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Contrasting patterns of sequence variation in steelhead populations reflect distinct evolutionary processes
Abstract Multiple evolutionary processes influence genome‐wide allele frequencies and quantifying effects of genetic drift, and multiple forms of selection remain challenging in natural populations. Here, we investigate variation at major effect loci in contrast to patterns of neutral drift across a wide collection of steelhead ( Oncorhynchus mykiss ) populations that have declined in abundance due to anthropogenic impacts. Whole‐genome resequencing of 74 populations of steelhead revealed genome‐wide patterns (~8 million SNPs) consistent with expected neutral population structure. However, allelic variation at major effect loci associated with adult migration timing (chromosome 28: GREB1L / ROCK1 ) and age at maturity (chromosome 25: SIX6 ) reflected how selection has acted on phenotypic variation in contrast with neutral structure. Variation at major effect loci was influenced by evolutionary processes with differing signals between the strongly divergent Coastal and Inland lineages, while allele frequencies within and among populations within the Inland lineage have been driven by local natural selection as well as recent anthropogenic influences. Recent anthropogenic effects appeared to have influenced the frequency of major effect alleles including artificial selection for specific traits in hatchery stocks with subsequent gene flow into natural populations. Selection from environmental factors at various scales has also likely influenced variation for major effect alleles. These results reveal evolutionary mechanisms that influence allele frequencies at major effect loci that are critical for conservation of phenotypic traits and life history variation of this protected species.
Structure and sequence evolution in the pennycress ( Thlaspi arvense ) pangenome
Eukaryotic genomes harbor many forms of variation, including nucleotide diversity and structural polymorphisms, which experience natural selection and contribute to genome evolution and biodiversity. Harnessing this variation for agriculture hinges on our ability to detect, quantify, catalog, and deploy genetic diversity. Here, we explore seven complete genomes of the emerging biofuel crop pennycress ( Thlaspi arvense ) drawn from across the species' current genetic diversity to catalog variation in genome structure and content. Across this new pangenome resource, we find contrasting evolutionary modes in different genomic zones. Gene-poor, repeat-rich pericentromeric regions experience frequent rearrangements, including repeated centromere repositioning. By contrast, conserved gene-dense chromosome arms maintain large-scale synteny across accessions even in fast-evolving NOD-like receptor immune genes, where microsynteny breaks down across species, but gene cluster positioning macrosynteny is maintained. Our findings highlight that multiple elements of the genome experience dynamic evolution that conserves functional content on the chromosome scale but allows repositioning and presence–absence variation on a local scale. This diversity is invisible to classical reference-based strategies and highlights the strength and utility of pangenomic resources. These results provide a valuable case study of rapid genomic structural evolution within a species and powerful resources for crop development in an emerging biofuel crop.
Targeted sequence design within the coarse-grained polymer genome
Coarse-grained modeling, machine learning, and optimization enable efficient design of polymers with target properties.
Correction for Thompson et al., “Fatty Acid and Alcohol Metabolism in Pseudomonas putida : Functional Analysis Using Random Barcode Transposon Sequencing”
Volume 86, no. 21, 2020, e01665-20, https://doi.org/10.1128/AEM.01665-20. Readers should note that when the authors created the deletion mutant of PP_2675, they deleted the entire region between the gene’s start and stop codons. However, this also deleted the DNA that codes for the first 14 amino acids of the overlapping ORF PP_2676. Additionally, the originally published URL for the JBEI public strain repository was incorrect. The correct link to all strains and plasmids in this study is https://public-registry.jbei .org/folders/641.
Nitrogen Metabolism in Pseudomonas putida : Functional Analysis Using Random Barcode Transposon Sequencing
Pseudomonas putida KT2440 has long been studied for its diverse and robust metabolisms, yet many genes and proteins imparting these growth capacities remain uncharacterized. Using pooled mutant fitness assays, we identified genes and proteins involved in the assimilation of 52 different nitrogen containing compounds. To assay amino acid biosynthesis, 19 amino acid drop-out conditions were also tested. From these 71 conditions, significant fitness phenotypes were elicited in 672 different genes including 100 transcriptional regulators and 112 transport-related proteins. We divide these conditions into 6 classes, and propose assimilatory pathways for the compounds based on this wealth of genetic data. To complement these data, we characterize the substrate range of three promiscuous aminotransferases relevant to metabolic engineering efforts in vitro. So we examine the specificity of five transcriptional regulators, explaining some fitness data results and exploring their potential to be developed into useful synthetic biology tools. In addition, we use manifold learning to create an interactive visualization tool for interpreting our BarSeq data, which will improve the accessibility and utility of this work to other researchers.
Draft Genome Sequence of Mycobacterium sp. Strain JC1 DSM 3803
Mycobacterium sp. strain JC1 DSM3803 is one of the few known bacteria predicted to possess the xylulose monophosphate (XuMP) pathway of C1 carbon assimilation. The draft genome is 7,921,603 bp with a GC content of 66.88% and will allow more in depth investigation of the bacterium’s unique metabolisms.
