Wang, XuewenChen, ShiyuChen, ShiyuYssel, A.E.J. (Anna)Chaluvadi, Srinivasa R.Johnson, Matthew S.Gangashetty, PrakashHamidou, FalalouSanogo, Moussa D.Zwaenepoel, ArthurWallace, JasonVan de Peer, YvesBennetzen, Jeffrey L.Van Deynze, Allen2022-03-102022-03-102021-03Wang, X., Chen, S., Ma, X. et al. 2021, 'Genome sequence and genetic diversity analysis of an under-domesticated orphan crop, white fonio (Digitaria exilis)', GigaScience, vol. 10, no. 3, pp. 1-12.2047-217X (online)10.1093/gigascience/giab013http://hdl.handle.net/2263/84425Supplementary Figure S1. A. Comparison of the contiguity of the Niatia Genome and CM05836 [21] genome. B. Comparison of contig tig00001331 corresponding to 100 consecutive segments anchored on the same chromosome 3B and tig00010942 corresponding to 65 consecutive segments on the chromosome 5A on the Abrouk et al. [21] genome.Supplementary Figure S2. The k-mer distribution of raw Illumina reads at k-mer value 33 bp.Supplementary Figure S3. A. Marginal posterior distributions for 2 independent chains (green and orange) and induced marginal prior distributions (blue) for internal node ages (t n11 to t n19, see panel C), overall mean substitution rate (mu), mean substitution rate for different codon positions (mu1,mu2, andmu3), and variance parameter of the uncorrelated relaxed clock (sigma2 1, sigma2 2, and sigma2 3) for the 3 codon positions. B. Trace plots for the MCMC chains associated with panel (A).Supplementary Figure S4. There are 10,075 families that have 2 copies in fonio and 1 copy in Setaria italica, and 90% of 2-copy families are located in synteny blocks. The above 4 examples indicate the high degree of collinearity and synteny between S. italica and fonio.Supplementary Figure S5. GO of single-copy, contracted genes in fonio.Supplementary Figure S6. GO enrichment for expanded genes in D. exilis and relative to O. sativa.Supplementary Figure S7. Phylogenetic tree of the SSH-like genes from fonio and related species. The genes shaded in light blue are the family members most closely related to SSH-1 in O. sativa and D. exilis. Genes are named according to their PLAZA identifiers. Abbreviations for species names are as follows: Bradi (Brachypodium distachyon), pgl GLEAN (Cenchrus amercianus), Digex (Digitaria exilis), Oropetium (Oropetium thomaeum), OsR (Oryza sativa), Seita (Setaria italica), Sobic (Sorghum bicolor), and Zm (Zea mays).Supplementary Figure S8. Phylogenetic tree of the dw3 gene family of fonio and related species.Supplementary Figure S9. Gene family tree for GW2-A-like genes in fonio and related species. This figure also includes the genes from 2 additional Pooid species, barley (Hordeum vulgare) (HORV) and wheat (Triticum turgidum) (TRITD).Supplementary Table S1. Comparison of genome assembly statistics of fonio.Supplementary Table S2. Statistics for the gene annotation.Supplementary Table S3. Annotated non-coding RNA genes.Supplementary Table S4. Orthologs for suppression of Shattering1 genes.Supplementary Table S5. Orthologs of Dwarf Gene-3.Supplementary Table S6. Orthologs of Grain Weight-2 genes.Supplementary Table S7. Passport data for accessions and samples used for diversity study (see Supplementary Tables Excel file).Supplementary Table S8. Single-nucleotide polymorphism database used for diversity study (see Supplementary Tables Excel file).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.en© The Author(s) 2021. This is an Open Access article distributed under the terms of the Creative Commons Attribution License.DomesticationGene amplificationGene lossMilletPolyploidyArticle