Department of Genetics, University of Georgia, Athens, GA 30602, USA.
Department of Plant Sciences, Seed Biotechnology Center, University of California, 1 Shields Ave. Davis, CA 95616, USA.
Gigascience. 2021 Mar 12;10(3). doi: 10.1093/gigascience/giab013.
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.
Digitaria exilis，即白高粱，是西非一种次要但至关重要的作物，因其在炎热、干燥和低肥力环境中的强适应性以及其谷物在人类营养方面的卓越品质而备受重视。然而，它的发展受到植物育种和改良程度低的阻碍。
我们使用长读长 SMRT-cell 技术对高粱进行了测序，得到了一个约 761Mb 的组装，包含 3329 个 contigs（N50，1.73Mb；L50，126）。该组装达到了很高的完成度，具有 >99%的 BUSCO 分数。高粱基因组被鉴定为四倍体，大部分基因组作为同源重复保留，总体差异约为 4.3%，不包括插入缺失。高粱内的 2 个基因组被发现从约 310 万年前开始独立分化。重复含量（>49%）对于这个大小的草基因组来说相当标准，但 Gypsy 和 Copia 长末端重复反转录转座子的比例（约 6.7）被发现异常高。鉴定出了几个与未来作物改良相关的基因，包括爆裂性、株高和粒大小。对高粱群体遗传学的分析，主要在马里进行，表明该作物具有广泛的遗传多样性，主要分布在与萨赫勒和苏丹草原区域相吻合的南北梯度上。
我们为一种重要的非洲作物提供了高质量的组装、注释和多样性分析。这些信息的可用性应该为未来进一步驯化和改良高粱提供支持。
