Digitaria exilis
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA644458 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR12199500.fastq.gz | Fastqsanger.gz | |||
| SRR12199600.fastq.gz | Fastqsanger.gz | |||
| SRR12199501.fastq.gz | Fastqsanger.gz | |||
| SRR12199601.fastq.gz | Fastqsanger.gz | |||
| SRR12199502.fastq.gz | Fastqsanger.gz |
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Project description:Fonio millet genome unlocks African orphan crop diversity for agriculture in a changing climate
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Project description: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. 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. 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.
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Project description:Digitaria exilis cultivar:Niatia Genome sequencing and assembly
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Project description:Low iron and high phytic acid content make fonio based meals a poor source of bioavailable iron. Phytic acid degradation in fonio porridge using whole grain cereals as phytase source and effect on iron bioavailability when added to iron fortified fonio meals were investigated. Grains, nuts and seeds collected in Mali markets were screened for phytic acid and phytase activity. We performed an iron absorption study in Beninese women (n?=?16), using non-dephytinised fonio porridge (FFP) and dephytinised fonio porridge (FWFP; 75% fonio-25% wheat), each fortified with (57)Fe or (58)Fe labeled FeSO4. Iron absorption was quantified by measuring the erythrocyte incorporation of stable iron isotopes. Phytic acid varied from 0.39 (bambara nut) to 4.26 g/100 g DM (pumpkin seed), with oilseeds values higher than grains and nuts. Phytase activity ranged from 0.17±1.61 (fonio) to 2.9±1.3 phytase unit (PU) per g (whole wheat). Phytic acid was almost completely degraded in FWFP after 60 min of incubation (pH?5.0, 50°C). Phytate?iron molar ratios decreased from 23.7?1 in FFP to 2.7?1 in FWFP. Iron fortification further reduced phytate?iron molar ratio to 1.9?1 in FFP and 0.3?1 in FWFP, respectively. Geometric mean (95% CI) iron absorption significantly increased from 2.6% (0.8-7.8) in FFP to 8.3% (3.8-17.9) in FWFP (P<0.0001). Dephytinisation of fonio porridge with intrinsic wheat phytase increased fractional iron absorption 3.2 times, suggesting it could be a possible strategy to decrease PA in cereal-based porridges.
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Project description:Fonio (Digitaria exilis Stapf) is an ancient African cereal that represents a rich source of carbohydrate, fat, fiber, vitamins, minerals, and sulfur-containing amino acids. Processing and utilization of fonio require adequate knowledge of its structural, chemical, and nutritional characteristics. The present work evaluates the structural, techno-functional, and gelling properties of fonio and compares them to other major gluten-free cereals (rice, maize, sorghum, and millet). Fonio flour presented significantly higher water absorption index and swelling power, while it scored a lower water solubility index than the reference flours. The pasting viscosity profile of fonio was similar to that of rice, with equivalent peak viscosity but a breakdown viscosity 24% lower than rice, indicative of higher stability and resistance to shearing and heating. Rheological properties demonstrated that fonio generates gels with remarkably strong structures. At 15% concentration, fonio gel withstood stress 579% higher than those observed in the reference flours without breaking its structure. Fonio flour presented the highest gelatinization enthalpy (11.45 J/g) and a narrow gelatinization temperature range (9.96 °C), indicative of a better-packed starch structure than the other analyzed flours. The texture of the gels made with fonio showed higher firmness over the evaluated period. These combined results suggest that fonio is a suitable ingredient for gel-like food formulations.
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Project description:Identification and sequencing of lignin biosynthesis, lignification and lignin pathway control in the orphan grain crop, Digitaria exilis
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Project description:Within the family Geminiviridae, the emergence of new species results from their high mutation and recombination rates. In this study, we report the variability and evolution of digitaria streak virus (DSV), a mastrevirus isolated in 1986 from the grass Digitaria setigera in an island of the Vanuatu archipelago. Viral DNA of DSV samples was amplified from D. setigera specimens, derived from the naturally infected original plant, which were propagated in different laboratories in France and Italy for more than 20 years. From the consensus sequences, the nucleotide substitution rate was estimated for the period between a sample and the original sequence published in 1987, as well as for the period between samples. In addition, the intra-host genetic complexity and diversity of 8 DSV populations with a total of 165 sequenced haplotypes was characterized. The evolutionary rate of DSV was estimated to be between 1.13 × 10-4 and 9.87 × 10-4 substitutions/site/year, within the ranges observed in other single-stranded DNA viruses and RNA viruses. Bioinformatic analyses revealed high variability and heterogeneity in DSV populations, which confirmed that mutant spectra are continuously generated and are organized as quasispecies. The analysis of polymorphisms revealed nucleotide substitution biases in viral genomes towards deamination and oxidation of single-stranded DNA. The differences in variability in each of the genomic regions reflected a dynamic and modular evolution in the mutant spectra that was not reflected in the consensus sequences. Strikingly, the most variable region of the DSV genome, encoding the movement protein, showed rapid fixation of the mutations in the consensus sequence and a concomitant dN/dS ratio of 6.130, which suggests strong positive selection in this region. Phylogenetic analyses revealed a possible divergence in three genetic lineages from the original Vanuatu DSV isolate.
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