
==== Front
Wellcome Open Res
Wellcome Open Res
Wellcome Open Research
2398-502X
F1000 Research Limited London, UK

39221441
10.12688/wellcomeopenres.22823.1
Data Note
Articles
The genome sequence of a segmented worm, Terebella lapidaria Linnaeus, 1767
[version 1; peer review: 3 approved]

Darbyshire Teresa Investigation Resources Writing – Original Draft Preparation https://orcid.org/0000-0003-2256-9807
1
Adkins Patrick Investigation Resources Writing – Original Draft Preparation Writing – Review & Editing 2
Holmes Anna Investigation Resources 1
Bishop John Investigation Resources 2
Mieszkowska Nova Investigation Resources https://orcid.org/0000-0002-9570-7759
2
Marine Biological Association Genome Acquisition Lab
Darwin Tree of Life Barcoding collective
Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team
Wellcome Sanger Institute Scientific Operations: Sequencing Operations
Wellcome Sanger Institute Tree of Life Core Informatics team
Tree of Life Core Informatics collective
Darwin Tree of Life Consortiuma
1 Amgueddfa Cymru, Cardiff, Wales, UK
2 The Marine Biological Association, Plymouth, England, UK
a mark.blaxter@sanger.ac.uk
No competing interests were disclosed.

7 8 2024
2024
9 43224 7 2024
Copyright: © 2024 Darbyshire T et al.
2024
https://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

We present a genome assembly from an individual Terebella lapidaria (segmented worm; Annelida; Polychaeta; Terebellida; Terebellidae). The genome sequence spans 765.20 megabases. Most of the assembly is scaffolded into 16 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 15.97 kilobases in length.

Terebella lapidaria
a segmented worm
genome sequence
chromosomal
Terebellida
Wellcome Trust218328 206194 This work was supported by Wellcome through core funding to the Wellcome Sanger Institute [206194, <a href=https://doi.org/10.35802/206194>https://doi.org/10.35802/206194</a>] and the Darwin Tree of Life Discretionary Award [218328, <a href=https://doi.org/10.35802/218328>https://doi.org/10.35802/218328 </a>]. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
==== Body
pmcSpecies taxonomy

Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Protostomia; Spiralia; Lophotrochozoa; Annelida; Polychaeta; Sedentaria; Canalipalpata; Terebellida; Terebelliformia; Terebellidae ; Terebella; Terebella lapidaria Linnaeus, 1767 (NCBI:txid1131437).

Background

Terebella lapidaria Linnaeus, 1767 is a large-bodied polychaete of the family Terebellidae sensu stricto, originally described from the Mediterranean Sea ( Gil, 2011; Lavesque et al., 2021). It has also been recorded from the Adriatic and Aegean Seas as well as the Atlantic coast of France and the southern coast of the UK ( Fauvel, 1927; Gil, 2011; Lavesque et al., 2021; Linnaeus, 1767; NBN Trust Partnership, 2024), although its status in Atlantic regions is considered uncertain at this time until specimens can be compared to those from the Mediterranean ( Lavesque et al., 2021). Around the UK specifically, Terebella lapidaria has been recorded from Devon and Cornwall, along the south-west coast of England and the Bristol Channel, and is considered a non-native species of interest to Northern Ireland.

This species primarily inhabits shallow and intertidal waters, under rocks, in rock or shale crevices, shale gravel or muddy bottoms ( Gil, 2011; Lavesque et al., 2021; Marine Biological Association, 1957). They can reach 80–160 segments in size and up to 9 centimetres in length ( Fauvel, 1927).

The genus Terebella is characterised by having notochaetae on more than 25 segments with no clear definition between thorax and abdomen, and three pairs of branched branchiae. Of 37 species currently recognised within the genus, only T. lapidaria and Terebella banksyi Lavesque, Daffe, Londoño-Mesa & Hutchings, 2021 occur either around or in close proximity to the UK. Terebella banksyi is currently known only from its type locality in Arcachon Bay, France. The two species can be distinguished through the placement of the branchial pairs (on segments II–IV on T. lapidaria and discontinuous on segments II–III and segment V on T. banksyi) and the number of nephridial and genital papillae (five pairs on T. lapidaria, twelve pairs on T. banksyi) ( Lavesque et al., 2021).

