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.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.

Highlights

  • 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

  • The large stretches of gene content and gene collinearity retention observed between our largest contiguous assemblies (Fig. 1C) do demonstrate, that there has been no large number of small rearrangements of these genomes over the past 3.1 million years (My)

  • Our sequence of the white fonio (D. exilis) genome indicates its recent tetraploid origin and the retention of most of the genes duplicated in this process

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Summary

Background

White fonio (Digitaria exilis, NCBI:txid1010633) is a vital cereal crop of West Africa, where it is commonly known as fonio or acha. The large stretches of gene content and gene collinearity retention observed between our largest contiguous assemblies (Fig. 1C) do demonstrate, that there has been no large number of small rearrangements of these genomes over the past 3.1 My. To see the expansions and contractions of gene families, broomcorn millet (Panicum miliaceum L.) was added in the phylogenetic analysis because it experienced a recent tetraploidization estimated at ∼5.8 mya that is similar to fonio. Orthofinder results indicated that members of this gene family are present in single copy in all of the examined grass species, except fonio and maize (Supplementary Fig. S9 and Table S6). Further (both broader and deeper) germplasm analyses will be useful for resolving these issues

Conclusions
Findings
19. Pacific Biosciences
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