Chromosome-level genome assembly of a benthic associated Syngnathiformes species: the common dragonet, Callionymus lyra

  1. Sven Winter
  2. Stefan Prost
  3. Jordi de Raad
  4. Raphael T. F. Coimbra
  5. Magnus Wolf
  6. Marcel Nebenführ
  7. Annika Held
  8. Melina Kurzawe
  9. Ramona Papapostolou
  10. Jade Tessien
  11. Julian Bludau
  12. Andreas Kelch
  13. Sarah Gronefeld
  14. Yannis Schöneberg
  15. Christian Zeitz
  16. Konstantin Zapf
  17. David Prochotta
  18. Maximilian Murphy
  19. Monica M. Sheffer
  20. Moritz Sonnewald
  21. Maria A. Nilsson
  22. Axel Janke

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Abstract

Background The common dragonet, Callionymus lyra, is one of three Callionymus species inhabiting the North Sea. All three species show strong sexual dimorphism. The males show strong morphological differentiation, e.g., species-specific colouration and size relations, while the females of different species have few distinguishing characters. Callionymus belongs to the ‘benthic associated clade’ of the order Syngnathiformes. The ‘benthic associated clade’ so far is not represented by genome data and serves as an important outgroup to understand the morphological transformation in ‘long-snouted’ syngnatiformes such as seahorses and pipefishes. Findings Here, we present the chromosome-level genome assembly of C. lyra. We applied Oxford Nanopore Technologies’ long-read sequencing, short-read DNBseq, and proximity-ligation-based scaffolding to generate a high-quality genome assembly. The resulting assembly has a contig N50 of 2.2 Mbp and a scaffold N50 of 26.7 Mbp. The total assembly length is 568.7 Mbp, of which over 538 Mbp were scaffolded into 19 chromosome-length scaffolds. The identification of 94.5% complete BUSCO genes indicates high assembly completeness. Additionally, we sequenced and assembled a multi-tissue transcriptome with a total length of 255.5 Mbp that was used to aid the annotation of the genome assembly. The annotation resulted in 19,849 annotated transcripts and identified a repeat content of 27.7%. Conclusions The chromosome-level assembly of C. lyra provides a high-quality reference genome for future population genomic, phylogenomic, and phylogeographic analyses.

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  1. GigaByte

    Gigabyte doi: 10.46471/gigabyte.6

    Reviewer 2. Yunyun Lv

    Do you understand and agree to our policy of having open and named reviews, and having the your review included with the published papers. (If no, please inform the editor that you cannot review this manuscript.) Yes

    Is the language of sufficient quality? Yes

    Are all data available and do they match the descriptions in the paper? No

    Are the data and metadata consistent with relevant minimum information or reporting standards? See GigaDB checklists for examples http://gigadb.org/site/guide No

    Is the data acquisition clear, complete and methodologically sound? Yes

    Is there sufficient detail in the methods and data-processing steps to allow reproduction? Yes

    Is there sufficient data validation and statistical analyses of data quality? Yes

    Is the validation suitable for this type of data? Yes

    Is there sufficient information for others to reuse this dataset or integrate it with other data? No

    Any Additional Overall Comments to the Author This study presents a chromosome-level genome assembly of common dragonet. Hi-C method was applied to generate the high-quality genomic assembly. The result is valuable for further genomic analysis. However, some basic question should be solved or answered in the article to give a clearer insight.

    Line 35 findings section: The annotated total gene number and their quality should be evaluated and presented in the findings section. Line73-Line75：This sentence contains much speculation. I feel it should be removed or just mention the sympatry of their living location. Line 220: The section mainly described the method of gene annotation, however, the corresponding result is absent. These results are important to perform the various comparative genomic analysis. Thus, a detailed description of gene annotation result should be required in the revision. Line 238: Availability of supporting data; I searched the project accession number in NCBI database, but found no result. Thus, the supporting data is not unavailable in current.

    Line 33，type error: “syngnatiforms” should be syngnatiformes

    Recommendation Major Revision

  2. GigaByte

    Now published

    Reviewer 1. Chao Bian

    Do you understand and agree to our policy of having open and named reviews, and having the your review included with the published papers. (If no, please inform the editor that you cannot review this manuscript.)

    Yes

    Is the language of sufficient quality? Yes

    Are all data available and do they match the descriptions in the paper? Yes

    Are the data and metadata consistent with relevant minimum information or reporting standards? See GigaDB checklists for examples http://gigadb.org/site/guide Yes

    Is the data acquisition clear, complete and methodologically sound? Yes

    Is there sufficient detail in the methods and data-processing steps to allow reproduction? Yes

    Is there sufficient data validation and statistical analyses of data quality? Yes

    Is the validation suitable for this type of data? Yes

    Is there sufficient information for others to reuse this dataset or integrate it with other data? Yes

    Any Additional Overall Comments to the Author?

    This paper, entitled ‘Chromosome-level genome assembly of a benthic associated Syngnathiformes species: the common dragonet, Callionymus lyra’, has provided a reference genome of the common dragonet with a high contig and scaffold N50 values. The genome size estimation, gene and repeat annotation were also performed in this study. The analysis approaches, such as genome assembling, annotation, are solid and well performed.

    However, for the gene annotation, there was no homology-based annotation for gene annotation. On the other hand, why the authors have not used the HISAT or Tophat to map the RNA reads onto genome to predict the gene structure. I really rarely see the transcriptome annotation by using the trinity assembly.

    In addition, I still consider that the first published genome should have at least one analysis point for illuminating the molecular mechanism of the special character of this species. Only an assembly and some genes will largely reduce the impacts and interests for this fascinating fish species.

    Some minor mistakes should be changed: The decimal place through whole paper should be uniformed. Line 41, 538 Mbp should be 538.0 Mbp. Line 45, 27.66% should be 27.7%. Line 76, change “suggest” to “suggests”. Line 83 and line 94, for “see [9]” and “by [10]”, the author’s name should be indicated in text, like “see XX’s study [9]”. Line 104, tissue should be tissues. Line 120 and line 131, change ‘562’ to ‘562.0’, and change ‘645’ to ‘645.0’. Line 156, explains should be explain.

    Recommendation

    Major Revision

  3. Version published to 10.46471/gigabyte.6
  4. Version published to 10.1101/2020.09.08.287078v1 on bioRxiv