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

10.12688/wellcomeopenres.20997.1
Data Note
Articles
The genome sequence of great wood-rush, Luzula sylvatica (Huds) Gaudin
[version 1; peer review: 2 approved]

Goodwin Zoë A. Investigation Resources Writing – Original Draft Preparation 1
Bell David Investigation Resources Writing – Original Draft Preparation Writing – Review & Editing https://orcid.org/0000-0002-1059-8777
1
Hart Michelle L. Investigation Resources Writing – Original Draft Preparation Writing – Review & Editing 1
Hollingsworth Peter M. Investigation Resources Writing – Original Draft Preparation Writing – Review & Editing https://orcid.org/0000-0003-0602-0654
1
Royal Botanic Garden Edinburgh Genome Acquisition Lab
Plant Genome Sizing collective
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 Royal Botanic Garden Edinburgh, Edinburgh, Scotland, UK
a mark.blaxter@sanger.ac.uk
No competing interests were disclosed.

1 3 2024
2024
9 1242 2 2024
Copyright: © 2024 Goodwin ZA 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 specimen of Luzula sylvatica (great wood-rush; Tracheophyta; Magnoliopsida; Poales; Juncaceae). The genome sequence is 444.5 megabases in span. Most of the assembly is scaffolded into 6 chromosomal pseudomolecules. The mitochondrial and plastid genome assemblies have lengths of 633.36 kilobases and 201.32 kilobases in length, respectively.

Luzula sylvatica
great wood-rush
genome sequence
chromosomal
Poales
Wellcome Trust206194 218328 This work was supported by Wellcome through core funding to the Wellcome Sanger Institute (206194) and the Darwin Tree of Life Discretionary Award (218328). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
==== Body
pmcSpecies taxonomy

Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliopsida; Mesangiospermae; Liliopsida; Petrosaviidae; commelinids; Poales; Juncaceae; Luzula; Luzula sylvatica (Huds.) Gaudin (NCBI:txid59018).

Background

The genome of great wood-rush, Luzula sylvatica (Huds.) Gaudin, was sequenced as part of the Darwin Tree of Life Project, a collaborative effort to sequence all named eukaryotic species in the Atlantic Archipelago of Britain and Ireland.

Luzula sylvatica is a densely tufted herbaceous perennial ( Stace et al., 2019). It is a European temperate species and is widespread throughout Britain and Ireland, although less common in central and eastern England and central Ireland ( Stroh et al., 2023). Its range in Britain and Ireland is stable, although it has declined in central and eastern England since the 1960s ( Stroh et al., 2023).

It is shade tolerant and typically found in woodlands, moorlands, stream sides, and on montane ledges. It has a broad altitudinal range, from sea-level to 1040 m ( Stroh et al., 2023). The flowers are hermaphrodite and observations on other Luzula species show that although the predominant mode of pollination is wind pollination, insect pollination may also occur ( Huang et al., 2013). No hybrids of Luzula are recorded from Britain and Ireland ( Stace et al., 2015).

Within Britain and Ireland the species is diploid (2n = 12), with chromosome counts made on native material from three different populations in England, Ireland and Scotland ( Dempsey et al., 1994; Gornall & Bailey, 1993). In this paper we present a high-quality reference genome as a foundation resource for future studies.

Genome sequence report

The genome was sequenced from Luzula sylvatica ( Figure 1) collected from Royal Botanic Garden Edinburgh (Inverleith), Scotland, UK (55.97, –3.21). Using flow cytometry, the genome size (1C-value) was estimated to be 0.58 pg, equivalent to 580 Mb. A total of 33-fold coverage in Pacific Biosciences single-molecule HiFi long reads was generated. Primary assembly contigs were scaffolded with chromosome conformation Hi-C data. Manual assembly curation corrected 93 missing joins or mis-joins and removed 7 haplotypic duplications, reducing the assembly length by 1.13% and the scaffold number by 50.65%, and increasing the scaffold N50 by 1.12%.

Figure 1. Photograph of the herbarium voucher of the Luzula sylvatica (lpLuzSylv1) specimen used for genome sequencing.

