About This Project
Cacti are used for food, have been linked to healthier diets and disease prevention, and even serve as a stopgap crop for livestock forage in times of drought. They are also important ornamental plants. In this project, our team will sequence the whole genome of cacti to reveal genomic insight into the drought-tolerant plant. It will be the first plant genome sequenced in Cactaceae. Our team will collaborate with the Beijing Genome Institute to sequence the cactus genome using Illumina HiSeq technology.
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What is the context of this research?
Cactus are an especially important emerging crop, as they are far more efficient in converting water to dry matter than traditional crops due to a specialized photosynthetic pathway - crassulacean-acid metabolism (CAM) metabolism. With CAM metabolism, atmospheric carbon dioxide is only taken up during the night, when the stomates are open. A staple in Latin American and Native American cultures, Opuntia fruits (tunas) and vegetables (nopalitos) are also popular in Mediterranean and Caribbean countries and are attracting growing interest as new products for the USA. For example, the tonnage of nopalitos consumed annually in Mexico approximately equals the tonnage of cauliflower consumed in the USA.
What is the significance of this project?
This will be the first plant in family Cactaceae to be sequenced.
Despite 20 years of work in field testing and selecting elite clones of cactus, there is a nearly complete lack of knowledge of its genes, and the genetic control of its economically important traits. A comprehensive program is needed to guide germplasm evaluation and genetic improvement of this important botanical model, arid-region staple, and emerging US crop.
What are the goals of the project?
- Understand the structure of the gene pool and develop strategies for effective collection, characterization and utilization of germplasm;
- Develop and implement genomic tools to accelerate crop improvement,
- Explore the molecular/physiological basis of novel adaptations of cacti to arid conditions, both for their further improvement, and also toward enhancing the stress resistance of other crops.
Using high-throughput Illumina sequencing (paired-end, 150bp HiSeq runs), we will generate 45 giga-bases of the Cactus genome.
Our genome analysis team will analyze sequencing data by ourselves, so the genome analysis fee and labor fee will not be included in this budget.
The Orchid genome was recently published in Nature Genetics (The genome sequence of the orchid Phalaenopsis equestris), and we hope to publish similarly impactful publications from this work, such as Science, Nature, Nature Genetics or PNAS.
If you would donate $100 or more, you will be a number of cactus genome database and receive a hard copy of the cactus genome paper!
Meet the Team
If you want to participate in the cactus genome project, please contact us. We are seeking collaborators who love plants.
Peng Jiang received an MS and PhD from University of Georgia over the last six years. He loves to study ornamental plant genomics and genetics.
Hui Guo is a plant genome expert who received his PhD from University of Georgia, and has experience in assembly and analysis of plant genomes.
Some of plant genome projects from our team:
The genome of the mesopolyploid crop species Brassica rapa Nature genetics
Also, we are establishing an ornamental plant genome database at www.genegarden.com. You will find the cactus genome data in this database when it is published.
Press and Media
Our team is establishing an ornamental plant genome database at www.genegarden.com. You will find the cactus genome data in this database when it's published.
Gene search site in the GeneGarden. (A) The home page of the GeneGarden. The home page is the main entry page, providing quick access to resources through graphical menus. Every GeneGarden page consistently contains the same toolbar at the top with links to each section. (B) The organism page shows biology and ornamental details of landscape plants. (C) Genomic data type summary of each ornamental plants. (D) Genes can be searched by various categories, such as by species, name and keywords from functional annotation such as GO terms, InterPro protein domain name and KEGG pathway terms. (E) The gene details page has various tabs to show the data. The annotated sequence page is shown. (F) A JBrowse page linked from the alignment tab of the gene detail page. Users can return to the gene detail page from JBrowse.
Several important plant genomes, such as tomato, cotton, and sorghum, have been sequenced by University of Georgia. Our team members have participated in those plant genome projects.
The tomato genome has been selected as the cover of Nature.
Gigablog guest posting:
Tunas, mature cactus fruits, range from ~100-200 grams in mass, and about 13% in sugar content (among commercial types). A wide range of colors exist -- US consumers prefer deep purple fruit, however other countries prefer orange, green, white, or yellow.
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