Mangroves and salt marsh species are known to synthesize a wide spectrum of polysaccharides and polyphenols including flavonoids and other secondary metabolites which interfere with the extraction of pure genomic DNA. Although a plethora of plant DNA isolation protocols exist, extracting DNA from mangroves and salt marsh species is a challenging task. This study describes a rapid and reliable cetyl trimethylammonium bromide (CTAB) protocol suited specifically for extracting DNA from plants which are rich in polysaccharides and secondary metabolites, and the protocol also excludes the use of expensive liquid nitrogen and toxic phenols. Purity of extracted DNA was excellent as evident by A260/A280 ratio ranging from 1.78 to 1.84 and A260/A230 ratio was >2, which also suggested that the preparations were sufficiently free of proteins and polyphenolics/polysaccharide compounds. DNA concentration ranged from 8.8 to 9.9 μg μL−1. The extracted DNA was amenable to RAPD, restriction digestion, and PCR amplification of plant barcode genes (matK and rbcl). The optimized method is suitable for both dry and fresh leaves. The success of this method in obtaining high-quality genomic DNA demonstrated the broad applicability of this method.

Mounting evidence suggests that terrestrialization of plants started in streptophyte green algae, favoured by their dual existence in freshwater and subaerial/terrestrial environments. Here, we present the genomes of Mesostigma viride and Chlorokybus atmophyticus, two sister taxa in the earliest-diverging clade of streptophyte algae dwelling in freshwater and subaerial/terrestrial environments, respectively. We provide evidence that the common ancestor of M. viride and C. atmophyticus (and thus of streptophytes) had already developed traits associated with a subaerial/terrestrial environment, such as embryophyte-type photorespiration, canonical plant phytochrome, several phytohormones and transcription factors involved in responses to environmental stresses, and evolution of cellulose synthase and cellulose synthase-like genes characteristic of embryophytes. Both genomes differed markedly in genome size and structure, and in gene family composition, revealing their dynamic nature, presumably in response to adaptations to their contrasting environments. The ancestor of M. viride possibly lost several genomic traits associated with a subaerial/terrestrial environment following transition to a freshwater habitat.

Genome analysis of the pico-eukaryotic marine green alga Prasinoderma coloniale CCMP 1413 unveils the existence of a novel phylum within green plants (Viridiplantae), the Prasinodermophyta, which diverged before the split of Chlorophyta and Streptophyta. Structural features of the genome and gene family comparisons revealed an intermediate position of the P. coloniale genome (25.3 Mb) between the extremely compact, small genomes of picoplanktonic Mamiellophyceae (Chlorophyta) and the larger, more complex genomes of early-diverging streptophyte algae. Reconstruction of the minimal core genome of Viridiplantae allowed identification of an ancestral toolkit of transcription factors and flagellar proteins. Adaptations of P. coloniale to its deep-water, oligotrophic environment involved expansion of light-harvesting proteins, reduction of early light-induced proteins, evolution of a distinct type of C 4 photosynthesis and carbon-concentrating mechanism, synthesis of the metal-complexing metabolite picolinic acid, and vitamin B 1 , B 7 and B 12 auxotrophy. The P. coloniale genome provides first insights into the dawn of green plant evolution.

Background The expanding world population is expected to double the worldwide demand for food by 2050. Eighty-eight percent of countries currently face a serious burden of malnutrition, especially in Africa and south and southeast Asia. About 95% of the food energy needs of humans are fulfilled by just 30 species, of which wheat, maize, and rice provide the majority of calories. Therefore, to diversify and stabilize the global food supply, enhance agricultural productivity, and tackle malnutrition, greater use of neglected or underutilized local plants (so-called orphan crops, but also including a few plants of special significance to agriculture, agroforestry, and nutrition) could be a partial solution. Results Here, we present draft genome information for five agriculturally, biologically, medicinally, and economically important underutilized plants native to Africa: Vigna subterranea , Lablab purpureus , Faidherbia albida , Sclerocarya birrea , and Moringa oleifera . Assembled genomes range in size from 217 to 654 Mb. In V. subterranea , L. purpureus , F. albida , S. birrea , and M. oleifera , we have predicted 31,707, 20,946, 28,979, 18,937, and 18,451 protein-coding genes, respectively. By further analyzing the expansion and contraction of selected gene families, we have characterized root nodule symbiosis genes, transcription factors, and starch biosynthesis-related genes in these genomes. Conclusions These genome data will be useful to identify and characterize agronomically important genes and understand their modes of action, enabling genomics-based, evolutionary studies, and breeding strategies to design faster, more focused, and predictable crop improvement programs.

Moutai is a world-famous traditional Chinese liquor with complex taste and aroma, which are considered to be strongly influenced by the quality of fermentation starters (Daqu). However, the role of microbial communities in the starters has not been fully understood. In this study, we revealed the microbial composition of 185 Moutai starter samples, covering three different types of starters across immature and mature phases, and functional gene composition of mature starter microbiome. Our results showed that microbial composition patterns of immature starters varied, but they eventually were similar and steady when they became mature starters, after half-year storage and subsequent mixing. To help identify two types of immature starters, we selected seven operational taxonomic unit (OTU) markers by leave-one-out cross validation (LOOCV) and an OTU classified as Saccharopolyspora was the most decisive one. For mature starters, we identified a total of 16 core OTUs, one of which annotated as Bacillus was found positively associated with saccharifying power. We also identified the functional gene and microbial composition in starch and cellulose hydrolysis pathways. Microbes with higher abundances of alpha-glucosidase, alpha-amylase, and glucoamylase probably contributed to high saccharifying power. Overall, this study reveals the features of Moutai starter microbial communities in different phases and improves understanding of the relationships between microbiota and functional properties of the starters.