Near chromosome-level and highly repetitive genome assembly of the snake pipefish Entelurus aequoreus (Syngnathiformes: Syngnathidae)
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Editors Assessment:
The snake pipefish, Entelurus aequoreus, is a species of fish that dwells in open seagrass habitats in the northern Atlantic. As a pipefish, it is a member of the Syngnathidae family of fish which also includes seahorses and seadragons. In recent years it has expanded its population size and range into arctic waters. To better understand these demographic changes genomic data is useful, and to address this a high-quality reference genome has been produced. Building on a previous short-read reference, a near chromosome-scale genome assembly for the snake pipefish was assembled using PacBio CLR and Hi-C reads. After revisions the authors provided more details on the assembly metrics, the final assembly has a length of 1.6 Gbp, with scaffold and contig N50s of 62.3 Mbp and 45.0 Mbp respectively. Demographic inference analysis of the snake pipefish genome using this data enables tracing of population changes over the past 1 million years, and this reference will allow further analyses and studies relating these to changes in climate.
**This evaluation refers to version 1 of the preprint
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Abstract
The snake pipefish, Entelurus aequoreus (Linnaeus, 1758), is a slender, up to 60 cm long, northern Atlantic fish that dwells in open seagrass habitats and has recently expanded its distribution range. The snake pipefish is part of the family Syngnathidae (seahorses and pipefish) that has undergone several characteristic morphological changes, such as loss of pelvic fins and elongated snout. Here, we present a highly contiguous, near chromosome-scale genome of the snake pipefish assembled as part of a university master’s course. The final assembly has a length of 1.6 Gbp in 7,391 scaffolds, a scaffold and contig N50 of 62.3 Mbp and 45.0 Mbp and L50 of 12 and 14, respectively. The largest 28 scaffolds (>21 Mbp) span 89.7% of the assembly length. A BUSCO completeness score of 94.1% and a mapping rate above 98% suggest a high assembly completeness. Repetitive elements cover 74.93% of the genome, one of the highest proportions so far identified in vertebrate genomes. Demographic modeling using the PSMC framework indicates a peak in effective population size (50 – 100 kya) during the last interglacial period and suggests that the species might largely benefit from warmer water conditions, as seen today. Our updated snake pipefish assembly forms an important foundation for further analysis of the morphological and molecular changes unique to the family Syngnathidae.
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Editors Assessment:
The snake pipefish, Entelurus aequoreus, is a species of fish that dwells in open seagrass habitats in the northern Atlantic. As a pipefish, it is a member of the Syngnathidae family of fish which also includes seahorses and seadragons. In recent years it has expanded its population size and range into arctic waters. To better understand these demographic changes genomic data is useful, and to address this a high-quality reference genome has been produced. Building on a previous short-read reference, a near chromosome-scale genome assembly for the snake pipefish was assembled using PacBio CLR and Hi-C reads. After revisions the authors provided more details on the assembly metrics, the final assembly has a length of 1.6 Gbp, with scaffold and contig N50s of 62.3 Mbp and 45.0 Mbp respectively. Demographic inference …
Editors Assessment:
The snake pipefish, Entelurus aequoreus, is a species of fish that dwells in open seagrass habitats in the northern Atlantic. As a pipefish, it is a member of the Syngnathidae family of fish which also includes seahorses and seadragons. In recent years it has expanded its population size and range into arctic waters. To better understand these demographic changes genomic data is useful, and to address this a high-quality reference genome has been produced. Building on a previous short-read reference, a near chromosome-scale genome assembly for the snake pipefish was assembled using PacBio CLR and Hi-C reads. After revisions the authors provided more details on the assembly metrics, the final assembly has a length of 1.6 Gbp, with scaffold and contig N50s of 62.3 Mbp and 45.0 Mbp respectively. Demographic inference analysis of the snake pipefish genome using this data enables tracing of population changes over the past 1 million years, and this reference will allow further analyses and studies relating these to changes in climate.
