Genomic adaptation of giant viruses in polar oceans

寒冷域と温暖域ではウイルスの遺伝子組成が異なる --巨大ウイルスの環境適応--. 京都大学プレスリリース. 2023-10-13.Despite being perennially frigid, polar oceans form an ecosystem hosting high and unique biodiversity. Various organisms show different adaptive strategies in this habitat, but how viruses adapt to this environment is largely unknown. Viruses of phyla Nucleocytoviricota and Mirusviricota are groups of eukaryote-infecting large and giant DNA viruses with genomes encoding a variety of functions. Here, by leveraging the Global Ocean Eukaryotic Viral database, we investigate the biogeography and functional repertoire of these viruses at a global scale. We first confirm the existence of an ecological barrier that clearly separates polar and nonpolar viral communities, and then demonstrate that temperature drives dramatic changes in the virus–host network at the polar–nonpolar boundary. Ancestral niche reconstruction suggests that adaptation of these viruses to polar conditions has occurred repeatedly over the course of evolution, with polar-adapted viruses in the modern ocean being scattered across their phylogeny. Numerous viral genes are specifically associated with polar adaptation, although most of their homologues are not identified as polar-adaptive genes in eukaryotes. These results suggest that giant viruses adapt to cold environments by changing their functional repertoire, and this viral evolutionary strategy is distinct from the polar adaptation strategy of their hosts

A workflow for genome-wide mapping of archaeal transcription factors with ChIP-seq

Deciphering the structure of gene regulatory networks across the tree of life remains one of the major challenges in postgenomic biology. We present a novel ChIP-seq workflow for the archaea using the model organism Halobacterium salinarum sp. NRC-1 and demonstrate its application for mapping the genome-wide binding sites of natively expressed transcription factors. This end-to-end pipeline is the first protocol for ChIP-seq in archaea, with methods and tools for each stage from gene tagging to data analysis and biological discovery. Genome-wide binding sites for transcription factors with many binding sites (TfbD) are identified with sensitivity, while retaining specificity in the identification the smaller regulons (bacteriorhodopsin-activator protein). Chromosomal tagging of target proteins with a compact epitope facilitates a standardized and cost-effective workflow that is compatible with high-throughput immunoprecipitation of natively expressed transcription factors. The Pique package, an open-source bioinformatics method, is presented for identification of binding events. Relative to ChIP-Chip and qPCR, this workflow offers a robust catalog of protein–DNA binding events with improved spatial resolution and significantly decreased cost. While this study focuses on the application of ChIP-seq in H. salinarum sp. NRC-1, our workflow can also be adapted for use in other archaea and bacteria with basic genetic tools

Prediction of Ecological Function in the Microbiome Using Machine Learning on the Graph Spectra of Coevolving Subnetworks

