Yue Chang1,2, Huan Liu1,2,3, Min Liu1,2,3, Xuezhu Liao1,2,3, Sunil Kumar Sahu1,2,3, Yuan Fu1,2, Bo Song1,2, Shifeng Cheng1,2, Robert Kariba4, Samuel Muthemba4, Prasad S Hendre4, Sean Mayes5,6,7, Wai Kuan Ho6,7, Anna E J Yssel8, Presidor Kendabie5, Sibo Wang1,2, Linzhou Li1,2, Alice Muchugi4, Ramni Jamnadass4, Haorong Lu1,2, Shufeng Peng1,2, Allen Van Deynze4,9, Anthony Simons4, Howard Yana-Shapiro4,9, Yves Van de Peer10,11,8, Xun Xu1,2, Huanming Yang1,2, Jian Wang1,2, Xin Liu1,2,3,12. 1. BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China. 2. China National GeneBank, BGI-Shenzhen, Jinsha Road, Shenzhen 518120, China. 3. State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China. 4. African Orphan Crops Consortium, World Agroforestry Centre (ICRAF), United Nations Avenue, Nairobi 00100, Kenya. 5. Plant and Crop Sciences, Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire LE12 5RD, UK. 6. Biosciences, University of Nottingham Malaysia Campus, Jalan Broga 43500 Semenyih, Selangor, Malaysia. 7. Crops For the Future, Jalan Broga, 43500 Semenyih, Selangor, Malaysia. 8. Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria 0028, South Africa. 9. University of California, 1 Shields Ave, Davis, CA 95616, USA. 10. Center for Plant Systems Biology, VIB, Ghent B-9052, Belgium. 11. Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent B-9052, Belgium. 12. BGI-Fuyang, BGI-Shenzhen, Fuyang 236009, China.
Abstract
BACKGROUND: The expanding world population is expected to double the worldwide demand for food by 2050. Eighty-eight percent of countries currently face a serious burden of malnutrition, especially in Africa and south and southeast Asia. About 95% of the food energy needs of humans are fulfilled by just 30 species, of which wheat, maize, and rice provide the majority of calories. Therefore, to diversify and stabilize the global food supply, enhance agricultural productivity, and tackle malnutrition, greater use of neglected or underutilized local plants (so-called orphan crops, but also including a few plants of special significance to agriculture, agroforestry, and nutrition) could be a partial solution. RESULTS: Here, we present draft genome information for five agriculturally, biologically, medicinally, and economically important underutilized plants native to Africa: Vigna subterranea, Lablab purpureus, Faidherbia albida, Sclerocarya birrea, and Moringa oleifera. Assembled genomes range in size from 217 to 654 Mb. In V. subterranea, L. purpureus, F. albida, S. birrea, and M. oleifera, we have predicted 31,707, 20,946, 28,979, 18,937, and 18,451 protein-coding genes, respectively. By further analyzing the expansion and contraction of selected gene families, we have characterized root nodule symbiosis genes, transcription factors, and starch biosynthesis-related genes in these genomes. CONCLUSIONS: These genome data will be useful to identify and characterize agronomically important genes and understand their modes of action, enabling genomics-based, evolutionary studies, and breeding strategies to design faster, more focused, and predictable crop improvement programs.
BACKGROUND: The expanding world population is expected to double the worldwide demand for food by 2050. Eighty-eight percent of countries currently face a serious burden of malnutrition, especially in Africa and south and southeast Asia. About 95% of the food energy needs of humans are fulfilled by just 30 species, of which wheat, maize, and rice provide the majority of calories. Therefore, to diversify and stabilize the global food supply, enhance agricultural productivity, and tackle malnutrition, greater use of neglected or underutilized local plants (so-called orphan crops, but also including a few plants of special significance to agriculture, agroforestry, and nutrition) could be a partial solution. RESULTS: Here, we present draft genome information for five agriculturally, biologically, medicinally, and economically important underutilized plants native to Africa: Vigna subterranea, Lablab purpureus, Faidherbia albida, Sclerocarya birrea, and Moringa oleifera. Assembled genomes range in size from 217 to 654 Mb. In V. subterranea, L. purpureus, F. albida, S. birrea, and M. oleifera, we have predicted 31,707, 20,946, 28,979, 18,937, and 18,451 protein-coding genes, respectively. By further analyzing the expansion and contraction of selected gene families, we have characterized root nodule symbiosis genes, transcription factors, and starch biosynthesis-related genes in these genomes. CONCLUSIONS: These genome data will be useful to identify and characterize agronomically important genes and understand their modes of action, enabling genomics-based, evolutionary studies, and breeding strategies to design faster, more focused, and predictable crop improvement programs.
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