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1. Unveiling microbial diversity: harnessing long-read sequencing technology

   https://doi.org/10.1038/s41592-024-02262-1  

   Agustinho, Daniel P.; Fu, Yilei; Menon, Vipin K.; Metcalf, Ginger A.; Treangen, Todd J.; Sedlazeck, Fritz J. (April 2024, Nature Methods)
2. Functional sequencing read annotation for high precision microbiome analysis

   https://doi.org/10.1093/nar/gkx1209  

   Zhu, Chengsheng; Miller, Maximilian; Marpaka, Srinayani; Vaysberg, Pavel; Rühlemann, Malte C; Wu, Guojun; Heinsen, Femke-Anouska; Tempel, Marie; Zhao, Liping; Lieb, Wolfgang; et al (November 2017, Nucleic Acids Research)
3. Optimized sample selection for cost-efficient long-read population sequencing

   https://doi.org/10.1101/gr.264879.120  

   Ranallo-Benavidez, T. Rhyker; Lemmon, Zachary; Soyk, Sebastian; Aganezov, Sergey; Salerno, William J.; McCoy, Rajiv C.; Lippman, Zachary B.; Schatz, Michael C.; Sedlazeck, Fritz J. (May 2021, Genome Research)

   null (Ed.)
4. Improved contiguity of the threespine stickleback genome using long-read sequencing

   https://doi.org/10.1093/g3journal/jkab007  

   Nath, Shivangi; Shaw, Daniel E; White, Michael A (February 2021, G3 Genes|Genomes|Genetics)

   Macqueen, D (Ed.)

   Abstract While the cost and time for assembling a genome has drastically decreased, it still remains a challenge to assemble a highly contiguous genome. These challenges are rapidly being overcome by the integration of long-read sequencing technologies. Here, we use long-read sequencing to improve the contiguity of the threespine stickleback fish (Gasterosteus aculeatus) genome, a prominent genetic model species. Using Pacific Biosciences sequencing, we assembled a highly contiguous genome of a freshwater fish from Paxton Lake. Using contigs from this genome, we were able to fill over 76.7% of the gaps in the existing reference genome assembly, improving contiguity over fivefold. Our gap filling approach was highly accurate, validated by 10X Genomics long-distance linked-reads. In addition to closing a majority of gaps, we were able to assemble segments of telomeres and centromeres throughout the genome. This highlights the power of using long sequencing reads to assemble highly repetitive and difficult to assemble regions of genomes. This latest genome build has been released through a newly designed community genome browser that aims to consolidate the growing number of genomics datasets available for the threespine stickleback fish. 

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5. Pathways to polar adaptation in fishes revealed by long‐read sequencing

   https://doi.org/10.1111/mec.16501  

   Hotaling, Scott; Desvignes, Thomas; Sproul, John S.; Lins, Luana S. F.; Kelley, Joanna L. (June 2022, Molecular Ecology)

   Abstract Long‐read sequencing is driving a new reality for genome science in which highly contiguous assemblies can be produced efficiently with modest resources. Genome assemblies from long‐read sequences are particularly exciting for understanding the evolution of complex genomic regions that are often difficult to assemble. In this study, we utilized long‐read sequencing data to generate a high‐quality genome assembly for an Antarctic eelpout,Ophthalmolycus amberensis, the first for the globally distributed family Zoarcidae. We used this assembly to understand howO. amberensishas adapted to the harsh Southern Ocean and compared it to another group of Antarctic fishes: the notothenioids. We showed that selection has largely acted on different targets in eelpouts relative to notothenioids. However, we did find some overlap; in both groups, genes involved in membrane structure, thermal tolerance and vision have evidence of positive selection. We found evidence for historical shifts of transposable element activity inO. amberensisand other polar fishes, perhaps reflecting a response to environmental change. We were specifically interested in the evolution of two complex genomic loci known to underlie key adaptations to polar seas: haemoglobin and antifreeze proteins (AFPs). We observed unique evolution of the haemoglobin MN cluster in eelpouts and related fishes in the suborder Zoarcoidei relative to other Perciformes. For AFPs, we identified the first species in the suborder with no evidence ofafpIIIsequences (Cebidichthys violaceus) in the genomic region where they are found in all other Zoarcoidei, potentially reflecting a lineage‐specific loss of this cluster. Beyond polar fishes, our results highlight the power of long‐read sequencing to understand genome evolution. 

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