Genomic Projects
CONSERVING RARE PLANTS THROUGH GENOMICS
Welcome to the Green Biome Institute's Project Page. On this page, you will find information about the GBI's various activities.
You can get an overview of what we are doing by viewing The Inventory of Rare Plant Samples, which is a n extensive list of rare plant samples we are following. A list of all California Native Plant Society's endangered plants can be found in this spreadsheet. I n addition, the spreadsheet includes seed bank information, plants with medicinal properties, botanical garden inventories, and rare plants rankings from federal, state, and Colorado databases. Along with this information, the status of the GBI's genomic analysis efforts is included.
By 2026, the GBI will create draft genomic profiles of 300 endangered California plants. The profiles will include:
- Genomic DNA Sequencing
- Transcriptome Sequencing
- Chloroplast Sequencing
- Purported gene listing based on Busco-equivalent genes discovered
- Purported genes listing based on the Augustus Gene Prediction program (ref).
- Smithsonian DNA Barcode Sequences
- Microbiome data from plant leaves, including fungal (ITS) and bacterial (16S) profiles
- Metabolome data from Mass Spec Instrument analysis
- Potential medicinal value
In collaboration with our partners, the GBI also performs genomic studies on select, targeted plants to assist in optimizing breeding programs and conservation management programs.
Genomics
Rare Plants Nuclear Genomes
The GBI performs short-read sequencing on Illumina instruments and increasingly,
long-read sequencing on Oxford Nanopore systems. Assembly and analysis are
performed using freely available software organized into a workflow on Amazon Web
Services. See our project spreadsheet to understand our current projects and status.
Rare Plants DNA Barcode Sequence Listing
Each plant is analyzed for the presence of four unique DNA barcodes as specified by a recent publication of the Smithsonian Institution. The GBI will verify the presence of these barcodes including, rbcL, matK, trnH-psbA, and ITS.
Rare Plants Transcriptome
The GBI intends the transcriptome of all plants as sample availability allows.
The GBI will provide Chloroplast's genomes when samples allow.
We will provide 2 types of gene listings which may be useful to researchers. The first is a list of the genes based on Busco software comparison to Viridiplantae gene database. The second is a list of genes based on Augustus software.
A profile of all known Bacteria present based on 16S primer sets.
Medicinal Properties
Plant extracts are prepared in alcohols or water and their metabolite make up is analyzed by Mass Spec.
Discs composed of plant extracts are incubated on bacterial plates. Plates are analyzed that cause bacterial inhibition.
Additional Projects
The Green Biome Institute has cooperated with partners to analyze plant collections using ddRAD sequencing to discover genomic diversity in these collections. If you are interested in pursuing a similar project please contact the Director of the GBI.
The Green Biome Institute has partnered with the leading botanical gardens and conservation organizations in providing genomic analysis for endangered plants.Our most recent project was in cooperation with Santa Barbara Botanical Gardens.
The GBI works with field botanist and biologists to secure rare plant samples from gardens and the wild in a non harmful fashion.
The GBI students isolate all plant nucleic acids and metabolites. In addition to sequencing these sample themselves (most often long read sequencing on Oxford nanopore) the students utilize the wonderful services of the Berkeley QB3 Sequencing center for short read Illumina sequencing.
The combined short and long reads allow for the best and most helpful data results.