The genome of Terebella lapidaria was sequenced as part of the Darwin Tree of Life Project, and represents the first of its kind for this species.

Genome sequence report

The genome of an adult Terebella lapidaria ( Figure 1) was sequenced using Pacific Biosciences single-molecule HiFi long reads, generating a total of 22.32 Gb (gigabases) from 2.37 million reads, providing approximately 34-fold coverage. Primary assembly contigs were scaffolded with chromosome conformation Hi-C data, which produced 137.71 Gbp from 911.98 million reads, yielding an approximate coverage of 180-fold. Specimen and sequencing information is summarised in Table 1.

Figure 1. Photograph of the Terebella lapidaria (wtTerLapi1) specimen used for genome sequencing.

Table 1. Specimen and sequencing data for Terebella lapidaria.

Project information	
Study title	Terebella lapidaria ((a segmented worm))	
Umbrella BioProject	PRJEB59382	
Species	Terebella lapidaria	
BioSample	SAMEA8724784	
NCBI taxonomy ID	1131437	
Specimen information	
Technology	ToLID	BioSample accession	Organism part	
PacBio long read sequencing	wtTerLapi1	SAMEA8724848	Anterior body	
Hi-C sequencing	wtTerLapi3	SAMEA110451062	Mid body	
RNA sequencing	wtTerLapi3	SAMEA110451061	Posterior body	
Sequencing information	
Platform	Run accession	Read count	Base count (Gb)	
Hi-C Illumina NovaSeq 6000	ERR10851521	9.12e+08	137.71	
PacBio Sequel IIe	ERR10841323	5.49e+05	4.02	
PacBio Sequel IIe	ERR10841324	2.37e+06	22.32	
RNA Illumina NovaSeq X	ERR12765137	6.82e+07	10.3	

Manual assembly curation corrected 32 missing joins or mis-joins and 13 haplotypic duplications, reducing the assembly length by 0.8% and the scaffold number by 3.03%. The final assembly has a total length of 765.20 Mb in 576 sequence scaffolds with a scaffold N50 of 44.0 Mb ( Table 2). The snail plot in Figure 2 provides a summary of the assembly statistics, while the distribution of assembly scaffolds on GC proportion and coverage is shown in Figure 3. The cumulative assembly plot in Figure 4 shows curves for subsets of scaffolds assigned to different phyla. Most (97.22%) of the assembly sequence was assigned to 16 chromosomal-level scaffolds. Chromosome-scale scaffolds confirmed by the Hi-C data are named in order of size ( Figure 5; Table 3). While not fully phased, the assembly deposited is of one haplotype. Contigs corresponding to the second haplotype have also been deposited. The mitochondrial genome was also assembled and can be found as a contig within the multifasta file of the genome submission.

Table 2. Genome assembly data for Terebella lapidaria, wtTerLapi1.1.

Genome assembly	
Assembly name	wtTerLapi1.1	
Assembly accession	GCA_949152475.1	
Accession of alternate haplotype	GCA_949152485.1	
Span (Mb)	765.20	
Number of contigs	820	
Contig N50 length (Mb)	6.7	
Number of scaffolds	576	
Scaffold N50 length (Mb)	44.0	
Longest scaffold (Mb)	100.83	
Assembly metrics *	Benchmark	
Consensus quality (QV)	60.0	≥ 50	
k-mer completeness	100.0%	≥ 95%	
BUSCO **	C:96.3%[S:95.0%,D:1.3%],
F:1.9%,M:1.8%,n:954	C ≥ 95%	
Percentage of assembly
mapped to chromosomes	97.22%	≥ 95%	
Sex chromosomes	None	localised homologous pairs	
Organelles	Mitochondrial genome: 15.97 kb	complete single alleles	
* Assembly metric benchmarks are adapted from column VGP-2020 of “Table 1: Proposed standards and metrics for defining genome assembly quality” from Rhie et al. (2021).

