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1. Aureococcus anophagefferens strain CCMP1851: draft genome of a second Kratosvirus quantuckense- susceptible host strain for an emerging host–giant virus model system

   https://doi.org/10.1128/mra.00292-24  

   Chase, Emily E; Truchon, Alexander R; Schepens, William W; Wilhelm, Steven W (June 2024, Microbiology Resource Announcements)

   Hudson, André O (Ed.)

   ABSTRACT Here, we report the draft genome ofAureococcus anophagefferensstrain CCMP1851, which is susceptible to the virusKratosvirus quantuckense. CCMP1851 complements an available genome for a virus-resistant strain (CCMP1850) isolated from the same bloom. Future studies can now use this genome to examine genetic hints of virus resistance and susceptibility. 

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2. A high‐quality chromosome‐level genome assembly of a generalist herbivore, Trichoplusia ni

   https://doi.org/10.1111/1755-0998.12966  

   Chen, Wenbo; Yang, Xiaowei; Tetreau, Guillaume; Song, Xiaozhao; Coutu, Cathy; Hegedus, Dwayne; Blissard, Gary; Fei, Zhangjun; Wang, Ping (January 2019, Molecular Ecology Resources)

   Abstract The cabbage looper,Trichoplusia ni, is a globally distributed highly polyphagous herbivore and an important agricultural pest.T. nihas evolved resistance to various chemical insecticides, and is one of the only two insect species that have evolved resistance to the biopesticideBacillus thuringiensis(Bt) in agricultural systems and has been selected for resistance to baculovirus infections. We report a 333‐Mb high‐qualityT. nigenome assembly, which has N50 lengths of scaffolds and contigs of 4.6 Mb and 140 Kb, respectively, and contains 14,384 protein‐coding genes. High‐density genetic maps were constructed to anchor 305 Mb (91.7%) of the assembly to 31 chromosomes. Comparative genomic analysis ofT. niwithBombyx morishowed enrichment of tandemly duplicated genes inT. niin families involved in detoxification and digestion, consistent with the broad host range ofT. ni. High levels of genome synteny were found betweenT. niand other sequenced lepidopterans. However, genome synteny analysis ofT. niand theT. niderived cell line High Five (Hi5) indicated extensive genome rearrangements in the cell line. These results provided the first genomic evidence revealing the high instability of chromosomes in lepidopteran cell lines known from karyotypic observations. The high‐qualityT. nigenome sequence provides a valuable resource for research in a broad range of areas including fundamental insect biology, insect‐plant interactions and co‐evolution, mechanisms and evolution of insect resistance to chemical and biological pesticides, and technology development for insect pest management. 

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3. Closed circular genome sequence of a Microcystis aeruginosa PCC7806 Δ mcyB (UTK) non-toxic mutant

   https://doi.org/10.1128/MRA.00700-23  

   Stark, Gwendolyn F; Truchon, Alexander R; Dittmann, Elke; Wilhelm, Steven W (November 2023, Microbiology Resource Announcements)

   Becket, Elinne (Ed.)

   ABSTRACT Here we report the complete, closed genome of the non-toxicMicrocystis aeruginosaPCC7806 ΔmcyBmutant strain. This genome is 5,103,923 bp long, with a GC content of 42.07%. Compared to the published wild-type genome (Microcystis aeruginosaPCC7806SL), there is evidence of accumulated mutations beyond the inserted chloramphenicol resistance marker. 

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4. Draft genome of Bacillus subtilis strain YB955, prophage-cured derivative of strain 168

   https://doi.org/10.1128/mra.00263-24  

   Perez, Ryan King; Chavez_Rios, Jocelyn Sofia; Grifaldo, Jessica; Regner, Kurt; Pedraza-Reyes, Mario; Robleto, Eduardo A (August 2024, Microbiology Resource Announcements)

   Roux, Simon (Ed.)

   ABSTRACT We report the genome sequence ofBacillus subtilisstrain YB955, a prophage-cured strain used as a model in DNA repair, bacterial physiology, and mutagenesis studies. The assembled and annotated draft genome contains 4,031 coding genes, 5 rRNAs, and 73 tRNAs. Compared to 168, YB955 has a 134,402 bp deletion. 

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5. Pan-genome-scale metabolic modeling of Bacillus subtilis reveals functionally distinct groups

   https://doi.org/10.1128/msystems.00923-24  

   Neal, Maxwell; Brakewood, William; Betenbaugh, Michael; Zengler, Karsten (November 2024, mSystems)

   Faust, Karoline (Ed.)

   ABSTRACT Bacillus subtilisis an important industrial and environmental microorganism known to occupy many niches and produce many compounds of interest. Although it is one of the best-studied organisms, much of this focus including the reconstruction of genome-scale metabolic models has been placed on a few key laboratory strains. Here, we substantially expand these prior models to pan-genome-scale, representing 481 genomes ofB. subtiliswith 2,315 orthologous gene clusters, 1,874 metabolites, and 2,239 reactions. Furthermore, we incorporate data from carbon utilization experiments for eight strains to refine and validate its metabolic predictions. This comprehensive pan-genome model enables the assessment of strain-to-strain differences related to nutrient utilization, fermentation outputs, robustness, and other metabolic aspects. Using the model and phenotypic predictions, we divideB. subtilisstrains into five groups with distinct patterns of behavior that correlate across these features. The pan-genome model offers deep insights intoB. subtilis’metabolism as it varies across environments and provides an understanding as to how different strains have adapted to dynamic habitats. IMPORTANCEAs the volume of genomic data and computational power have increased, so has the number of genome-scale metabolic models. These models encapsulate the totality of metabolic functions for a given organism.Bacillus subtilisstrain 168 is one of the first bacteria for which a metabolic network was reconstructed. Since then, several updated reconstructions have been generated for this model microorganism. Here, we expand the metabolic model for a single strain into a pan-genome-scale model, which consists of individual models for 481B. subtilisstrains. By evaluating differences between these strains, we identified five distinct groups of strains, allowing for the rapid classification of any particular strain. Furthermore, this classification into five groups aids the rapid identification of suitable strains for any application. 

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