ArticleGigaScience2021
Genome sequence and genetic diversity analysis of an under-domesticated orphan crop, white fonio (Digitaria exilis).
Article in GigaScience, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- Research and developmental strategies to hasten the improvement of orphan crops.GM crops & food · 2025Review
- Phylogenetic networks empower biodiversity research.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Independent domestication and cultivation histories of two West African indigenous fonio millet crops.Nature communications · 2025Article
- A chromosome-scale genome assembly of Timorese crabgrass (Digitaria radicosa): a useful genomic resource for the Poaceae.G3 (Bethesda, Md.) · 2024Article
- Milletdb: a multi-omics database to accelerate the research of functional genomics and molecular breeding of millets.Plant biotechnology journal · 2023Article
- Pangenomic analysis identifies structural variation associated with heat tolerance in pearl millet.Nature genetics · 2023Article
- Genomic Distribution of Pro-VirulentInternational journal of molecular sciences · 2023Article
- Development of genomic resources for Rhodes grass (Frontiers in plant science · 2023Article
- Beyond a reference genome: pangenomes and population genomics of underutilized and orphan crops for future food and nutrition security.The New phytologist · 2022Review
- Pangenomes as a Resource to Accelerate Breeding of Under-Utilised Crop Species.International journal of molecular sciences · 2022Review
- Plant genome sequence assembly in the era of long reads: Progress, challenges and future directions.Quantitative plant biology · 2022Review
- Revitalization of small millets for nutritional and food security by advanced genetics and genomics approaches.Frontiers in genetics · 2022Review
- Advances in Cereal Crop Genomics for Resilience under Climate Change.Life (Basel, Switzerland) · 2021Review
- Genome sequence and genetic diversity analysis of an under-domesticated orphan crop, white fonio (Digitaria exilis).GigaScience · 2021Article
- Current Advancements and Limitations of Gene Editing in Orphan Crops.Frontiers in plant science · 2021Review
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Authors and funding
14 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundDigitaria 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.
findingsWe 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.
conclusionsWe 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.
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