** BUSCO scores based on the metazoa_odb10 BUSCO set using version 5.4.3. C = complete [S = single copy, D = duplicated], F = fragmented, M = missing, n = number of orthologues in comparison. A full set of BUSCO scores is available at https://blobtoolkit.genomehubs.org/view/wtTerLapi1_1/dataset/wtTerLapi1_1/busco.

Figure 2. Genome assembly of Terebella lapidaria, wtTerLapi1.1: metrics.

The BlobToolKit Snailplot shows N50 metrics and BUSCO gene completeness. The main plot is divided into 1,000 size-ordered bins around the circumference with each bin representing 0.1% of the 765,247,992 bp assembly. The distribution of scaffold lengths is shown in dark grey with the plot radius scaled to the longest scaffold present in the assembly (100,833,644 bp, shown in red). Orange and pale-orange arcs show the N50 and N90 scaffold lengths (43,950,887 and 34,304,479 bp), respectively. The pale grey spiral shows the cumulative scaffold count on a log scale with white scale lines showing successive orders of magnitude. The blue and pale-blue area around the outside of the plot shows the distribution of GC, AT and N percentages in the same bins as the inner plot. A summary of complete, fragmented, duplicated and missing BUSCO genes in the metazoa_odb10 set is shown in the top right. An interactive version of this figure is available at https://blobtoolkit.genomehubs.org/view/wtTerLapi1_1/dataset/wtTerLapi1_1/snail.

Figure 3. Genome assembly of Terebella lapidaria, wtTerLapi1.1: BlobToolKit GC-coverage plot.

Sequences are coloured by phylum. Circles are sized in proportion to sequence length. Histograms show the distribution of sequence length sum along each axis. An interactive version of this figure is available at https://blobtoolkit.genomehubs.org/view/wtTerLapi1_1/dataset/wtTerLapi1_1/blob.

Figure 4. Genome assembly of Terebella lapidaria, wtTerLapi1.1: BlobToolKit cumulative sequence plot.

The grey line shows cumulative length for all sequences. Coloured lines show cumulative lengths of sequences assigned to each phylum using the buscogenes taxrule. An interactive version of this figure is available at https://blobtoolkit.genomehubs.org/view/wtTerLapi1_1/dataset/wtTerLapi1_1/cumulative.

Figure 5. Genome assembly of Terebella lapidaria, wtTerLapi1.1: Hi-C contact map of the wtTerLapi1.1 assembly, visualised using HiGlass.

Chromosomes are shown in order of size from left to right and top to bottom. An interactive version of this figure may be viewed at https://genome-note-higlass.tol.sanger.ac.uk/l/?d=BaRPjPiNRWWAmO2tmlp1Kw.

Table 3. Chromosomal pseudomolecules in the genome assembly of Terebella lapidaria, wtTerLapi1.

INSDC accession	Name	Length (Mb)	GC%	
OX424555.1	1	100.83	41.0	
OX424556.1	2	61.85	41.5	
OX424557.1	3	56.41	42.0	
OX424558.1	4	48.06	41.0	
OX424559.1	5	45.2	41.5	
OX424560.1	6	44.13	41.0	
OX424561.1	7	43.95	41.5	
OX424562.1	8	43.11	41.0	
OX424563.1	9	41.54	42.0	
OX424564.1	10	41.56	41.0	
OX424565.1	11	40.88	41.0	
OX424566.1	12	40.61	41.5	
OX424567.1	13	37.36	41.0	
OX424568.1	14	34.35	41.0	
OX424569.1	15	34.3	40.5	
OX424570.1	16	28.56	40.5	
OX424571.1	MT	0.02	34.5	

The estimated Quality Value (QV) of the final assembly is 60.0 with k-mer completeness of 100.0%, and the assembly has a BUSCO v5.4.3 completeness of 96.3% (single = 95.0%, duplicated = 1.3%), using the metazoa_odb10 reference set ( n = 954).

