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Wellcome Open Res
Wellcome Open Res
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10.12688/wellcomeopenres.19664.2
Data Note
Articles
The genome sequence of wood avens, Geum urbanum L., 1753
[version 2; peer review: 3 approved]

Christenhusz Maarten J. M. Investigation Resources Writing – Review & Editing https://orcid.org/0000-0003-1398-8743
1
Lu Meng Writing – Original Draft Preparation Writing – Review & Editing https://orcid.org/0000-0002-2921-1632
23
Royal Botanic Gardens Kew Genome Acquisition Lab
Royal Botanic Garden Edinburgh Genome Acquisition Lab
Plant Genome Sizing collective
Darwin Tree of Life Barcoding collective
Wellcome Sanger Institute Tree of Life programme
Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective
Tree of Life Core Informatics collective
Darwin Tree of Life Consortiuma
1 Royal Botanic Gardens Kew, Richmond, England, UK
2 The University of Edinburgh, Edinburgh, Scotland, UK
3 Royal Botanic Garden Edinburgh, Edinburgh, Scotland, UK
a mark.blaxter@sanger.ac.uk
No competing interests were disclosed.

16 7 2024
2023
8 37110 7 2024
Copyright: © 2024 Christenhusz MJM 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 Geum urbanum the (wood avens; Streptophyta; Magnoliopsida; Rosales; Rosaceae). The genome sequence is 1,304.9 megabases in span. Most of the assembly is scaffolded into 21 chromosomal pseudomolecules. The mitochondrial and plastid genomes have also been assembled and are 335.5 and 156.1 kilobases in length respectively. Gene annotation of this assembly on Ensembl identified 50,336 protein-coding genes.

Geum urbanum
wood avens
genome sequence
chromosomal; Rosales
Wellcome Trust218328 Wellcome Trust206194 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>). Revised Amendments from Version 1

The genome assembly presented here has been annotated by the European Bioinformatics Institute since the first version of this data note, and we have updated the article by linking to the annotation data and method.
==== Body
pmcSpecies taxonomy

Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae; rosids; fabids; Rosales; Rosaceae; Rosoideae; Colurieae; Geum; Geum urbanum (Linnaeus 1753) (NCBI:txid57919).

Background

Geum urbanum L. (Rosaceae) is a widespread European perennial herb, the range of which extends to western Asia, western Siberia, and the northwest coast of Africa ( Taylor, 1997). It is native to Britain and Ireland and occurs abundantly, except in some parts of northern Scotland and Ireland ( Preston et al., 2002; Stace et al., 2019). Implied by its common name, wood avens, G. urbanum typically grows in woodland, shrubland, and hedgerows with well-drained conditions, but is also found in disturbed and more open habitats, waste grounds, gardens and parks ( Ruhsam et al., 2011; Taylor, 1997). It is a predominantly self-pollinating species with the outcrossing rates ranging from 0.058 to 0.177 in natural populations ( Ruhsam et al., 2010), yet its small, erect, yellow flowers can still attract pollinators ( Figure 1). The achene fruits of G. urbanum have a single hook ( Figure 1), which makes the seeds well-adapted to dispersal by animals ( Chen et al., 2013; Gorb & Gorb, 2002; Smedmark & Eriksson, 2006).

Figure 1. Ge um urbanum (not the sampled specimen) growing in secondary woodland.

( a) The plant habit with five-petal flowers in late May. ( b) Two small insects visiting the flower of G. urbanum. ( c) A fruiting head of G. urbanum. Photos taken by Meng Lu.

Cytogenetic evidence shows that G. urbanum is an ancient hexaploid (2 n = 42) ( Gajewski, 1957; Gajewski, 1958), with molecular studies suggesting that allopolyploidisation gave rise to this hexaploid lineage in Rosoideae ( Gajewski, 1957; Smedmark et al., 2005; Smedmark et al., 2003). However, recent genetic studies show that this species largely behaves as a diploid, although with some additional duplicated gene copies ( Jordan et al., 2018; Ruhsam, 2009). This species is known for its rampant hybridisation with a closely related species, G. rivale, where both occur in close proximity. These two species have several contrasting attributes, including mating system, flower morphology and habitat preference. Apart from its interesting biological features, many of the secondary metabolites of G. urbanum have important pharmacological uses ( Al-Snafi, 2019).

This genome will be extremely helpful for evolutionary studies aimed at understanding historical and contemporary hybridisation ( Jordan et al., 2018; Ruhsam et al., 2011) and the genetic basis of the selfing syndrome ( Sicard & Lenhard, 2011). It will also further contribute to uncovering the potential medical value of compounds produced by G. urbanum.

