A chromosome-level reference genome for Pacific herring (Clupea pallasii) from the Bering Sea
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Editors Assessment:
Here is a Data Release article sharing the reference genome of the Pacific herring (Clupea pallasii), a species with broad ecological, economic, and cultural importance. This specimen coming from the eastern Bering Sea which are genetically quite different from those from the Gulf of Alaska. This high-quality chromosome-scale reference was built from Hi-C and PacBio Hifi reads, creating a 795MB assembly anchoring to 26 chromosomes. There was initially a mixup with the data availability but after review this was resolved and all data is publicly available. This data allows study of cryptic diversity in Clupea and its evolutionary history in the subarctic.
This evaluation refers to version 1 of the preprint
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Abstract
ABSTRACT Pacific herring (Clupea pallasii) serve as a critical trophic link between plankton and many marine species targeted by fisheries. With a broad distribution throughout the North Pacific Ocean, from the Arctic to temperate latitudes, herring hold ecological, economic, and cultural importance. Despite this importance, genomic resources for this species, such as reference genome sequences, have only recently become available. To date, only one scaffold-level reference genome, representing a specimen from the Gulf of Alaska (Vancouver; 1,379 scaffolds), has been published to NCBI. Addressing this data gap, we produced a high quality 795 Mb genome sequence organized into 26 chromosomes combining long read sequencing with short read sequencing of proximity ligation libraries. Our assembly is highly complete (BUSCO score of 97.7%) and contiguous (922 contigs, N50 = 7,338,470, L50 = 38; 26 scaffolds, N50 = 31,494,017; L50 = 12). Pacific herring from the Bering Sea are genetically differentiated from those south of the Aleutian Islands and the Alaska Peninsula, making a reference genome from the eastern Bering Sea an important addition to the Pacific herring’s genomic toolbox.
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Editors Assessment:
Here is a Data Release article sharing the reference genome of the Pacific herring (Clupea pallasii), a species with broad ecological, economic, and cultural importance. This specimen coming from the eastern Bering Sea which are genetically quite different from those from the Gulf of Alaska. This high-quality chromosome-scale reference was built from Hi-C and PacBio Hifi reads, creating a 795MB assembly anchoring to 26 chromosomes. There was initially a mixup with the data availability but after review this was resolved and all data is publicly available. This data allows study of cryptic diversity in Clupea and its evolutionary history in the subarctic.
This evaluation refers to version 1 of the preprint
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Pacific herring (Clupea pallasii) serve as a critical trophic link between plankton and many marine species targeted by fisheries. With a broad distribution throughout the North Pacific Ocean, from the Arctic to temperate latitudes, herring hold ecological, economic, and cultural importance. Despite this importance, genomic resources for this species, such as reference genome sequences, have only recently become available. To date, only one scaffold-level reference genome, representing a specimen from the Gulf of Alaska (Vancouver; 1,379 scaffolds), has been published to NCBI. Addressing this data gap, we produced a high quality 795Mb genome sequence organized into 26 chromosomes combining long read sequencing with short read sequencing of proximity ligation libraries. Our assembly is highly complete (BUSCO score of 97.7%) and …
Pacific herring (Clupea pallasii) serve as a critical trophic link between plankton and many marine species targeted by fisheries. With a broad distribution throughout the North Pacific Ocean, from the Arctic to temperate latitudes, herring hold ecological, economic, and cultural importance. Despite this importance, genomic resources for this species, such as reference genome sequences, have only recently become available. To date, only one scaffold-level reference genome, representing a specimen from the Gulf of Alaska (Vancouver; 1,379 scaffolds), has been published to NCBI. Addressing this data gap, we produced a high quality 795Mb genome sequence organized into 26 chromosomes combining long read sequencing with short read sequencing of proximity ligation libraries. Our assembly is highly complete (BUSCO score of 97.7%) and contiguous (922 contigs, N50 = 7,338,470, L50 = 38; 26 scaffolds, N50 = 31,494,017; L50 = 12). Pacific herring south of the Aleutian Islands and the Alaska Peninsula are genetically differentiated from those in the Bering Sea, making a reference genome from the eastern Bering Sea an important addition to the Pacific herring’s genomic toolbox.
A peer reviewed version of this paper is published in GigaByte (doi: 10.46471/gigabyte.182) with open peer reviews under a CC-BY license. These reviews were as follows:
Reviewer 1. Mats Pettersson
Are all data available and do they match the descriptions in the paper?
No. I could not find any records associated with accession JBTGUN000000000. However, the supplied biosample ID (SAMN54268497) is correct, and leads to this project: PRJNA1392659, which contains the expected datasets.
Additional Comments:
Except for the accession mixup indicated above, I have no critical comments. I am convinced this genome is of high quality, and will prove a useful resource for the scientific community..
Reviewer 2. Shengyong Xu
Are all data available and do they match the descriptions in the paper?
No. The authors reported that the final assembly consisted of 26 scaffolds, with an N50 of 31 Mb and an L50 of 12; however, the final assembly comprised 322 sequences (GenBank accession JBTGUN000000000.1), including 26 chromosome-level scaffolds and 296 unanchored sequences. The authors should have included information on the unanchored sequences in their statistics to avoid the misunderstanding that the final assembly contains only 26 chromosome-level sequences.
Is there sufficient detail in the methods and data-processing steps to allow reproduction?
No. In the phylogenetic analysis, the authors should describe the process for accessing and filtering 500 protein-coding genes.
Additional Comments:
- Table 1, GC content data should be rounded to two decimal places, consistent with the description in the main text. 2. Line 3, Page 7, in "Genome assembly validation" section, the scaffold data entries 323, 1496, and 1380 appear to contain mitochondrial genome sequences; the authors are advised to verify this. 3. What do the percentages on the branches of the phylogenetic tree in Figure 2 denote? The authors should provide specific notes. Furthermore, the 68% support level suggests potential taxonomic misidentification; the authors need to clarify the accuracy of the species identification, for example, by conducting DNA barcoding analysis using mitochondrial 12S or COI gene fragments.
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