December 3, 2015, San Diego, Beijing, and Cali, Colombia - Novogene, a leading genomics solution provider with the largest Illumina-based sequencing capacity in China, and the International Center for Tropical Agriculture (CIAT), a global agricultural research and development organization and custodian of the world's largest cassava gene bank, are partnering to construct a pan-genome of cassava (Manihot esculenta) and one of its closest wild relatives (M. e. peruviana). This novel approach to global cassava genome research is designed to unravel the plant's complex evolutionary history and genetic diversity with the goal of increasing the production and nutritional value of a primary food source in Africa, Latin America and the Caribbean.
Under the pan-genome sequencing project, Novogene will sequence and assemble cassava genomes provided by CIAT from six different eco-geographic zones, and conduct comparative genomic analysis among these genomes in relation to M. e. peruviana. The pan-genome will include the cassava's core-genome, containing genes present in all of cassava's ecogeographic zones of domestication (Mesoamerican-Caribbean, Savanna, Andean, South America Lowland Forest, Amazon, Humid Atlantic Forest and Dry Atlantic Forest); the dispensable-genome, containing genes present in two or more ecogeographic zones; and unique genes specific to single ecogeographic adaptation regions, including those from M. e. peruviana.
Since the initial publication of the cassava reference genome, attempts have been made to characterize cassava through genome resequencing to unlock important sources of genetic diversity to improve varieties that will meet future productivity, nutrition and environmental challenges. However, resequencing has often failed to capture many types of structural variation related to agronomic traits, including copy number variation and presence-absence variation, especially for the most genetically diverse lines and the crop's wild relatives because the reference genome was developed using a single inbred genome. Next-generation sequencing and state-of-the-art assembly algorithms make the construction of pan-genome maps feasible, and the construction of genome maps for individual or multiple strains provides unprecedented opportunities to investigate detailed genetic diversity at the population level.
"This research represents a significant step forward in demonstrating the value of pan-genome de novo assemblies in building and characterizing the genes that pave the path to the domestication of cassava out of the Manihot tribe," stated Dr. Luis Augusto Becerra Lopez-Lavalle, Cassava Molecular Geneticist at CIAT, "and provides candidate genes for introgression into today's cassava for crop improvement." Added Dr Joe Tohme, AgBiodiversity Director of CIAT, "We welcomed the opportunity to partner with Novogene given their high-quality sequencing capabilities, cutting edge bioinformatics technology and expertise, and pan-genomic research experience."
"Novogene is a pioneer and world leader in the assembly and analysis of pan-genome maps," stated Dr. Ruiqiang Li, Founder and Chief Executive Officer of Novogene. "Our pan-genomic research studies, including the wild relative of cultivated soybean, have been published in leading scientific journals. We look forward to applying this experience and expertise to the creation of the cassava pan-genome with the objective of enhancing global cultivation of this important food source."
Cassava is the world's third most important source of dietary energy after maize and rice. Half-a-billion people in Africa as well as Latin America and the Caribbean depend on this root crop for food, and millions of Asian farmers grow it for industrial markets. Cassava can withstand harsh conditions, making it a key crop for protecting smallholder farming against climate change. Esteemed by smallholder farmers for its tolerance to drought and infertile soils, the crop is inherently eco-efficient, offering a reliable source of food as well as income from markets for a wide variety of food, feed, pharmaceutical and industrial products.
The International Center for Tropical Agriculture is a not-for-profit research and development organization dedicated to reducing poverty and hunger while protecting natural resources in developing countries. It is based in Cali, Colombia.
CIAT is part of the CGIAR Consortium, a global partnership that unites organizations engaged in research for a food-secure future. CGIAR research is dedicated to reducing rural poverty, increasing food security, improving human health and nutrition, and ensuring more sustainable management of natural resources. Donors include individual countries, major foundations, and international entities.
This project was made possible with the financial support of the Federal Ministry for Economic Cooperation and Development, Germany, with support from the German Society for International Cooperation (GIZ) GmbH.
Novogene Bioinformatics Technology Company, Ltd., headquartered in Beijing with branches in the US and UK, is a leading genomics solution provider with cutting edge bioinformatics expertise and the largest Illumina-based sequencing capacity in China. Committed to quality service and scientific excellence, Novogene has achieved rapid growth and industry recognition by working in partnership with diverse healthcare, educational and research institutions around the globe to realize the unlimited potential of the rapidly evolving world of genomics. The company has completed numerous major service projects with findings published by top-ranked journals such as Science and Nature. Novogene is the first company in China to purchase Illumina's HiSeq X 10 system and is the only Illumina Genome Network partner in China. Novogene Corporation is Novogene's U.S. subsidiary, based in San Diego, CA.
For more information, contact:
Luis Augusto Becerra Lopez-Lavalle
Principal Research Scientist and Cassava Molecular Geneticist
Agrobiodiversity Research Area - Cassava Program
International Center for Tropical Agriculture (CIAT)
Agrobiodiversity Research Area
International Center for Tropical Agriculture (CIAT)
Joyce Peng, Ph.D.
Global Marketing Director and General Manager