Genome sequence report

The genome was sequenced from a Geum urbanum specimen collected from a garden bed at the Royal Botanic Gardens, Kew (latitude 51.48, longitude –0.30). Using flow cytometry, the genome size (1C-value) was estimated to be 1.64 pg, equivalent to 1,610 Mb. A total of 27-fold coverage in Pacific Biosciences single-molecule HiFi long reads and 64-fold coverage in 10X Genomics read clouds were generated. Primary assembly contigs were scaffolded with chromosome conformation Hi-C data. Manual assembly curation corrected 5 missing joins or mis-joins and removed one haplotypic duplication, reducing the scaffold number by 13.33%.

The final assembly has a total length of 1,304.9 Mb in 26 sequence scaffolds with a scaffold N50 of 65.2 Mb ( Table 1). Most (99.95%) of the assembly sequence was assigned to 21 chromosomal-level scaffolds. Chromosome-scale scaffolds confirmed by the Hi-C data are named in order of size ( Figure 2– Figure 5; Table 2).

Table 1. Genome data for Geum urbanum, drGeuUrba1.1.

Project accession data	
Assembly identifier	drGeuUrba1.1	
Species	Geum urbanum	
Specimen	drGeuUrba1	
NCBI taxonomy ID	57919	
BioProject	PRJEB48840	
BioSample ID	SAMEA7522180	
Isolate information	leaf tissue; drGeuUrba1 – Monoecious	
Assembly metrics *	Benchmark	
Consensus quality (QV)	59.6	≥ 50	
k-mer completeness	99.99%	≥ 95%	
BUSCO **	C:98.7%[S:18.6%,D:80.1%],
F:0.3%,M:1.1%,n:2,326	C ≥ 95%	
Percentage of assembly mapped
to chromosomes	99.95%	≥ 95%	
Sex chromosomes	Not applicable	localised homologous pairs	
Organelles	Mitochondrial and plastid
genomes assembled.	complete single alleles	
Raw data accessions	
PacificBiosciences SEQUEL II	ERR7419408, ERR7419409	
10X Genomics Illumina	ERR7417841–ERR7417844	
Hi-C Illumina	ERR7417845	
PolyA RNA-Seq Illumina	ERR9435030	
Genome assembly	
Assembly accession	GCA_946800695.1	
Accession of alternate haplotype	GCA_946800285.1	
Span (Mb)	1,304.9	
Number of contigs	113	
Contig N50 length (Mb)	19.5	
Number of scaffolds	26	
Scaffold N50 length (Mb)	65.2	
Longest scaffold (Mb)	94.2	
Genome annotation at Ensembl	
Number of protein-coding genes	50,336	
Number of non-coding genes	10,365	
Number of gene transcripts	75,552	
* 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 eudicots_odb10 BUSCO set using v5.3.2. 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/drGeuUrba1.1/dataset/CAMPEP01/busco.

Figure 2. Genome assembly of Geum urbanum, drGeuUrba1.1: 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 1,304,870,458 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 (94,240,583 bp, shown in red). Orange and pale-orange arcs show the N50 and N90 scaffold lengths (65,224,196 and 44,983,829 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 eudicots_odb10 set is shown in the top right. An interactive version of this figure is available at https://blobtoolkit.genomehubs.org/view/drGeuUrba1.1/dataset/CAMPEP01/snail.

Figure 3. Genome assembly of Geum urbanum, drGeuUrba1.1: GC coverage.

BlobToolKit GC-coverage plot. Scaffolds are coloured by phylum. Circles are sized in proportion to scaffold length. Histograms show the distribution of scaffold length sum along each axis. An interactive version of this figure is available at https://blobtoolkit.genomehubs.org/view/drGeuUrba1.1/dataset/CAMPEP01/blob.

Figure 4. Genome assembly of Geum urbanum, drGeuUrba1.1: cumulative sequence.

BlobToolKit cumulative sequence plot. The grey line shows cumulative length for all scaffolds. Coloured lines show cumulative lengths of scaffolds assigned to each phylum using the buscogenes taxrule. An interactive version of this figure is available at https://blobtoolkit.genomehubs.org/view/drGeuUrba1.1/dataset/CAMPEP01/cumulative.

Figure 5. Genome assembly of Geum urbanum, drGeuUrba1.1: Hi-C contact map.

Hi-C contact map of the drGeuUrba1.1 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=JSrsAc2aSfi-e9L51ilEkA.

