Section: Genomics
Topic: Genetics/genomics

Chromosome-level genome reference of the Caucasian dwarf goby Knipowitschia cf. caucasica, a new alien Gobiidae invading the River Rhine

Schoenle, Alexandra1 ; Guiglielmoni, Nadège1 ; Mainz, Tobias1; Greve, Carola2, 3; Hamadou, Alexander Ben2, 3; Heermann, Lisa1, 4 ; Borcherding, Jost1 ; Waldvogel, Ann-Marie1  
1 Institute of Zoology, University of Cologne, Zülpicher Str. 47b, 50674 Cologne, Germany
2 LOEWE Center for Translational Biodiversity Genomics, Senckenberganlage 25, 60325 Frankfurt am Main, Germany
3 Senckenberg Research Institute, Senckenberganlage 25, 60325 Frankfurt am Main, Germany
4 Federal Agency for Nature Conservation, Konstantinstr. 110, 53179 Bonn, Germany

Corresponding author(s): Waldvogel, Ann-Marie (a.waldvogel@uni-koeln.de)

10.24072/pcjournal.490 - Peer Community Journal, Volume 4 (2024), article no. e108.

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The Caucasian dwarf goby Knipowitschia cf. caucasica is a new invasive alien Gobiidae spreading in the Lower Rhine since 2019. Little is known about the invasion biology of the species and further investigations to reconstruct the invasion history are lacking genomic resources. We assembled a high-quality chromosome-scale reference genome of Knipowitschia cf. caucasica by combining PacBio, Omni-C and Illumina technologies. The size of the assembled genome is 956.58 Mb with a N50 scaffold length of 43 Mb, which includes 92.3 % complete Actinopterygii Benchmarking Universal Single-Copy Orthologs. 98.96 % of the assembly sequence was assigned to 23 chromosome-level scaffolds, with a GC-content of 42.83 %. Repetitive elements account for 53.08 % of the genome. The chromosome-level genome contained 26,404 transcripts with 23,210 multi-exons, of which 26,260 genes were functionally annotated. In summary, the high-quality genome assembly provides a fundamental basis to understand the adaptive advantage of the species.

Published online:
DOI: 10.24072/pcjournal.490
Type: Research article
Keywords: fish, reference genome, invasive alien species, goby

Schoenle, Alexandra 1; Guiglielmoni, Nadège 1; Mainz, Tobias 1; Greve, Carola 2, 3; Hamadou, Alexander Ben 2, 3; Heermann, Lisa 1, 4; Borcherding, Jost 1; Waldvogel, Ann-Marie 1

1 Institute of Zoology, University of Cologne, Zülpicher Str. 47b, 50674 Cologne, Germany
2 LOEWE Center for Translational Biodiversity Genomics, Senckenberganlage 25, 60325 Frankfurt am Main, Germany
3 Senckenberg Research Institute, Senckenberganlage 25, 60325 Frankfurt am Main, Germany
4 Federal Agency for Nature Conservation, Konstantinstr. 110, 53179 Bonn, Germany
License: CC-BY 4.0
Copyrights: The authors retain unrestricted copyrights and publishing rights 
@article{10_24072_pcjournal_490,
     author = {Schoenle, Alexandra and Guiglielmoni, Nad\`ege and Mainz, Tobias and Greve, Carola and Hamadou, Alexander Ben and Heermann, Lisa and Borcherding, Jost and Waldvogel, Ann-Marie},
     title = {Chromosome-level genome reference of the {Caucasian} dwarf goby {\protect\emph{Knipowitschia}} cf. \protect\emph{caucasica}, a new alien {Gobiidae} invading the {River} {Rhine}},
     journal = {Peer Community Journal},
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     year = {2024},
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%A Heermann, Lisa
%A Borcherding, Jost
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Schoenle, Alexandra; Guiglielmoni, Nadège; Mainz, Tobias; Greve, Carola; Hamadou, Alexander Ben; Heermann, Lisa; Borcherding, Jost; Waldvogel, Ann-Marie. Chromosome-level genome reference of the Caucasian dwarf goby Knipowitschia cf. caucasica, a new alien Gobiidae invading the River Rhine. Peer Community Journal, Volume 4 (2024), article  no. e108. doi : 10.24072/pcjournal.490. https://peercommunityjournal.org/articles/10.24072/pcjournal.490/

PCI peer reviews and recommendation, and links to data, scripts, code and supplementary information: 10.24072/pci.genomics.100376

Conflict of interest of the recommender and peer reviewers:
The recommender in charge of the evaluation of the article and the reviewers declared that they have no conflict of interest (as defined in the code of conduct of PCI) with the authors or with the content of the article.

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