Broomcorn millet (Panicum miliaceum L.) is the most water-efficient cereal and one of the earliest domesticated plants. Here we report its high-quality, chromosome-scale genome assembly using a combination of short-read sequencing, single-molecule real-time sequencing, Hi-C, and a high-density genetic map. Phylogenetic analyses reveal two sets of homologous chromosomes that may have merged ~5.6 million years ago, both of which exhibit strong synteny with other grass species. Broomcorn millet contains 55,930 protein-coding genes and 339 microRNA genes. We find Paniceae-specific expansion in several subfamilies of the BTB (broad complex/tramtrack/bric-a-brac) subunit of ubiquitin E3 ligases, suggesting enhanced regulation of protein dynamics may have contributed to the evolution of broomcorn millet. In addition, we identify the coexistence of all three C4 subtypes of carbon fixation candidate genes. The genome sequence is a valuable resource for breeders and will provide the foundation for studying the exceptional stress tolerance as well as C4 biology.
We conducted floristic and community analyses to compare the floristic composition, forest structure, taxonomic richness, and species diversity between two tiankeng (large doline, or sinkhole) habitats and two outside-tiankeng habitats of forest fragments in a degraded karst area in southwestern China. We found remarkably higher taxonomic richness in the tiankeng habitats than in the outside-tiankeng habitats at the species, generic, and familial levels. The inside-tiankeng habitats had higher floristic diversity but lower dominance. The remarkably higher uniqueness at all taxonomic levels and the much larger tree size in the two tiankeng habitats than in the outside-tiankeng habitats demonstrated the old-growth and isolated nature of the tiankeng flora. Plot-scale species richness, Shannon-Wiener index, Pielou’s evenness, and Berger-Parker dominance significantly differed across habitats. Heterogeneity in floristic composition at the species, generic, and familial levels was extremely significant across habitats. In pairwise comparisons, except for the Chuandong Tiankeng-Shenmu Tiankeng pair, all the pairs showed significant between-habitat heterogeneity in floristic composition. Our results suggest that as oases amidst the degraded karst landscape, tiankengs serve as modern refugia that preserve old-growth forest communities with their rich floristic diversity, and can provide a model for habitat conservation and forest restoration in that area.
Understanding diversity patterns and community structure of bryophytes will help integrate nature conservation at multiple biotic-group levels. We conducted a survey of ground bryophytes in a subtropical forest along an edge-to-interior gradient in South China. We recorded 11 liverwort species from 10 genera of seven families, and 26 moss species from 23 genera of 16 families in three transects. A two-way cluster analysis detected the environmental gradient between the forest edge and forest interior for bryophytes with habitat specificity. Functional diversity of bryophytes differed significantly across an edge-to-interior gradient. The range and median in both structural and functional diversity decreased remarkably from the forest edge to the interior. Multi-response permutation procedures showed significant differences in species composition between the forest-edge and forest-interior, and between the intermediate and forest-interior transects. Seven species were detected with a significant indicator value for indicating environmental conditions in the forest edge, while only one such species was found indicative of the intermediate transect. Our results demonstrate that remarkable edge effects exist for species composition and functional diversity patterns, and the forest edge is a marginal habitat with high biotic heterogeneity. Furthermore, functional diversity metrics are more sensitive to the edge effect than species diversity.
Based on a combination of next-generation sequencing and single-molecule sequencing, we obtained the whole-genome sequence of Bacillus megaterium strain TG1-E1, which is a highly salt-tolerant rhizobacterium that enhances plant tolerance to drought stress. The complete genome is estimated to be approximately 5.48 Mb containing a total of 5,858 predicted protein-coding DNA sequences.
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