Table 2. Chromosomal pseudomolecules in the genome assembly of Geum urbanum, drGeuUrba1.

INSDC
accession	Chromosome	Size
(Mb)	GC%	
OX326997.1	1	94.24	40.1	
OX326998.1	2	90.78	39.9	
OX326999.1	3	82.87	40	
OX327000.1	4	81.92	39.9	
OX327001.1	5	76.26	40	
OX327002.1	6	68.51	40.1	
OX327003.1	7	66.65	40.2	
OX327004.1	8	65.95	39.9	
OX327005.1	9	65.22	40.1	
OX327006.1	10	58.98	39.5	
OX327007.1	11	58.47	39.9	
OX327008.1	12	56.09	40.1	
OX327009.1	13	55.44	40.3	
OX327010.1	14	52.82	40.2	
OX327011.1	15	51.58	39.7	
OX327012.1	16	51.37	40.1	
OX327013.1	17	48.95	39.7	
OX327014.1	18	48.17	40	
OX327015.1	19	44.98	39.7	
OX327016.1	20	43.17	40.1	
OX327017.1	21	41.87	39.8	
OX327018.1	MT	0.34	44.4	
OX327019.1	Pltd	0.16	36.8	

Genome annotation report

The Geum urbanum genome assembly (GCA_946800695.1) was annotated at the European Bioinformatics Institute (EBI) on Ensembl Rapid Release. The resulting annotation includes 75,552 transcribed mRNAs from 50,336 protein-coding and 10,365 non-coding genes ( Table 2; https://rapid.ensembl.org/Geum_urbanum_GCA_946800695.1/Info/Index). The average transcript length is 2,623.32. There are 1.24 coding transcripts per gene and 5.16 exons per transcript.

The estimated Quality Value (QV) of the final assembly is 59.6 with k-mer completeness of 99.99%, and the assembly has a BUSCO v5.3.2 completeness of 98.7% (single = 18.6%, duplicated = 80.1%), using the eudicots_odb10 reference set ( n = 2,326).

Metadata for specimens, spectral estimates, sequencing runs, contaminants and pre-curation assembly statistics can be found at https://links.tol.sanger.ac.uk/species/57919.

Methods

Sample acquisition, genome size estimation and nucleic acid extraction

A specimen of Geum urbanum (drGeuUrba1) was collected from Bed 227 of the Rhododendron Dell at the Royal Botanic Gardens, Kew (latitude 51.48, longitude –0.30) on 26 August 2020. The specimen was picked by hand from weedy vegetation on the edge of the lawn by Maarten Christenhusz (Royal Botanic Gardens, Kew), collection number 9055. The specimen was identified based on its morphology by Maarten Christenhusz, and was preserved by freezing at –80°C.

Using flow cytometry, the genome size (1C-value) was estimated using the fluorochrome propidium iodide and following the ‘one-step’ method outlined in Pellicer et al. (2021). Specifically for this species, the General Purpose Buffer (GPB) supplemented with 3% PVP and 0.08% (v/v) beta-mercaptoethanol was used for isolation of nuclei ( Loureiro et al., 2007), and the internal calibration standard was Petroselinum crispum ‘Champion Moss Curled’ with an assumed 1C-value of 2,200 Mb ( Obermayer et al., 2002).

DNA was extracted at the Tree of Life laboratory, Wellcome Sanger Institute (WSI). The drGeuUrba1 sample was weighed and dissected on dry ice with tissue set aside for Hi-C sequencing. Leaf tissue was cryogenically disrupted to a fine powder using a Covaris cryoPREP Automated Dry Pulveriser, receiving multiple impacts. High molecular weight (HMW) DNA was extracted using the Illustra Nucleon PhytoPure HMW DNA extraction kit. HMW DNA was sheared into an average fragment size of 12–20 kb in a Megaruptor 3 system with speed setting 30. Sheared DNA was purified by solid-phase reversible immobilisation using AMPure PB beads with a 1.8× ratio of beads to sample to remove the shorter fragments and concentrate the DNA sample. The concentration of the sheared and purified DNA was assessed using a Nanodrop spectrophotometer and Qubit Fluorometer and Qubit dsDNA High Sensitivity Assay kit. Fragment size distribution was evaluated by running the sample on the FemtoPulse system.

RNA was extracted from leaf tissue of drGeuUrba1 in the Tree of Life Laboratory at the WSI using TRIzol, according to the manufacturer’s instructions. RNA was then eluted in 50 μl RNAse-free water and its concentration assessed using a Nanodrop spectrophotometer and Qubit Fluorometer using the Qubit RNA Broad-Range (BR) Assay kit. Analysis of the integrity of the RNA was done using Agilent RNA 6000 Pico Kit and Eukaryotic Total RNA assay.