Metagenome Sequencing to Explore Phylogenomics of Terrestrial Cyanobacteria
Cyanobacteria are ubiquitous microorganisms with crucial ecosystem functions, yet most knowledge of their biology is from aquatic taxa. We have constructed metagenomes for 50 taxonomically well-characterized terrestrial cyanobacterial cultures. These data will support phylogenomic studies of evolutionary relationships and gene content among these unique algae and their aquatic relatives.
Thaumarchaea Genome Sequences from a High Arctic Active Layer
The role of archaeal ammonia oxidizers often exceeds that of bacterial ammonia oxidizers in marine and terrestrial environments but has been understudied in permafrost, where thawing has the potential to release ammonia. Here, three thaumarchaea genomes were assembled and annotated from metagenomic data sets from carbon-poor Canadian High Arctic active-layer cryosols.
Draft Genome Sequence of Tumebacillus sp. Strain BK434, Isolated from the Roots of Eastern Cottonwood
A Gram-positive bacterium was isolated from the root of an eastern cottonwood tree ( Populus deltoides ) in Georgia and identified as a Tumebacillus species with 99% 16S rRNA nucleotide identity to Tumebacillus avium . The genome is 4.6 Mbp and encodes 4,072 proteins and 251 RNAs.
Metatranscriptomic Sequencing of Winter and Spring Planktonic Communities from Lake Erie, a Laurentian Great Lake
Previous reports suggest planktonic and under-ice winter microbial communities in Lake Erie are dominated by diatoms. Here, we report the assembled metatranscriptomes of 79 Lake Erie surface water microbial communities spanning both the winter (28 samples) and spring (51 samples) months over spatial, temporal, and climatic gradients in 2019 through 2020.
Draft Metagenome Sequences of the Sphagnum (Peat Moss) Microbiome from Ambient and Warmed Environments across Europe
We present 49 metagenome assemblies of the microbiome associated with Sphagnum (peat moss) collected from ambient, artificially warmed, and geothermally warmed conditions across Europe. These data will enable further research regarding the impact of climate change on plant-microbe symbiosis, ecology, and ecosystem functioning of northern peatland ecosystems.
Draft Genome Sequence of Agrobacterium fabrum ARqua1
Agrobacterium fabrum ARqua1 is a hybrid of Agrobacterium fabrum C58C bearing the megaplasmid pRiA4b. ARqua1 is used by many plant researchers to generate transgenic roots. The draft genome of ARqua1 includes a 249,350-bp contig that likely covers all of pRiA4b, and it will be a valuable resource to plant biologists.
Genome sequences of key bacterial symbionts of entomopathogenic nematodes: Xenorhabdus cabanillasii DSM17905, Xenorhabdus ehlersii DSM16337, Xenorhabdus japonica DSM16522, Xenorhabdus koppenhoeferii DSM18168, and Xenorhabdus mauleonii DSM17908
ABSTRACT Xenorhabdus species are bacterial symbionts of entomopathogenic Steinernema nematodes, in which they produce diverse secondary metabolites implicated in pathogenesis. To expand resources for natural product prospecting and exploration of host-symbiont-pathogen relationships, the genomes of Xenorhabdus cabanillasi, Xenorhabdus ehlersii , Xenorhabdus japonica , Xenorhabdus koppenhoeferii , and Xenorhabdus mauleonii were analyzed.
Methylome and Complete Genome Sequence of Parageobacillus toebii DSM 14590 T , a Thermophilic Bacterium
ABSTRACT Here, we present the first complete genome assembly of the thermophilic bacterium Parageobacillus toebii DSM 14590 T . The P. toebii DSM 14590 T genome consists of a 3,270,071-bp circular chromosome and a 52,989-bp native plasmid.
Draft Genome Sequences of 14 Bacterial Isolates from the Rhizosphere of Bioenergy Sorghum
We report the draft genomes of a collection of 15 bacteria, isolated from the rhizosphere soil of bioenergy sorghum (Sorghum bicolor (L.) Moench). These isolates belong to the genera, Acidovorax, Nocardioides, Agrobacterium, Peribacillus, Caulobacter, Cupriavidus, Pseudomonas, Rhizobium, Sphingomonas, Priestia, Dyadobacter, Roseomonas, Ideonella, and Bacillus.
Friend or Foe: Draft Genome Sequence of Bradyrhizobium sp. Strain SRS-191
We report the genomic features of Bradyrhizobium sp. strain SRS-191, which was isolated from a former nuclear legacy site in Aiken, South Carolina, USA. With a genome size of 7,621,400 bp, the strain harbored genes not only for environmentally beneficial traits (e.g., heavy metal resistance, nitrogen fixation, and aromatic biodegradation) but also for antimicrobial resistance.
Complete Genome Sequence of Phormidium yuhuli AB48, Isolated from an Industrial Photobioreactor Environment
We report the genome of Phormidium yuhuli AB48, which includes a circular chromosome and a circular plasmid (4,747,469 bp and 51,599 bp, respectively). This is currently the only closed reference genome of an isolate of the Phormidium genus, based on the Genome Taxonomy Database (GTDB), providing a potential model system for sustainable biotechnology innovation.