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A draft genome of 906 scaffolds of 115.8 Mb was created for Desmodesmus armatus , a diploid, lipid- and storage carbohydrate-accumulating microalga proven relevant for large-scale, outdoor cultivation, and serves as a model alga platform for improving photosynthetic efficiency and carbon assimilation for next-generation bioenergy production.
Species of Nannochloropsis are single-celled Stramenopiles commonly used in microalgae-based technologies for the manufacturing of bioproducts. Nannochloropsis oceanica QH25 was isolated from an algal cultivation pond located in Imperial, Texas (USA). We used PacBio continuous long read (CLR) sequencing to produce a highly contiguous 29.34 Mb genome.
We present genome assemblies of six Brucella melitensis strains isolated from goats and humans in Tanzania’s Kagera region. These sequences provide insight into circulating Brucella strains in Tanzania and East Africa. These data will support future comparative genomics, epidemiological investigations, and regional brucellosis control strategies.
The genomes of Methylomonas sp. strain EFPC1 and Methylococcus sp. strain EFPC2 isolated from a mercury-contaminated stream in Oak Ridge Tennessee, were sequenced.
We report eight genomes from representatives of the phylum Acidobacteria subdivisions 1 and 3, isolated from soils. The genome sizes range from 4.9 to 6.7 Mb. Genomic analysis reveals putative genes for low- and high-affinity respiratory oxygen reductases, high-affinity hydrogenases, and the capacity to use a diverse collection of carbohydrates.
This study presents the draft genome of Rossellomorea marisflavi DL-A, a malathion-degrading bacterium isolated from the North Oconee River in Athens, GA, USA. The DL-A genome is 4.27 Mb in size and comprises 4,271 coding sequences with proteins.
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.
We grew a soil enrichment culture to identify organisms that anaerobically oxidize phenazine-1-carboxylic acid. A strain of Citrobacter portucalensis was isolated from this enrichment and sequenced by both Illumina and PacBio technologies. It has a genome with a length of 5.3 Mb, a G+C content of 51.8%, and at least one plasmid.
Abstract Pseudomonads are ubiquitous bacteria with importance in medicine, soil, agriculture, and biomanufacturing. We report a novel Pseudomonas putida phage, MiCath, which is the first known phage infecting P. putida S12, a strain increasingly used as a synthetic biology chassis. MiCath was isolated from garden soil under a tomato plant using P. putida S12 as a host and was also found to infect four other P. putida strains. MiCath has a ~ 61 kbp double-stranded DNA genome which encodes 97 predicted open reading frames (ORFs); functions could only be predicted for 48 ORFs using comparative genomics. Functions include structural phage proteins, other common phage proteins (e.g., terminase), a queuosine gene cassette, a cas4 exonuclease, and an endosialidase. Restriction digestion analysis suggests the queuosine gene cassette encodes a pathway capable of modification of guanine residues. When compared to other phage genomes, MiCath shares at most 74% nucleotide identity over 2% of the genome with any sequenced phage. Overall, MiCath is a novel phage with no close relatives, encoding many unique gene products.
Ten distinct isolates from the genus Pseudomonas were isolated in culture. The genomes of these isolates were sequenced using the Illumina MiSeq platform and assembled in order to provide insight into the metabolic and carbon-degrading potential of bacteria residing in soils at high latitudes.
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.
Abstract Aspergillus flavus is an opportunistic pathogen of crops, including peanuts and maize, and is the second leading cause of aspergillosis in immunocompromised patients. A. flavus is also a major producer of the mycotoxin, aflatoxin, a potent carcinogen, which results in significant crop losses annually. The A. flavus isolate NRRL 3357 was originally isolated from peanut and has been used as a model organism for understanding the regulation and production of secondary metabolites, such as aflatoxin. A draft genome of NRRL 3357 was previously constructed, enabling the development of molecular tools and for understanding population biology of this particular species. Here, we describe an updated, near complete, telomere-to-telomere assembly and re-annotation of the eight chromosomes of A. flavus NRRL 3357 genome, accomplished via long-read PacBio and Oxford Nanopore technologies combined with Illumina short-read sequencing. A total of 13,715 protein-coding genes were predicted. Using RNA-seq data, a significant improvement was achieved in predicted 5’ and 3’ untranslated regions, which were incorporated into the new gene models.
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.
Cryphonectria parasitica is the causal agent of chestnut blight, a fungal disease that almost entirely eliminated mature American chestnut from North America over a 50-year period. Here, we formally report the genome of C. parasitica EP155 using a Sanger shotgun sequencing approach. After finishing and integration with simple-sequence repeat markers, the assembly was 43.8 Mb in 26 scaffolds (L 50 = 5; N 50 = 4.0Mb). Eight chromosomes are predicted: five scaffolds have two telomeres and six scaffolds have one telomere sequence. In total, 11,609 gene models were predicted, of which 85% show similarities to other proteins. Finally, this genome resource has already increased the utility of a fundamental plant pathogen experimental system through new understanding of the fungal vegetative incompatibility system, with significant implications for enhancing mycovirus-based biological control.
We present draft genomes of two Paraburkholderia strains and two Burkholderia strains. Three strains were isolated from surrounding soils and one from roots of switchgrass (Panicum virgatum) in Michigan, USA.
Rhodococcus bacterial strains are characterized by wide metabolic versatility and extraordinary resistance to environmental stresses. The high versatility and adaptability of Rhodococcus strains is partly related with large and complex genomes (up to 10.1 Mbp) including high genetic redundancy and the presence of several circular and linear (mega)plasmids, which harbour peculiar catabolic and biosynthetic genes. Within Rhodococcus genus, R. opacus strain PD630 is considered a model oleaginous strain for its ability to produce and accumulate lipids (mostly triacyglycerols, TAGs) using different carbon sources, including low-cost and renewable resources such as lignocellulose. Notably, under specific growth conditions, this strain is capable of accumulating up to 80% of its cellular dry weight in TAGs; that is a rare feature in the prokaryotic and eukaryotic kingdoms. Multi-omic approaches have been applied to obtain system-level information about metabolic and regulatory pathways involved in these biosynthetic processes. Novel molecular tools for genome editing (CRISPR/Cas9 and recombineering) have been recently developed highlighting the possible utilization of R. opacus PD630 as synthetic biology platform for lipids production.
Larkinella sp. strain BK230, a heterotrophic bacterium of the phylum Bacteroidetes , was isolated from the roots of a field-grown eastern cottonwood tree ( Populus deltoides ) located in Georgia. The draft 7.27-Mb genome has a G+C content of 53.4% and contains 6,026 coding sequences, including 41 tRNA genes.
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.