Metadata for specimens, BOLD barcode results, spectra estimates, sequencing runs, contaminants and pre-curation assembly statistics are given at https://links.tol.sanger.ac.uk/species/1131437.

Methods

Sample acquisition

Adult specimens of Terebella lapidaria were collected Batten Bay, Devon, UK (latitude 50.36, longitude –4.13) on 2020-11-15. The specimens were collected by Patrick Adkins, John Bishop, Nova Mieszkowska (all Marine Biological Association) and Teresa Darbyshire and Anna Holmes (both Amgueddfa Cymru) and identified by Teresa Darbyshire. The specimens were preserved by liquid nitrogen. One specimen (specimen ID MBA-201115-002C, ToLID wtTerLapi1) was used for PacBio DNA sequencing, and another (specimen ID MBA-201115-002E, ToLID wtTerLapi3) for Hi-C and RNA sequencing.

The initial species identification was verified by an additional DNA barcoding process according to the framework developed by Twyford et al. (2024). A small sample was dissected from the specimen and stored in ethanol, while the remaining parts of the specimen were shipped on dry ice to the Wellcome Sanger Institute (WSI). The tissue was lysed, the COI marker region was amplified by PCR, and amplicons were sequenced and compared to the BOLD database, confirming the species identification ( Crowley et al., 2023). Following whole genome sequence generation, the relevant DNA barcode region was also used alongside the initial barcoding data for sample tracking at the WSI ( Twyford et al., 2024). The standard operating procedures for Darwin Tree of Life barcoding have been deposited on protocols.io ( Beasley et al., 2023).

Nucleic acid extraction

The workflow for high molecular weight (HMW) DNA extraction at the WSI Tree of Life Core Laboratory includes a sequence of core procedures: sample preparation; sample homogenisation, DNA extraction, fragmentation, and clean-up. In sample preparation, the wtTerLapi1 sample was weighed and dissected on dry ice ( Jay et al., 2023). Tissue from the anterior body was homogenised using a PowerMasher II tissue disruptor ( Denton et al., 2023a).

HMW DNA was extracted using the Automated MagAttract v1 protocol ( Sheerin et al., 2023). DNA was sheared into an average fragment size of 12–20 kb in a Megaruptor 3 system ( Todorovic et al., 2023). Sheared DNA was purified by solid-phase reversible immobilisation ( Strickland et al., 2023): in brief, the method employs AMPure PB beads to eliminate shorter fragments and concentrate the DNA. The concentration of the sheared and purified DNA was assessed using a Nanodrop spectrophotometer and Qubit Fluorometer using the Qubit dsDNA High Sensitivity Assay kit. Fragment size distribution was evaluated by running the sample on the FemtoPulse system.

RNA was extracted from posterior body tissue of wtTerLapi3 in the Tree of Life Laboratory at the WSI using the RNA Extraction: Automated MagMax™ mirVana protocol ( do Amaral et al., 2023). The RNA concentration was assessed using a Nanodrop spectrophotometer and a Qubit Fluorometer using the Qubit RNA Broad-Range Assay kit. Analysis of the integrity of the RNA was done using the Agilent RNA 6000 Pico Kit and Eukaryotic Total RNA assay.

Protocols developed by the WSI Tree of Life laboratory are publicly available on protocols.io ( Denton et al., 2023b).

Sequencing

Pacific Biosciences HiFi circular consensus DNA sequencing libraries were constructed according to the manufacturers’ instructions. Poly(A) RNA-Seq libraries were constructed using the NEB Ultra II RNA Library Prep kit. DNA and RNA sequencing was performed by the Scientific Operations core at the WSI on Pacific Biosciences Sequel IIe (HiFi) and Illumina NovaSeq X (RNA-Seq) instruments. Hi-C data were also generated from mid-body tissue of wtTerLapi3 using the Arima-HiC v2 kit. The Hi-C sequencing was performed using paired-end sequencing with a read length of 150 bp on the Illumina NovaSeq 6000 instrument.

