Despite half a century of research, the biology of dinoflagellates remains enigmatic: they defy many functional and genetic traits attributed to typical eukaryotic cells. Genomic approaches to study dinoflagellates are often stymied due to their large, multi-gigabase genomes. Members of the genusSymbiodiniumare photosynthetic endosymbionts of stony corals that provide the foundation of coral reef ecosystems. Their smaller genome sizes provide an opportunity to interrogate evolution and functionality of dinoflagellate genomes and endosymbiosis. We sequenced the genome of the ancestralSymbiodinium microadriaticumand compared it to the genomes of the more derivedSymbiodinium minutumandSymbiodinium kawagutiiand eukaryote model systems as well as transcriptomes from other dinoflagellates. Comparative analyses of genome and transcriptome protein sets show that all dinoflagellates, not onlySymbiodinium, possess significantly more transmembrane transporters involved in the exchange of amino acids, lipids, and glycerol than other eukaryotes. Importantly, we find that onlySymbiodiniumharbor an extensive transporter repertoire associated with the provisioning of carbon and nitrogen. Analyses of these transporters show species-specific expansions, which provides a genomic basis to explain differential compatibilities to an array of hosts and environments, and highlights the putative importance of gene duplications as an evolutionary mechanism in dinoflagellates andSymbiodinium.

Recent big data analyses have illuminated marine microbial diversity from a global perspective, focusing on planktonic microorganisms. Here, we analyze 2.5 terabases of newly sequenced datasets and theTaraOceans metagenomes to study the diversity of biofilm-forming marine microorganisms. We identify more than 7,300 biofilm-forming ‘species’ that are undetected in seawater analyses, increasing the known microbial diversity in the oceans by more than 20%, and provide evidence for differentiation across oceanic niches. Generation of a gene distribution profile reveals a functional core across the biofilms, comprised of genes from a variety of microbial phyla that may play roles in stress responses and microbe-microbe interactions. Analysis of 479 genomes reconstructed from the biofilm metagenomes reveals novel biosynthetic gene clusters and CRISPR-Cas systems. Our data highlight the previously underestimated ocean microbial diversity, and allow mining novel microbial lineages and gene resources.

Mangroves are unique, and endangered, coastal ecosystems that play a vital role in the tropical and subtropical environments. A comprehensive description of the microbial communities in these ecosystems is currently lacking, and additional studies are required to have a complete understanding of the functioning and resilience of mangroves worldwide. In this work, we carried out a metagenomic study by comparing the microbial community of mangrove sediment with the rhizosphere microbiome of Avicennia marina, in northern Red Sea mangroves, along the coast of Saudi Arabia. Our results revealed that rhizosphere samples presented similar profiles at the taxonomic and functional levels and differentiated from the microbiome of bulk soil controls. Overall, samples showed predominance by Proteobacteria, Bacteroidetes and Firmicutes, with high abundance of sulfate reducers and methanogens, although specific groups were selectively enriched in the rhizosphere. Functional analysis showed significant enrichment in 'metabolism of aromatic compounds', 'mobile genetic elements', 'potassium metabolism' and 'pathways that utilize osmolytes' in the rhizosphere microbiomes. To our knowledge, this is the first metagenomic study on the microbiome of mangroves in the Red Sea, and the first application of unbiased 454-pyrosequencing to study the rhizosphere microbiome associated with A. marina. Our results provide the first insights into the range of functions and microbial diversity in the rhizosphere and soil sediments of gray mangrove (A. marina) in the Red Sea.

Bread wheat (Triticum aestivum) is a globally dominant crop and major source of calories and proteins for the human diet. Compared with its wild ancestors, modern bread wheat shows lower genetic diversity, caused by polyploidisation, domestication and breeding bottlenecks^1,2. Wild wheat relatives represent genetic reservoirs, and harbour diversity and beneficial alleles that have not been incorporated into bread wheat. Here we establish and analyse extensive genome resources for Tausch’s goatgrass (Aegilops tauschii), the donor of the bread wheat D genome. Our analysis of 46 Ae. tauschii genomes enabled us to clone a disease resistance gene and perform haplotype analysis across a complex disease resistance locus, allowing us to discern alleles from paralogous gene copies. We also reveal the complex genetic composition and history of the bread wheat D genome, which involves contributions from genetically and geographically discrete Ae. tauschii subpopulations. Together, our results reveal the complex history of the bread wheat D genome and demonstrate the potential of wild relatives in crop improvement.

The computational search for promoters in prokaryotes remains an attractive problem in bioinformatics. Despite the attention it has received for many years, the problem has not been addressed satisfactorily. In any bacterial genome, the transcription start site is chosen mostly by the sigma (σ) factor proteins, which control the gene activation. The majority of published bacterial promoter prediction tools target σ⁷⁰ promoters in Escherichia coli. Moreover, no σ-specific classification of promoters is available for prokaryotes other than for E. coli. Here, we introduce bTSSfinder, a novel tool that predicts putative promoters for five classes of σ factors in Cyanobacteria (σ^A, σ^C, σ^H, σ^G and σ^F) and for five classes of sigma factors in E. coli (σ⁷⁰, σ³⁸, σ³², σ²⁸ and σ²⁴). Comparing to currently available tools, bTSSfinder achieves higher accuracy (MCC = 0.86, F₁-score = 0.93) compared to the next best tool with MCC = 0.59, F₁-score = 0.79) and covers multiple classes of promoters. bTSSfinder is available standalone and online at http://www.cbrc.kaust.edu.sa/btssfinder. Supplementary data are available at Bioinformatics online.

Animals endemic to deep-sea hydrothermal vents often form obligatory symbioses with bacteria, maintained by intricate host–symbiont interactions. Most genomic studies on holobionts have not investigated both sides to similar depths. Here, we report dual symbiosis in the peltospirid snail Gigantopelta aegis with two gammaproteobacterial endosymbionts: a sulfur oxidiser and a methane oxidiser. We assemble high-quality genomes for all three parties, including a chromosome-level host genome. Hologenomic analyses reveal mutualism with nutritional complementarity and metabolic co-dependency, highly versatile in transporting and using chemical energy. Gigantopelta aegis likely remodels its immune system to facilitate dual symbiosis. Comparisons with Chrysomallon squamiferum, a confamilial snail with a single sulfur-oxidising gammaproteobacterial endosymbiont, show that their sulfur-oxidising endosymbionts are phylogenetically distant. This is consistent with previous findings that they evolved endosymbiosis convergently. Notably, the two sulfur-oxidisers share the same capabilities in biosynthesising nutrients lacking in the host genomes, potentially a key criterion in symbiont selection.