Xuewen Wang1, Shiyu Chen2, Xiao Ma3, Anna E J Yssel4,5, Srinivasa R Chaluvadi1, Matthew S Johnson6, Prakash Gangashetty7, Falalou Hamidou7, Moussa D Sanogo8, Arthur Zwaenepoel3, Jason Wallace9, Yves Van de Peer3,4,10, Jeffrey L Bennetzen1, Allen Van Deynze2. 1. Department of Genetics, University of Georgia, Athens, GA 30602, USA. 2. Department of Plant Sciences, Seed Biotechnology Center, University of California, 1 Shields Ave. Davis, CA 95616, USA. 3. Bioinformatics & Systems Biology, VIB / Ghent University, Technologiepark 71, 9052 Zwijnaarde, Belgium. 4. Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria 0028, South Africa. 5. Centre for Bioinformatics and Computational Biology, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria 0028, South Africa. 6. Institute of Plant Breeding, Genetics, and Genomics, University of Georgia, 111 Riverbend Rd, Athens, GA 30602, USA. 7. International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), BP 12404, Niamey, Niger. 8. Institut d'Economie Rurale, Ministere de l'Agriculture, Cinzana, BP 214, Ségou, Mali. 9. Department of Crop and Soil Sciences, University of Georgia, 3111 Carlton St Bldg, Athens, GA 30602, USA. 10. College of Horticulture, Nanjing Agricultural University, Nanjing, China.
Abstract
BACKGROUND: Digitaria exilis, white fonio, is a minor but vital crop of West Africa that is valued for its resilience in hot, dry, and low-fertility environments and for the exceptional quality of its grain for human nutrition. Its success is hindered, however, by a low degree of plant breeding and improvement. FINDINGS: We sequenced the fonio genome with long-read SMRT-cell technology, yielding a ∼761 Mb assembly in 3,329 contigs (N50, 1.73 Mb; L50, 126). The assembly approaches a high level of completion, with a BUSCO score of >99%. The fonio genome was found to be a tetraploid, with most of the genome retained as homoeologous duplications that differ overall by ∼4.3%, neglecting indels. The 2 genomes within fonio were found to have begun their independent divergence ∼3.1 million years ago. The repeat content (>49%) is fairly standard for a grass genome of this size, but the ratio of Gypsy to Copia long terminal repeat retrotransposons (∼6.7) was found to be exceptionally high. Several genes related to future improvement of the crop were identified including shattering, plant height, and grain size. Analysis of fonio population genetics, primarily in Mali, indicated that the crop has extensive genetic diversity that is largely partitioned across a north-south gradient coinciding with the Sahel and Sudan grassland domains. CONCLUSIONS: We provide a high-quality assembly, annotation, and diversity analysis for a vital African crop. The availability of this information should empower future research into further domestication and improvement of fonio.
BACKGROUND:Digitaria exilis, white fonio, is a minor but vital crop of West Africa that is valued for its resilience in hot, dry, and low-fertility environments and for the exceptional quality of its grain for human nutrition. Its success is hindered, however, by a low degree of plant breeding and improvement. FINDINGS: We sequenced the fonio genome with long-read SMRT-cell technology, yielding a ∼761 Mb assembly in 3,329 contigs (N50, 1.73 Mb; L50, 126). The assembly approaches a high level of completion, with a BUSCO score of >99%. The fonio genome was found to be a tetraploid, with most of the genome retained as homoeologous duplications that differ overall by ∼4.3%, neglecting indels. The 2 genomes within fonio were found to have begun their independent divergence ∼3.1 million years ago. The repeat content (>49%) is fairly standard for a grass genome of this size, but the ratio of Gypsy to Copia long terminal repeat retrotransposons (∼6.7) was found to be exceptionally high. Several genes related to future improvement of the crop were identified including shattering, plant height, and grain size. Analysis of fonio population genetics, primarily in Mali, indicated that the crop has extensive genetic diversity that is largely partitioned across a north-south gradient coinciding with the Sahel and Sudan grassland domains. CONCLUSIONS: We provide a high-quality assembly, annotation, and diversity analysis for a vital African crop. The availability of this information should empower future research into further domestication and improvement of fonio.
Authors: Michael S Campbell; MeiYee Law; Carson Holt; Joshua C Stein; Gaurav D Moghe; David E Hufnagel; Jikai Lei; Rujira Achawanantakun; Dian Jiao; Carolyn J Lawrence; Doreen Ware; Shin-Han Shiu; Kevin L Childs; Yanni Sun; Ning Jiang; Mark Yandell Journal: Plant Physiol Date: 2013-12-04 Impact factor: 8.340
Authors: Zhongwei Lin; Xianran Li; Laura M Shannon; Cheng-Ting Yeh; Ming L Wang; Guihua Bai; Zhao Peng; Jiarui Li; Harold N Trick; Thomas E Clemente; John Doebley; Patrick S Schnable; Mitchell R Tuinstra; Tesfaye T Tesso; Frank White; Jianming Yu Journal: Nat Genet Date: 2012-05-13 Impact factor: 38.330
Authors: Cassandria Geraldine Tay Fernandez; Benjamin John Nestor; Monica Furaste Danilevicz; Mitchell Gill; Jakob Petereit; Philipp Emanuel Bayer; Patrick Michael Finnegan; Jacqueline Batley; David Edwards Journal: Int J Mol Sci Date: 2022-02-28 Impact factor: 5.923