A microbial gene catalog of anaerobic digestion from full-scale biogas plants.

BACKGROUND: Biogas production with anaerobic digestion (AD) is one of the most promising solutions for both renewable energy production and resolving the environmental problem caused by the worldwide increase in organic waste. However, the complex structure of the microbiome in AD is poorly understood. FINDINGS: In this study, we constructed a microbial gene catalog of AD (22,840,185 genes) based on 1,817 Gb metagenomic data derived from digestate samples of 56 full-scale biogas plants fed with diverse feedstocks. Among the gene catalog, 73.63% and 2.32% of genes were taxonomically annotated to Bacteria and Archaea, respectively, and 57.07% of genes were functionally annotated with KEGG orthologous groups. Our results confirmed the existence of core microbiome in AD and showed that the type of feedstock (cattle, chicken, and pig manure) has a great influence on carbohydrate hydrolysis and methanogenesis. In addition, 2,426 metagenome-assembled genomes were recovered from all digestate samples, and all genomes were estimated to be ≥80% complete with ≤10% contamination. CONCLUSIONS: This study deepens our understanding of the microbial composition and function in the AD process and also provides a huge number of reference genome and gene resources for analysis of anaerobic microbiota.

The genome of the golden apple snail Pomacea canaliculata provides insight into stress tolerance and invasive adaptation.

Background: The golden apple snail (Pomacea canaliculata) is a freshwater snail listed among the top 100 worst invasive species worldwide and a noted agricultural and quarantine pest that causes great economic losses. It is characterized by fast growth, strong stress tolerance, a high reproduction rate, and adaptation to a broad range of environments. Results: Here, we used long-read sequencing to produce a 440-Mb high-quality, chromosome-level assembly of the P. canaliculata genome. In total, 50 Mb (11.4%) repeat sequences and 21,533 gene models were identified in the genome. The major findings of this study include the recent explosion of DNA/hAT-Charlie transposable elements, the expansion of the P450 gene family, and the constitution of the cellular homeostasis system, which contributes to ecological plasticity in stress adaptation. In addition, the high transcriptional levels of perivitelline genes in the ovary and albumen gland promote the function of nutrient supply and defense ability in eggs. Furthermore, the gut metagenome also contains diverse genes for food digestion and xenobiotic degradation. Conclusions: These findings collectively provide novel insights into the molecular mechanisms of the ecological plasticity and high invasiveness.

The genome of tapeworm Taenia multiceps sheds light on understanding parasitic mechanism and control of coenurosis disease.

Coenurosis, caused by the larval coenurus of the tapeworm Taenia multiceps, is a fatal central nervous system disease in both sheep and humans. Though treatment and prevention options are available, the control of coenurosis still faces presents great challenges. Here, we present a high-quality genome sequence of T. multiceps in which 240 Mb (96%) of the genome has been successfully assembled using Pacbio single-molecule real-time (SMRT) and Hi-C data with a N50 length of 44.8 Mb. In total, 49.5 Mb (20.6%) repeat sequences and 13, 013 gene models were identified. We found that Taenia spp. have an expansion of transposable elements and recent small-scale gene duplications following the divergence of Taenia from Echinococcus, but not in Echinococcus genomes, and the genes underlying environmental adaptability and dosage effect tend to be over-retained in the T. multiceps genome. Moreover, we identified several genes encoding proteins involved in proglottid formation and interactions with the host central nervous system, which may contribute to the adaption of T. multiceps to its parasitic life style. Our study not only provides insights into the biology and evolution of T. multiceps, but also identifies a set of species-specific gene targets for developing novel treatment and control tools for coenurosis.

Ancient horizontally transferred genes in the genome of California two-spot octopus, Octopus bimaculoides.

Horizontal gene transfer (HGT), a mechanism that shares genetic material between the host and donor from separated offspring branches, has been described as a means of producing novel and beneficial phenotypes for the host organisms. However, in molluscs, the second most diverse group, the existence of HGT is still controversial. In the present study, 12 HGT genes were identified from California two-spot octopus Octopus bimaculoides based on a similarity search, phylogenetic construction, gene composition analysis and PCR (Polymerase Chain Reaction) validation. Based on the phylogenetic topologies, ten HGT genes were identified to have been transferred into the possible molluscan ancestor, possibly before its radiation. Furthermore, most of the donor organisms were predicted to be familiar bacteria in marine environments. These horizontally transferred genes were under a strong negative selection and could be transcribed in octopus functionally. The predicted biochemical functions of these genes include metabolism, neurotransmission, immune defense and tissue integrity. Seven Zn-metalloproteinases were validated as the main type of HGT genes in octopus with divergent motif composition, intron presence and phylogenetic relationship to the endogenous ones. Furthermore, the functions of Zn-metalloproteinase were predicted to be responsible for immune defense and tissue remolding. Three HGT genes were distributed mainly in the nervous system and were predicted to regulate the neurotransmission through glia-neuronal interactions. The results collectively indicated the existence of HGT in molluscs and its potential contribution to the evolution of octopus with regards to functional innovation and adaptability.