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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. Metagenome-Assembled Genome Sequences of Raphidiopsis raciborskii and Planktothrix agardhii from a Cyanobacterial Bloom in Kissena Lake, New York, USA

   https://doi.org/10.1128/MRA.01380-20  

   Martin, Robbie M.; Kausch, Michael; Yap, Kimarie; Wehr, John D.; Boyer, Gregory L.; Wilhelm, Steven W. (January 2021, Microbiology Resource Announcements)

   Stewart, Frank J. (Ed.)

   ABSTRACT Raphidiopsis raciborskii and Planktothrix agardhii are filamentous, potentially toxin-producing cyanobacteria that form nuisance blooms in fresh waters. Here, we report high-quality metagenome-assembled genome sequences of R. raciborskii and P. agardhii collected from a bloom in Kissena Lake, New York. 

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3. Metagenome-Assembled Genome Sequences of Raphidiopsis raciborskii and Planktothrix agardhii from a Cyanobacterial Bloom in Kissena Lake, New York, USA

   Martin, R.M.; Kausch, M.; Yap, K.; Wehr, J.D.; Boyer, G.L.; Wilhelm, G.L. (January 2021, Microbiology resource announcements)

   null (Ed.)

   Raphidiopsis raciborskii and Planktothrix agardhii are filamentous, poten- tially toxin-producing cyanobacteria that form nuisance blooms in fresh waters. Here, we report high-quality metagenome-assembled genome sequences of R. raciborskii and P. agardhii collected from a bloom in Kissena Lake, New York. 

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4. Genomic analyses provide insights into peach local adaptation and responses to climate change

   https://doi.org/10.1101/gr.261032.120  

   Li, Yong; Cao, Ke; Li, Nan; Zhu, Gengrui; Fang, Weichao; Chen, Changwen; Wang, Xinwei; Guo, Jian; Wang, Qi; Ding, Tiyu; et al (April 2021, Genome Research)

   The environment has constantly shaped plant genomes, but the genetic bases underlying how plants adapt to environmental influences remain largely unknown. We constructed a high-density genomic variation map of 263 geographically representative peach landraces and wild relatives. A combination of whole-genome selection scans and genome-wide environmental association studies (GWEAS) was performed to reveal the genomic bases of peach adaptation to diverse climates. A total of 2092 selective sweeps that underlie local adaptation to both mild and extreme climates were identified, including 339 sweeps conferring genomic pattern of adaptation to high altitudes. Using genome-wide environmental association studies (GWEAS), a total of 2755 genomic loci strongly associated with 51 specific environmental variables were detected. The molecular mechanism underlying adaptive evolution of high drought, strong UVB, cold hardiness, sugar content, flesh color, and bloom date were revealed. Finally, based on 30 yr of observation, a candidate gene associated with bloom date advance, representing peach responses to global warming, was identified. Collectively, our study provides insights into molecular bases of how environments have shaped peach genomes by natural selection and adds candidate genes for future studies on evolutionary genetics, adaptation to climate changes, and breeding. 

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5. Ecological divergence of syntopic marine bacterial species is shaped by gene content and expression

   https://doi.org/10.1038/s41396-023-01390-4  

   Nowinski, Brent; Feng, Xiaoyuan; Preston, Christina M.; Birch, James M.; Luo, Haiwei; Whitman, William B.; Moran, Mary Ann (March 2023, The ISME Journal)

   Abstract Identifying mechanisms by which bacterial species evolve and maintain genomic diversity is particularly challenging for the uncultured lineages that dominate the surface ocean. A longitudinal analysis of bacterial genes, genomes, and transcripts during a coastal phytoplankton bloom revealed two co-occurring, highly related Rhodobacteraceae species from the deeply branching and uncultured NAC11-7 lineage. These have identical 16S rRNA gene amplicon sequences, yet their genome contents assembled from metagenomes and single cells indicate species-level divergence. Moreover, shifts in relative dominance of the species during dynamic bloom conditions over 7 weeks confirmed the syntopic species’ divergent responses to the same microenvironment at the same time. Genes unique to each species and genes shared but divergent in per-cell inventories of mRNAs accounted for 5% of the species’ pangenome content. These analyses uncover physiological and ecological features that differentiate the species, including capacities for organic carbon utilization, attributes of the cell surface, metal requirements, and vitamin biosynthesis. Such insights into the coexistence of highly related and ecologically similar bacterial species in their shared natural habitat are rare. 

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