Genome assembly, curation and evaluation

Assembly

Original assembly of HiFi reads was performed using Hifiasm ( Cheng et al., 2021) with the --primary option. Haplotypic duplications were identified and removed with purge_dups ( Guan et al., 2020). Hi-C reads were further mapped with bwa-mem2 ( Vasimuddin et al., 2019) to the primary contigs, which were further scaffolded using the provided Hi-C data ( Rao et al., 2014) in YaHS ( Zhou et al., 2023) using the --break option. Scaffolded assemblies were evaluated using Gfastats ( Formenti et al., 2022), BUSCO ( Manni et al., 2021) and MERQURY.FK ( Rhie et al., 2020).

The mitochondrial genome was assembled using MitoHiFi ( Uliano-Silva et al., 2023), which runs MitoFinder ( Allio et al., 2020) and uses these annotations to select the final mitochondrial contig and to ensure the general quality of the sequence.

Assembly curation

The assembly was decontaminated using the Assembly Screen for Cobionts and Contaminants (ASCC) pipeline (article in preparation). Manual curation was primarily conducted using PretextView ( Harry, 2022), with additional insights provided by JBrowse2 ( Diesh et al., 2023) and HiGlass ( Kerpedjiev et al., 2018). Scaffolds were visually inspected and corrected as described by Howe et al. (2021). Any identified contamination, missed joins, and mis-joins were corrected, and duplicate sequences were tagged and removed. The entire process is documented at https://gitlab.com/wtsi-grit/rapid-curation (article in preparation).

Evaluation of the final assembly

A Hi-C map for the final assembly was produced using bwa-mem2 ( Vasimuddin et al., 2019) in the Cooler file format ( Abdennur & Mirny, 2020). To assess the assembly metrics, the k-mer completeness and QV consensus quality values were calculated in Merqury ( Rhie et al., 2020). This work was done using Nextflow ( Di Tommaso et al., 2017) DSL2 pipelines “sanger-tol/readmapping” ( Surana et al., 2023a) and “sanger-tol/genomenote” ( Surana et al., 2023b). The genome was analysed within the BlobToolKit environment ( Challis et al., 2020) and BUSCO scores ( Manni et al., 2021; Simão et al., 2015) were calculated.

The genome assembly and evaluation pipelines were developed using the nf-core tooling ( Ewels et al., 2020), use MultiQC ( Ewels et al., 2016), and make extensive use of the Conda package manager, the Bioconda initiative ( Grüning et al., 2018), the Biocontainers infrastructure ( da Veiga Leprevost et al., 2017), and the Docker ( Merkel, 2014) and Singularity ( Kurtzer et al., 2017) containerisation solutions.

Table 4 contains a list of relevant software tool versions and sources.

Table 4. Software tools: versions and sources.

Software tool	Version	Source	
BlobToolKit	4.2.1	https://github.com/blobtoolkit/blobtoolkit	
BUSCO	5.3.2	https://gitlab.com/ezlab/busco	
Hifiasm	0.16.1-r375	https://github.com/chhylp123/hifiasm	
HiGlass	1.11.6	https://github.com/higlass/higlass	
Merqury	MerquryFK	https://github.com/thegenemyers/MERQURY.FK	
MitoHiFi	2	https://github.com/marcelauliano/MitoHiFi	
PretextView	0.2	https://github.com/wtsi-hpag/PretextView	
purge_dups	1.2.3	https://github.com/dfguan/purge_dups	
sanger-tol/genomenote	v1.0	https://github.com/sanger-tol/genomenote	
sanger-tol/readmapping	1.1.0	https://github.com/sanger-tol/readmapping/tree/1.1.0	
YaHS	1.2a	https://github.com/c-zhou/yahs	

Wellcome Sanger Institute – Legal and Governance

The materials that have contributed to this genome note have been supplied by a Darwin Tree of Life Partner. The submission of materials by a Darwin Tree of Life Partner is subject to the ‘Darwin Tree of Life Project Sampling Code of Practice’, which can be found in full on the Darwin Tree of Life website here. By agreeing with and signing up to the Sampling Code of Practice, the Darwin Tree of Life Partner agrees they will meet the legal and ethical requirements and standards set out within this document in respect of all samples acquired for, and supplied to, the Darwin Tree of Life Project.

