for drugs and green chemistry), conservation genetics (detecting inbreeding depression and resolving disputed taxonomy for genetic-rescue programs), and food security (transferring stress-tolerance genes from crop wild relatives into commercial varieties via genome editing). With sequencing costs dropping below $1,000 per high-quality reference genome, the focus has shifted to automated ultra-long DNA extraction and open, decentralized data sharing.

The key directions of biodiversity genomics are:

1. Reference Genome Generation: Producing chromosome-level assemblies for keystone and endangered species.
2. Environmental DNA (eDNA) Monitoring: Tracking biodiversity changes by sequencing DNA shed into soil and water.
3. Bioprospecting: Mining genomic databases for novel enzymes and secondary metabolites for industrial use.
4. Conservation Genetics: Assessing genetic diversity within isolated populations to guide breeding programs.

Sectoral value chain#

[Sample Collection] ──> [DNA Extraction] ──> [Sequencing] ──> [Bioinformatics Assembly]
                                  │
                          (Annotation)
                                  │
                                  ▼
[Ecosystem Monitoring] <─── [Open Data Archiving] <─────┘

Value chain levels#

Cross-cutting technologies of the sector:

• Long-Read Sequencing: Technologies like Nanopore and PacBio enabling highly continuous genome assemblies.
• Spatial Transcriptomics: Mapping gene expression directly within tissue sections to understand complex biology.
• Cloud Computing: Massive scalable infrastructure required to process petabytes of genomic data.

02US#

The United States acts as the central administrative hub for global biodiversity initiatives, coordinating standards and data protocols for the Earth BioGenome Project.

EBP coordination, High-throughput sequencing, Cloud infrastructure#

• EBP coordination hub: UC Davis (Harris Lewin’s working group) coordinates the global EBP network and its assembly-quality metrics (contig N50 above 1 Mb, base accuracy above Q40).
• Vertebrate Genomes Project: Erich Jarvis’s group at Rockefeller University drives the VGP, targeting reference genomes for all roughly 70,000 vertebrate species with PacBio HiFi reads.
• Smithsonian collections and NCBI: the Smithsonian Institution anchors specimen and voucher curation for US ecosystem-sequencing initiatives, while NCBI archives the open genomic data.

03CN#

China is heavily investing in massive sequencing infrastructure, leveraging automation to rapidly sequence thousands of Asian plant and animal species.

Stereo-seq, 10KP Project, Mass automation#

• Spatial genomics: BGI-Research pairs its proprietary Stereo-seq spatial-transcriptomics platform with whole-genome assembly of rare Asian plants.
• Large-scale projects: the 10,000 Plant Genomes (10KP) and companion eukaryote programmes sequence mosses, ferns, algae and endemic animals on BGI’s DNBSEQ platforms; the Kunming Institute of Zoology holds the leading databases of Chinese wild-mammal evolutionary zoogeography.
• National databases: the China National GeneBank (CNGB) securely hosts the country’s immense biodiversity datasets.

04EU#

The European Union focuses on deep ecological genomics, sequencing entire ecosystems to understand the impacts of climate change and discover novel bioproducts.

Darwin Tree of Life, Marine genomics, Data sovereignty#

• Darwin Tree of Life: the Wellcome Sanger Institute-led DtL project aims to sequence all roughly 70,000 eukaryotic species of Britain and Ireland, running one of the world’s highest-throughput de novo assembly pipelines.
• Marine bioprospecting: France’s Genoscope sequences ocean microbiomes (notably the Tara Oceans expeditions), screening for extremophile enzymes useful to green chemistry.
• Assembly algorithms and open data: the Max Planck Institute (Myers lab) develops the overlap-layout graph mathematics behind modern assemblers, and EMBL-EBI hosts open European bioinformatics infrastructure.

05Leading companies and research institutes#

06Tech stack and innovations#

Modern biodiversity genomics depends entirely on breakthroughs in extracting ultra-long DNA molecules and algorithmic assembly of highly repetitive regions.

1. UHMW DNA Extraction:
   • Nanobind magnetic disks (a nanosilica-coated surface) gently wind ultra-long DNA under mild rocking, keeping fragments above 100 kb that long-read sequencing needs.
   • gentle, low-shear lysis preserves megabase-scale chromosomes that spin-column kits would fragment.
2. Sequencing Technologies:
   • PacBio HiFi and Oxford Nanopore generate multi-kilobase reads above Q30 that resolve repetitive regions short reads cannot.
   • Hi-C chromatin conformation capture fixes chromatin with formaldehyde and proximity-ligates physically close DNA, producing the contact map that scaffolds contigs into chromosomes.
3. Bioinformatics Algorithms:
   • Hifiasm builds accurate contigs from HiFi reads, Purge_dups removes haplotype duplicates, and YaHS orders contigs into chromosome-scale scaffolds using Hi-C contacts.
   • AI annotation pipelines such as Braker3 rapidly label genes, regulatory elements and biosynthetic gene clusters across novel species.

07Value chains and production pipelines#

Industrial pipeline of Reference Genome Generation (EBP Standards)#

┌───────────────────────────┐      ┌───────────────────────────┐
│ 1. Tissue Sampling        │ ───> │ 2. UHMW DNA Extraction    │
└───────────────────────────┘      └───────────────────────────┘
                                                 │
                                                 ▼
┌───────────────────────────┐      ┌───────────────────────────┐
│ 4. Bioinformatics Assembly│ <─── │ 3. Long-Read Sequencing   │
└───────────────────────────┘      └───────────────────────────┘
              │
              ▼
┌───────────────────────────┐      ┌───────────────────────────┐
│ 5. Gene Annotation        │ ───> │ 6. Public Release         │
└───────────────────────────┘      └───────────────────────────┘

Stage 1: Tissue Sampling

Field biologists collect fresh tissue samples, instantly freezing them in liquid nitrogen to perfectly preserve cellular DNA integrity.

Stage 2: UHMW DNA Extraction

Laboratories utilize specialized magnetic nanodisks to gently isolate ultra-high molecular weight DNA without mechanical shearing.

Stage 3: Long-Read Sequencing

Extracted DNA is processed through Nanopore or PacBio systems, generating massive datasets of continuous, multi-kilobase reads.

Stage 4: Bioinformatics Assembly

Supercomputers run complex graph algorithms to piece the reads together, utilizing Hi-C data to scaffold the contigs into full chromosomes.

Stage 5: Gene Annotation

Automated AI pipelines scan the assembled chromosomes to identify genes, regulatory elements, and structural variants.

Stage 6: Public Release

The fully curated, high-quality reference genome is uploaded to central databases like GenBank or ENA for open scientific access.