Chapter 1. We propose a method for predicting the ecological function of host-associated microbes using neural networks trained on a feature space of labeled ecological interactions from the literature. The feature space is constructed over the Laplacian spectral density distributions of the networks formed by linking the phylogenies of the host and microbial clades through their ecological associations. A classifier trained on 51 interactions with known ecology and 100 simulated controls was used predict the ecological function in the microbimes of 14 species of wild-caught cichlid fish from the Lake Tanganyika adaptive radiation observed using 16S rRNA sequencing. Chapter 2. Genomic patterns of divergence are examined using whole-genome resequencing of three sympatric cichlid species pairs with similar functional and ecological differentiation but different ages, revealing a signature of genomic divergence. Regions of elevated relative differentiation exhibit increased absolute differentiation. We detect a signature of convergent evolution across all three species pairs. Our results suggest that functional phenotypic differentiation is associated with a signature of genomic divergence. Chapter 3. We show that evolutionary innovations can result in competitive inferiority and extinction. The modified pharyngeal jaws of cichlid fishes and several marine fish, a classic example of evolutionary innovation, are not universally beneficial. Analysis of dietary evolution across marine fish lineages reveals that the innovation compromises access to predator niches. This competitive inferiority shaped the adaptive radiation of cichlids in Lake Tanganyika and played a pivotal, previously unrecognized role in the mass extinction of cichlid fishes in Lake Victoria after Nile perch invasion. Chapter 4. We map protein sequences from the Global Ocean Survey to protein families and use non-negative matrix factorization (NMF) to approximate linear combinations of ecological components with characteristic functional and site profiles. We identify functional signatures, estimate functional distance between sites, and find that an NMF-filtered measure is more strongly correlated with environmental distance than a comparable PCA-filtered measure. We find that functional distance is more strongly correlated with environmental distance than geographic distance in agreement with prior studies. Chapter 5. We describe the unique technical, logistical, organizational, and ethical issues from the 2013 Indigo V Indian Ocean Expedition research cruise from Cape Town, South Africa, to Phuket, Thailand aboard the S/Y Indigo V. An inventory the surface water population of bacterioplankton was collected and basic measurements of ocean physics and chemistry were tabulated. Chapter 6. We report on the microbial diversity across the Indian Ocean and a lagoon in the Chagos Archipelago. The community within the lagoon differed from adjacent community despite constant water exchange, driven by photosynthetic cyanobacterium Synechococcus. Enrichment of photosynthesis-related transcripts and nutrient cycling indicate influence of primary production on community structure. A five-fold diurnal increase in viral transcripts within the lagoon suggests concomitant bacteriophage influence. Chapter 7. We present a novel ChIP-seq workflow for archaea using Halobacterium salinarum sp. NRC-1 and map binding sites of natively expressed transcription factors. Relative to ChIP-Chip and qPCR, it improves spatial resolution and reduces cost. Chapter 8. Pique is a user-friendly, freely licensed ChIP-Seq peak finding application for bacterial and archaeal ChIP-Seq experiments. Output is provided in standardized file formats for manual curation and data exploration. Chapter 9. With appropriate handling, 3D printers produce sterile components from non-sterile thermoplastic feedstock without post-fabrication treatment. Chapter 10. We present a method for fabricating single-use microtiter plates with volumes calibrated for each sample, allowing the use of multichannel pipettes for general liquid handling operations. Many custom plates can be 3D printed simultaneously, resulting in substantial savings in cost and time. Chapter 11. The growth kinetics of 48 strains of building-associated bacteria were measured aboard the International Space Station. One strain, Bacillus safensis JPL-MERTA-8-2, grew 60% better in microgravity

Df and Dxy values for 10kb blocks from Kivu pair

Df and Dxy values for 10kb blocks from Kivu pai

Data from: Evaluating genomic divergence and parallelism in replicate ecomorphs from young and old cichlid adaptive radiations

Comparative genomic studies of closely related species typically focus on single species pairs at one given stage of divergence. That makes it difficult to infer the continuum of evolutionary process during speciation and beyond. Here, we use whole-genome resequencing to examine genomic patterns of divergence in three sympatric cichlid species pairs with very similar functional and ecological differentiation, but different ages. We find a strong signature of increasing genomic divergence with time in both the mitochondrial genome and the nuclear genome. In contrast to many other systems, we find that in these cichlids regions of elevated relative differentiation also exhibit increased absolute differentiation. We detect a signature of convergent evolution in a comparison of outlier regions across all three species pair comparisons but the extent of it is modest, and regions that are strongly divergent in any one pair tend to be only slightly elevated in the other pairs, consistent with a repeatable but polygenic basis of traits that characterize the ecomorphs. Our results suggest that strong functional phenotypic differentiation, as seen in all three species pairs, is generally associated with a clear signature of genomic divergence, even in the youngest species pair

Df and Dxy values for 10kb blocks from Victoria pair

Df and Dxy values for 10kb blocks from Victoria pai

Recombination should not be an afterthought.

This month’s Genome Watch highlights how the search for the origins of SARS-CoV-2 emphasizes the need for integrated phylogenetic methods