Sequencing

Pacific Biosciences HiFi circular consensus and 10X Genomics read cloud 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 were performed by the Scientific Operations core at the WSI on Pacific Biosciences SEQUEL II (HiFi), Illumina HiSeq 4000 (RNA-Seq) and Illumina NovaSeq 6000 (10X) instruments. Hi-C data were also generated from leaf tissue of drGeuUrba1 using the Arima v2 kit and sequenced on the Illumina NovaSeq 6000 instrument.

Genome assembly, curation and evaluation

Assembly was carried out with Hifiasm ( Cheng et al., 2021) and haplotypic duplication was identified and removed with purge_dups ( Guan et al., 2020). One round of polishing was performed by aligning 10X Genomics read data to the assembly with Long Ranger ALIGN, calling variants with FreeBayes ( Garrison & Marth, 2012). The assembly was then scaffolded with Hi-C data ( Rao et al., 2014) using YaHS ( Zhou et al., 2023). The assembly was checked for contamination and corrected as described previously ( Howe et al., 2021). Manual curation was performed using HiGlass ( Kerpedjiev et al., 2018) and Pretext ( Harry, 2022). The mitochondrial and chloroplast genomes were assembled using MBG ( Rautiainen & Marschall, 2021) from PacBio HiFi reads mapping to related genomes: a representative circular sequence was selected for each from the graph based on read coverage.

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.

Table 3 contains a list of relevant software tool versions and sources.

Table 3. Software tools: versions and sources.

Software tool	Version	Source	
BlobToolKit	4.0.7	https://github.com/blobtoolkit/blobtoolkit	
BUSCO	5.3.2	https://gitlab.com/ezlab/busco	
FreeBayes	1.3.1-17-gaa2ace8	https://github.com/freebayes/freebayes	
Hifiasm	0.15.3	https://github.com/chhylp123/hifiasm	
HiGlass	1.11.6	https://github.com/higlass/higlass	
Long Ranger
ALIGN	2.2.2	https://support.10xgenomics.com/genome-exome/
software/pipelines/latest/advanced/other-pipelines	
MBG	-	https://github.com/maickrau/MBG	
Merqury	MerquryFK	https://github.com/thegenemyers/MERQURY.FK	
PretextView	0.2	https://github.com/wtsi-hpag/PretextView	
purge_dups	1.2.3	https://github.com/dfguan/purge_dups	
YaHS	1	https://github.com/c-zhou/yahs	

Genome annotation

The Ensembl Genebuild annotation system ( Aken et al., 2016) was used to generate annotation for the Geum urbanum assembly (GCA_946800695.1) in Ensembl Rapid Release at the EBI. Annotation was created primarily through alignment of transcriptomic data to the genome, with gap filling via protein-to-genome alignments of a select set of proteins from UniProt ( UniProt Consortium, 2019).

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.

Acknowledgements

We thank Richard A. Ennos and Alex D. Twyford for helpful comments on the introduction section.

Data availability

European Nucleotide Archive: Geum urbanum. Accession number PRJEB48840; https://identifiers.org/ena.embl/PRJEB48840. ( Wellcome Sanger Institute, 2022)

The genome sequence is released openly for reuse. The Geum urbanum 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. Raw data and assembly accession identifiers are reported in Table 1.

Author information

Members of the Royal Botanic Gardens Kew Genome Acquisition Lab are listed here: https://doi.org/10.5281/zenodo.4786680.

Members of the Royal Botanic Garden Edinburgh Genome Acquisition Lab are listed here: https://doi.org/10.5281/zenodo.4786682.

Members of the Plant Genome Sizing collective are listed here: https://doi.org/10.5281/zenodo.7994306.

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 programme are listed here: https://doi.org/10.5281/zenodo.4783585.

Members of Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective are listed here: https://doi.org/10.5281/zenodo.4790455.

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

10.21956/wellcomeopenres.25107.r90007
Reviewer response for version 2
Maharajan Theivanayagam 1Referee
1 Division of Plant Molecular Biology and Biotechnology, Department of Biosciences, Rajagiri College of Social Sciences, Cochin, Kerala, India
1 9 2024 Copyright: © 2024 Maharajan T
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.
The author(s) is/are employees of the US Government and therefore domestic copyright protection in USA does not apply to this work. The work may be protected under the copyright laws of other jurisdictions when used in those jurisdictions.
Version 2recommendationapprove
Accept the manuscript without further delay

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

No

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

Partly

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

No

Are the protocols appropriate and is the work technically sound?