Further, the Wellcome Sanger Institute employs a process whereby due diligence is carried out proportionate to the nature of the materials themselves, and the circumstances under which they have been/are to be collected and provided for use. The purpose of this is to address and mitigate any potential legal and/or ethical implications of receipt and use of the materials as part of the research project, and to ensure that in doing so we align with best practice wherever possible. The overarching areas of consideration are:

•     Ethical review of provenance and sourcing of the material

•     Legality of collection, transfer and use (national and international)

Each transfer of samples is further undertaken according to a Research Collaboration Agreement or Material Transfer Agreement entered into by the Darwin Tree of Life Partner, Genome Research Limited (operating as the Wellcome Sanger Institute), and in some circumstances other Darwin Tree of Life collaborators.

Data availability

European Nucleotide Archive: Terebella lapidaria (a segmented worm). Accession number PRJEB59382; https://identifiers.org/ena.embl/PRJEB59382 ( Wellcome Sanger Institute, 2023). The genome sequence is released openly for reuse. The Terebella lapidaria genome sequencing initiative is part of the Darwin Tree of Life (DToL) project. All raw sequence data and the assembly have been deposited in INSDC databases. The genome will be annotated using available RNA-Seq data and presented through the Ensembl pipeline at the European Bioinformatics Institute. Raw data and assembly accession identifiers are reported in Table 1 and Table 2.

Author information

Members of the Marine Biological Association Genome Acquisition Lab are listed here: https://doi.org/10.5281/zenodo.8382513.

Members of the Darwin Tree of Life Barcoding collective are listed here: https://doi.org/10.5281/zenodo.4893703.

Members of the Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team are listed here: https://doi.org/10.5281/zenodo.10066175.

Members of Wellcome Sanger Institute Scientific Operations: Sequencing Operations are listed here: https://doi.org/10.5281/zenodo.10043364.

Members of the Wellcome Sanger Institute Tree of Life Core Informatics team are listed here: https://doi.org/10.5281/zenodo.10066637.

Members of the Tree of Life Core Informatics collective are listed here: https://doi.org/10.5281/zenodo.5013541.

Members of the Darwin Tree of Life Consortium are listed here: https://doi.org/10.5281/zenodo.4783558.

10.21956/wellcomeopenres.25130.r95053
Reviewer response for version 1
Wasmuth James 1Referee https://orcid.org/0000-0002-9516-212X

1 Faculty of Veterinary Medicine, University of Calgary, Calgary, Alberta, Canada
6 9 2024 Copyright: © 2024 Wasmuth J
2024
https://creativecommons.org/licenses/by/4.0/ This is an open access peer review report distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Version 1recommendationapprove
The authors present a high quality genome assembly for Terebella lapidaria.

Background

The presented rationale for creating a genome assembly for T. lapidaria could be improved. The authors should elaborate on "[T]he first of its kind for this species." At which taxonomic rank is this assembly the first? Are there additional compelling reasons for sequencing this species: conservation, invasive species, model of animal development/biochemistry? I'm genuinely interested.

Data report

The authors should comment on the high proportion of contamination from Brachiopoda that is identified by Blobtools (Figure 3). Further, in Figure 4 the light green Annelida line obscured by the darker green Brachiopod line.

Methods

BUSCO: The authors need to confirm which version of they used: in the main text 5.4.3 vs in table 4 5.3.2. They should also specify which alignment tools they used within BUSCO (e.g. augustus vs metaeuk) as these can lead to considerable differences in the score.

Other considerations

Given that the authors carried out RNA-Seq, I would have welcomed a first pass at genome annotation; how many protein coding genes could be prediction.

The mitochondrial genome has been assembled but no annotation is presented, e.g. size, tRNAs, genes.