**This evaluation refers to version 1 of the preprint
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AbstractThe snake pipefish, Entelurus aequoreus (Linnaeus, 1758), is a slender, up to 60 cm long, northern Atlantic fish that dwells in open seagrass habitats and has recently expanded its distribution range. The snake pipefish is part of the family Syngnathidae (seahorses and pipefish) that has undergone several characteristic morphological changes, such as loss of pelvic fins and elongated snout. Here, we present a highly contiguous, near chromosome-scale genome of the snake pipefish assembled as part of a university master’s course. The final assembly has a length of 1.6 Gbp in 7,391 scaffolds, a scaffold and contig N50 of 62.3 Mbp and 45.0 Mbp and L50 of 12 and 14, respectively. The largest 28 scaffolds (>21 Mbp) span 89.7% of the assembly length. A BUSCO completeness score of 94.1% and a mapping rate above 98% suggest a high …
AbstractThe snake pipefish, Entelurus aequoreus (Linnaeus, 1758), is a slender, up to 60 cm long, northern Atlantic fish that dwells in open seagrass habitats and has recently expanded its distribution range. The snake pipefish is part of the family Syngnathidae (seahorses and pipefish) that has undergone several characteristic morphological changes, such as loss of pelvic fins and elongated snout. Here, we present a highly contiguous, near chromosome-scale genome of the snake pipefish assembled as part of a university master’s course. The final assembly has a length of 1.6 Gbp in 7,391 scaffolds, a scaffold and contig N50 of 62.3 Mbp and 45.0 Mbp and L50 of 12 and 14, respectively. The largest 28 scaffolds (>21 Mbp) span 89.7% of the assembly length. A BUSCO completeness score of 94.1% and a mapping rate above 98% suggest a high assembly completeness. Repetitive elements cover 74.93% of the genome, one of the highest proportions so far identified in vertebrate genomes. Demographic modeling using the PSMC framework indicates a peak in effective population size (50 – 100 kya) during the last interglacial period and suggests that the species might largely benefit from warmer water conditions, as seen today. Our updated snake pipefish assembly forms an important foundation for further analysis of the morphological and molecular changes unique to the family Syngnathidae.
This work has been published in GigaByte Journal under a CC-BY 4.0 license (https://doi.org/10.46471/gigabyte.105), and has published the reviews under the same license as follows:
Reviewer 1. Yanhong Zhang
Are all data available and do they match the descriptions in the paper? No. There is no BioProject available for review at the link. Are the data and metadata consistent with relevant minimum information or reporting standards?
No. "the GigaDB repository:DOI:XXXXX." I am not sure that the authors have upload the data.
Is the data acquisition clear, complete and methodologically sound? No. I am not sure that the authors have uploaded the data.
Is there sufficient data validation and statistical analyses of data quality? No. I need more information.
Is the validation suitable for this type of data? No. I need more information.
Is there sufficient information for others to reuse this dataset or integrate it with other data? No. I need more information.
Any Additional Overall Comments to the Author:
In line 41, you mean “50-100 kya”?
The authors need to provide more details about the genomic data： Genome size estimation based on K-mer spectrum？ Statistics of genomic characteristics from K-mer? Statistics of Hi-C sequencing raw data, such as raw bases, clean bases. Statistics of the pseduchromosome assemblies using Hi-C data. The result of BUSCO assessment, how about complete BUSCOs? complete single-copy？ Statistics of gene predictions in the snake pipefish Statistics of the noncoding RNA in the snake pipefish genome. The author claims that all other data, including the repeat and gene annotation, was uploaded to the GigaDB repository: DOI: XXXXX. I cannot find these data. “DOI: XXXXX”? What does that mean?
Reviewer 2. Sarah Flanagan
Are all data available and do they match the descriptions in the paper?
No. I received an NCBI link which took me to the raw data files and a BioSample description, but it did not link to the assembled and annotated genome.
Is there sufficient detail in the methods and data-processing steps to allow reproduction?
Yes. Only one point was not clear to me in the methods -- please clarify in the text which data was used to generate consensus genome sequences using vcfutils (lines 240-241). How did this differ from the assembled and annotated genome?
Any Additional Overall Comments to the Author:
In the abstract and introduction, the description of the habitat of the species is confusing and it was not clear from the manuscript as written that there are two ecotypes, one that is pelagic and one that is coastal. Consider re-phrasing these sections (lines 31-32, 57-59, and 61-62) to better describe the habitat of this species.
Please also consider increasing the font size of the labels in Figure 1 -- the details are very difficult to read.
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