Broomcorn millet (Panicum miliaceum L.) has strong tolerance to abiotic stresses, and is probably one of the oldest crops, with its earliest cultivation that dated back to ca. ~10,000 years. We report here its genome assembly through a combination of PacBio sequencing, BioNano, and Hi-C (in vivo) mapping. The 18 super scaffolds cover ~95.6% of the estimated genome (~887.8 Mb). There are 63,671 protein-coding genes annotated in this tetraploid genome. About ~86.2% of the syntenic genes in foxtail millet have two homologous copies in broomcorn millet, indicating rare gene loss after tetraploidization in broomcorn millet. Phylogenetic analysis reveals that broomcorn millet and foxtail millet diverged around ~13.1 Million years ago (Mya), while the lineage specific tetraploidization of broomcorn millet may be happened within ~5.91 million years. The genome is not only beneficial for the genome assisted breeding of broomcorn millet, but also an important resource for other Panicum species.

Domestication of broomcorn millet (Panicum miliaceum) is one of the most significant events in prehistoric East Asia, providing sufficient food supply for the explosive growth of Neolithic populations and the transition into complex societies. However, to date, the process of broomcorn millet domestication is still largely unknown, partly due to the lack of clear diagnostic tools for distinguishing between millet and its related wild grasses in archaeological samples. Here, we examined the percentage of silicified epidermal long-cell undulated patterns in the glume and palea from inflorescence bracts in 21 modern varieties of broomcorn millet and 12 weed/feral-type Panicum ruderale collected across northern China. Our results show that the percentage of ηIII patterns in domesticated broomcorn millet (23.0% ± 5.9%; n = 63) is about 10% higher than in P. ruderale (10.8% ± 5.8%; n = 36), with quartiles of 17.2–28.3% and 5.1–15.5%, respectively. Owing to the increase in ηIII pattern percentage correlates significantly with a decrease in the grain length/width ratio, in the absence of exact wild ancestors of broomcorn millet, the characterization of phytolith differences between P. ruderale and P. miliaceum thus becomes an alternative approach to provide insight into origin of broomcorn millet.

Broomcorn millet (Panicum miliaceum L.), one of the first domesticated crops, has been grown in Northern China for at least 10,000 years. The species is presently a minor crop, and evaluation of its genetic diversity has been very limited. In this study, we analyzed the genetic diversity of 88 accessions of broomcorn millet collected from various provinces of China. Amplification with 67 simple sequence repeat (SSR) primers revealed moderate levels of diversity in the investigated accessions. A total of 179 alleles were detected, with an average of 2.7 alleles per locus. Polymorphism information content and expected heterozygosity ranged from 0.043 to 0.729 (mean = 0.376) and 0.045 to 0.771 (mean = 0.445), respectively. Cluster analysis based on the unweighted pair group method of mathematical averages separated the 88 accessions into four groups at a genetic similarity level of 0.633. A genetic structure assay indicated a close correlation between geographical regions and genetic diversity. The uncovered information will be valuable for defining gene pools and developing breeding programs for broomcorn millet. Furthermore, the millet-specific SSR markers developed in this study should serve as useful tools for assessment of genetic diversity and elucidation of population structure in broomcorn millet.

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Cultivated broomcorn millet (Panicum miliaceum L.), one of the most ancient crops, has long been an important staple food in the semiarid regions of Eurasia. Weedy broomcorn millet (Panicum ruderale (Kitag.) Chang comb. Nov.), the companion weed of cultivated broomcorn millet, is also widely distributed throughout Eurasia and can produce fertile offspring by crossing with cultivated broomcorn millet. The evolutionary and genetic relationships between weedy and cultivated broomcorn millets, and the explicit domestication areas and detailed spread routes of this cereal are still unclear. The genetic diversity and population structure of 200 accessions of weedy and cultivated broomcorn millets were explored to elucidate the genetic relationship between weedy and cultivated broomcorn millets, and to trace the explicit domestication areas and detailed spread routes of broomcorn millets by using 23 simple sequence repeats (SSR) markers. Our results show that the weedy populations in China may harbor the ancestral variations that gave rise to the domesticated broomcorn millet. The population structure pattern observed in the wild and domesticated broomcorn millets is consistent with the hypothesis that there may be at least two independent domestication areas in China for the cultivated broomcorn millet, the Loess Plateau and the Northeast China, with both following the westward spread routes. These two westward spread routes of cultivated broomcorn millet coincide exactly with the prehistoric Oasis Route and Steppe Route, respectively.

Influenza A virus (IAV) is a globally distributed zoonotic pathogen and causes a highly infectious respiratory disease with high morbidity and mortality in humans and animals. IAV has evolved various strategies to counteract the innate immune response, using different viral proteins. However, the mechanisms are not fully elucidated. In this study, we demonstrated that the nonstructural protein 2 (NS2) of H1N1 IAV negatively regulate the induction of type-I interferon. Co-immunoprecipitation experiments revealed that NS2 specifically interacts with interferon regulatory factor 7 (IRF7). NS2 blocks the nuclear translocation of IRF7 by inhibiting the formation of IRF7 dimers, thereby prevents the activation of IRF7 and inhibits the production of interferon-beta. Taken together, these findings revealed a novel mechanism by which the NS2 of H1N1 IAV inhibits IRF7-mediated type-I interferon production.

Broomcorn millet (Panicum miliaceum L.) is one of the earliest domesticated crops in the world. Weedy broomcorn millet [Panicum ruderale (Kitag.) Chang or Panicum miliaceum subsp. ruderale (Kitag.) Tzvel] is thought to be the descendant of the wild ancestor or the feral type of this cereal. The genealogical relationships and genetic divergence among these taxa have not been clarified. In this study, the genetic diversity and population structure of weedy and cultivated broomcorn millets were investigated by using the high-throughput sequencing technology, i.e., the specific-locus amplified fragment sequencing (SLAF-seq). Our analyses consistently revealed both the wild and the feral genotypes in the weedy broomcorn millets. The single nucleotide polymorphisms (SNPs) at the genomic level provided useful evidence to distinguish the wild and the endoferal/exoferal types of weedy broomcorn millets. The genetic divergence revealed between the cultivated broomcorn millet from eastern Eurasia and those from central-western Eurasia was probably derived from either the genetic introgression from weedy broomcorn millets along the spread routes or the founder effect, while the limited gene flow of broomcorn millets from eastern and central-western Eurasia was probably due to the different uses of broomcorn millets and eating habits of the local people.