Are sufficient details of methods and materials provided to allow replication by others?

Partly

Is the rationale for creating the dataset(s) clearly described?

Partly

Are the datasets clearly presented in a useable and accessible format?

Yes

Are the protocols appropriate and is the work technically sound?

Yes

Reviewer Expertise:

Invertebrate genomics, transcriptomics, evolutionary biochemistry

I confirm that I have read this submission and believe that I have an appropriate level of expertise to confirm that it is of an acceptable scientific standard.

10.21956/wellcomeopenres.25130.r93506
Reviewer response for version 1
Dayi Mehmet 1Referee https://orcid.org/0000-0002-5367-918X

1 Düzce University, Düzce,, Turkey
30 8 2024 Copyright: © 2024 Dayi M
2024
https://creativecommons.org/licenses/by/4.0/ This is an open access peer review report distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Version 1recommendationapprove
Background section

For the figure 1 (specimen figure) it would be good to use a bar describing length of the specimen since the authors mention about different lenght of this species (....They can reach 80–160 segments in size and up to 9 centimetres in length (Fauvel, 1927)....).

Genome sequence report

The BUSCO tool version number should be checked and be consistent with that mentioned in Table 4. 

Assembly curation section

The authors should provide more details about decontamination of the assembly since they used their own work which is in preparation (article in preparation). .... The assembly was decontaminated using the Assembly Screen for Cobionts and Contaminants (ASCC) pipeline (article in preparation).... 

Additionally, the authors provide more details and clear explanation of the entire process. In the current form of the method it is not clear since the authors again used their unpublished work (article in preparation). Besides, the link (https://gitlab.com/wtsi-grit/rapid-curation) provided for the entire process does not clearly show the entire process.

Are sufficient details of methods and materials provided to allow replication by others?

Partly

Is the rationale for creating the dataset(s) clearly described?

Partly

Are the datasets clearly presented in a useable and accessible format?

Yes

Are the protocols appropriate and is the work technically sound?

Yes

Reviewer Expertise:

Genome evolution.

I confirm that I have read this submission and believe that I have an appropriate level of expertise to confirm that it is of an acceptable scientific standard.

10.21956/wellcomeopenres.25130.r95060
Reviewer response for version 1
Nilsson Maria 1Referee https://orcid.org/0000-0002-8136-7263

1 Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Germany
29 8 2024 Copyright: © 2024 Nilsson M
2024
https://creativecommons.org/licenses/by/4.0/ This is an open access peer review report distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Version 1recommendationapprove
The nuclear genome has been sequenced from the marine segmented worm Terebella lapidaria. The species occur in the mediterranean but is also found in French and UK waters. Two individuals were used for the genome assembly. The individuals were DNA barcoded before the nuclear genome was sequenced.

The assembly is based on pacbio longread sequences and HiC. The final length of the manual curated assembly is 765Mb and contain 16 chromosomal pseudomolecules. It was not possible to assemble the sex chromosomes. The contig N50 length is 6.7 Mb. The BUSCO score, which counts the number of complete benchmarking genes is 96.3%.

The overall QV value is 60. The statistics indicate that it is a good assembly which is generally difficult to achieve from marine soft-bodied animals.

Minor comments:

1) in the background it is stated that the genome assembly of Terebella lapidaria is "the first of its kind". Please clarify in what sense it is the first, is it the first from that family, genus etc.?

Are sufficient details of methods and materials provided to allow replication by others?

Yes

Is the rationale for creating the dataset(s) clearly described?

Yes

Are the datasets clearly presented in a useable and accessible format?

Yes

Are the protocols appropriate and is the work technically sound?

Yes

Reviewer Expertise:

phylogenomics, transposable elements, mitogenomics

I confirm that I have read this submission and believe that I have an appropriate level of expertise to confirm that it is of an acceptable scientific standard.

Competing interests: No competing interests were disclosed.

Competing interests: No competing interests were disclosed.

Competing interests: No competing interests were disclosed.
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