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      A high-quality reference genome for the common creek chub, Semotilus atromaculatus

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          Abstract

          Creek chub ( Semotilus atromaculatus) is a leuciscid minnow species commonly found in anthropogenically disturbed environments, making it an excellent model organism to study human impacts on aquatic systems. Genomic resources for creek chub and other leuciscid species are currently limited. However, advancements in DNA sequencing now allow us to create genomic resources at a historically low cost. Here, we present a high quality, 239 contig reference genome for the common creek chub, created with PacBio HiFi sequencing. We compared the assembly quality of two pipelines: Pacific Biosciences’ Improved Phase Assembly (873 contigs) and Hifiasm (239 contigs). Quality and completeness of this genome is comparable to the zebrafish (Danioninae) and fathead minnow (Leuciscidae) genomes. The creek chub genome is highly syntenic to the zebrafish and fathead minnow genomes, and while our assembly does not resolve into the expected 25 chromosomes, synteny with zebrafish suggests that each creek chub chromosome is likely represented by 1–4 large contigs in our assembly. This reference genome is a valuable resource that will enhance genomic biodiversity studies of creek chub and other nonmodel leuciscid species common to disturbed environments.

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          Most cited references36

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          BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs.

          Genomics has revolutionized biological research, but quality assessment of the resulting assembled sequences is complicated and remains mostly limited to technical measures like N50.
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            Circos: an information aesthetic for comparative genomics.

            We created a visualization tool called Circos to facilitate the identification and analysis of similarities and differences arising from comparisons of genomes. Our tool is effective in displaying variation in genome structure and, generally, any other kind of positional relationships between genomic intervals. Such data are routinely produced by sequence alignments, hybridization arrays, genome mapping, and genotyping studies. Circos uses a circular ideogram layout to facilitate the display of relationships between pairs of positions by the use of ribbons, which encode the position, size, and orientation of related genomic elements. Circos is capable of displaying data as scatter, line, and histogram plots, heat maps, tiles, connectors, and text. Bitmap or vector images can be created from GFF-style data inputs and hierarchical configuration files, which can be easily generated by automated tools, making Circos suitable for rapid deployment in data analysis and reporting pipelines.
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              Improved metagenomic analysis with Kraken 2

              Although Kraken’s k-mer-based approach provides a fast taxonomic classification of metagenomic sequence data, its large memory requirements can be limiting for some applications. Kraken 2 improves upon Kraken 1 by reducing memory usage by 85%, allowing greater amounts of reference genomic data to be used, while maintaining high accuracy and increasing speed fivefold. Kraken 2 also introduces a translated search mode, providing increased sensitivity in viral metagenomics analysis.
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                Author and article information

                Contributors
                Role: Editor
                Journal
                G3 (Bethesda)
                Genetics
                g3journal
                G3: Genes|Genomes|Genetics
                Oxford University Press (US )
                2160-1836
                February 2024
                21 December 2023
                21 December 2023
                : 14
                : 2
                : jkad283
                Affiliations
                Department of Integrative Biology, University of Guelph , Guelph, ON N1G 2W1, Canada
                Department of Integrative Biology, University of Guelph , Guelph, ON N1G 2W1, Canada
                Department of Integrative Biology, University of Guelph , Guelph, ON N1G 2W1, Canada
                Department of Biology, Northern Michigan University, 1401 Presque Isle Avenue, Marquette, MI 49855, USA
                Author notes
                Corresponding author: Department of Integrative Biology, University of Guelph, 50 Stone Road East, Guelph, ON N1G 2W1, Canada. Email: apitura@ 123456uoguelph.ca

                Amanda V. Meuser and Amy R. Pitura Co-first authors.

                Conflicts of interest The authors declare no conflicts of interest.

                Author information
                https://orcid.org/0000-0001-9554-2002
                https://orcid.org/0000-0002-3153-4553
                https://orcid.org/0000-0002-9461-9140
                Article
                jkad283
                10.1093/g3journal/jkad283
                10849318
                38128526
                868cb314-1258-4569-ac86-9cdab2563c8c
                © The Author(s) 2023. Published by Oxford University Press on behalf of The Genetics Society of America.

                This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

                History
                : 14 July 2023
                : 10 October 2023
                : 05 January 2024
                Page count
                Pages: 9
                Funding
                Funded by: Digital Research Alliance of Canada, DOI 10.13039/501100021202;
                Funded by: Canada First Research Excellence Fund, DOI 10.13039/501100010785;
                Funded by: University of Guelph’s Food From Thought Research Support;
                Categories
                Genome Report
                AcademicSubjects/SCI01180
                AcademicSubjects/SCI01140

                Genetics
                semotilus atromaculatus,reference genome,creek chub,synteny,cyprinid,leuciscid
                Genetics
                semotilus atromaculatus, reference genome, creek chub, synteny, cyprinid, leuciscid

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