Partly

Reviewer Expertise:

Functional Genomics and Genome Editing

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.25107.r92345
Reviewer response for version 2
Chakraborty Abhisek 1Referee https://orcid.org/0009-0005-5393-889X

1 Johannes Gutenberg University of Mainz, Mainz, Germany
15 8 2024 Copyright: © 2024 Chakraborty A
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 2recommendationapprove
1. The Geum urbanum genome presented in this data note is a high-quality reference standard genome based on the reported assembly statistics. However, since previous studies indicated towards the polyploidy of this species, the authors should report the LAI score to further strengthen the assembly statistics. Also, the BUSCO score for the coding gene set should be reported.

2. Since the authors also assembled the mitochondrial and plastid genomes, these genome sequences should be deposited in a publicly available database. How many chloroplast and mitochondrial genes could be identified?

3. The scripts used for the analyses are valuable to the research community and should be publicly available.

4. In the abstract, “Most of the assembly” can be replaced with “99.95% of the assembly” for better readability.

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

Partly

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:

Genome assembly, Comparative Genomics, Evolutionary Genomics

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.21781.r86519
Reviewer response for version 1
Maharajan Theivanayagam 1Referee
1 Division of Plant Molecular Biology and Biotechnology, Department of Biosciences, Rajagiri College of Social Sciences, Cochin, Kerala, India
10 7 2024 Copyright: © 2024 Maharajan T
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 1recommendationreject
Results should be described in detail because there is no information on how many genes, transcription factors, and markers have been identified from the genome of Geum urbanum. Why did the authors not submit the genome sequences at NCBI and phytozome databases? How many differentially expressed genes and proteins are identified from this study?  Hence, I advise the authors to please refer to already published articles and improve the contents of the manuscript.

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

No

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

Partly

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

No

Are the protocols appropriate and is the work technically sound?

Partly

Reviewer Expertise:

Functional Genomics and Genome Editing

I confirm that I have read this submission and believe that I have an appropriate level of expertise to state that I do not consider it to be of an acceptable scientific standard, for reasons outlined above.

Sanger Tree of Life Team Wellcome Trust Sanger Institute, UK

10 7 2024 This data note reports on the whole genome assembly and its quality. This serves as a resource for researchers. It is not a research paper reporting on differentially expressed genes, transcription factors, and markers, although the resource is freely available to researchers who are studying the details of this species. The genome assembly is available on the NCBI ( GCA_946800695.1 ) as well as on ENA. We deposit the data on ENA, which is part of the INSDC, along with NCBI and the DNA DataBank of Japan (DDBJ). The INSDC's main policy is to provide permanent, free, and unrestricted access to all archived nucleotide data. The three organisations exchange data daily. Phytozome prioritises species sequenced at the Joint Genome Institute and selected species sequenced elsewhere and includes functional annotation. Since this genome assembly can be highly useful for researchers conducting functional annotation, we opted to deposit our data in the widely accessible INSDC databases. We believe that the current data note provides valuable information on the whole genome assembly and its quality, offering a crucial resource for further research. Given that our primary aim is to present the genome assembly rather than conduct a detailed functional annotation, we have ensured that the data is available through established and widely accessible platforms like NCBI and ENA. This approach aligns with our objective to make the genome data freely available to the research community. Since the first version of this data note, this Geum urbanum assembly has been annotated at the European Bioinformatics Institute (https://rapid.ensembl.org/Geum_urbanum_GCA_946800695.1/Info/Index), and we have updated the genome note in the second version to report on this annotation.

10.21956/wellcomeopenres.21781.r78942
Reviewer response for version 1
Wu Zinian 1Referee https://orcid.org/0000-0002-4121-4529

1 Institute of Grassland Research, Chinese Academy of Agricultural Sciences, Hohhot, China
9 5 2024 Copyright: © 2024 Wu Z
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
In this study, the high-quality genome of Geum urbanum was assembled. The Scaffold N50 was 65.2 MB, reaching the chromosome level. The estimated Quality Value ( QV ) of the final assembly is 59.6 with k-mer completeness of 99.99 %. and the assembly has a BUSCO v5.3.2 completeness of 98.7 %. It's a pretty perfect job. 

Recommendations:  LAI should be used to evaluate genome integrity. 

Complete the genome annotation and genome feature analysis as soon as possible.

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:

Identification and evaluation of plant germplasm resources

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.

Competing interests: No competing interests were disclosed.

Competing interests: No competing interests were disclosed.
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