The final assembly has a total length of 444.5 Mb in 36 sequence scaffolds with a scaffold N50 of 74.5 Mb ( Table 1). The snailplot 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 (96.69%) of the assembly sequence was assigned to 6 chromosomal-level scaffolds. Chromosome-scale scaffolds confirmed by the Hi-C data are named in order of size ( Figure 5; Table 2). Heterozygous inversions were observed on chromosome 5, in the region of 7.3 Mb to 22.9 Mb. While not fully phased, the assembly deposited is of one haplotype. Contigs corresponding to the second haplotype have also been deposited. The mitochondrial and plastid genomes were also assembled and can be found as contigs within the multifasta file of the genome submission.

Table 1. Genome data for Luzula sylvatica, lpLuzSylv1.1.

Project accession data	
Assembly identifier	lpLuzSylv1.1	
Species	Luzula sylvatica	
Specimen	lpLuzSylv1	
NCBI taxonomy ID	59018	
BioProject	PRJEB50874	
BioSample ID	SAMEA7535982	
Isolate information	lpLuzSylv1: leaf tissue (DNA and Hi-C sequencing)	
Assembly metrics *	Benchmark	
Consensus quality (QV)	59.9	≥ 50	
k-mer completeness	100.0%	≥ 95%	
BUSCO **	C:71.5%[S:66.4%,D:5.1%],
F:2.8%,M:25.7%,n:4,896	C ≥ 95%	
Percentage of
assembly mapped to
chromosomes	96.69%	≥ 95%	
Sex chromosomes	-	localised homologous pairs	
Organelles	Mitochondrial genome:
633.36 kb
Plastid genome: 201.32 kb	complete single alleles	
Raw data accessions	
PacificBiosciences
SEQUEL II	ERR8705854, ERR8705855	
Hi-C Illumina	ERR8702782	
Genome assembly	
Assembly accession	GCA_946800325.1	
Accession of
alternate haplotype	GCA_946800335.1	
Span (Mb)	444.5	
Number of contigs	186	
Contig N50 length (Mb)	5.3	
Number of scaffolds	36	
Scaffold N50 length (Mb)	74.5	
Longest scaffold (Mb)	77.24	
* 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 poales_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/CAMPEJ01/dataset/CAMPEJ01/busco.

Figure 2. Genome assembly of Luzula sylvatica, lpLuzSylv1.1: 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 445,370,405 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 (77,244,432 bp, shown in red). Orange and pale-orange arcs show the N50 and N90 scaffold lengths (74,526,441 and 60,551,003 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 poales_odb10 set is shown in the top right. An interactive version of this figure is available at https://blobtoolkit.genomehubs.org/view/CAMPEJ01/dataset/CAMPEJ01/snail.

Figure 3. Genome assembly of Luzula sylvatica, lpLuzSylv1.1: 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/CAMPEJ01/dataset/CAMPEJ01/blob.

Figure 4. Genome assembly of Luzula sylvatica, lpLuzSylv1.1: 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/CAMPEJ01/dataset/CAMPEJ01/cumulative.

Figure 5. Genome assembly of Luzula sylvatica, lpLuzSylv1.1: Hi-C contact map of the lpLuzSylv1.1 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=OgFWtEaJQnGD2mhY8BD_Cw.

Table 2. Chromosomal pseudomolecules in the genome assembly of Luzula sylvatica, lpLuzSylv1.

INSDC
accession	Chromosome	Length (Mb)	GC%	
OX326956.1	1	77.24	32.5	
OX326957.1	2	74.93	32.0	
OX326958.1	3	74.53	32.0	
OX326959.1	4	72.9	31.5	
OX326960.1	5	70.51	32.0	
OX326961.1	6	60.55	32.5	
OX326962.1	MT	0.63	45.5	
OX326963.1	Pltd	0.2	35.5	

The estimated Quality Value (QV) of the final assembly is 59.9 with k-mer completeness of 100.0%, and the assembly has a BUSCO v5.3.2 completeness of 71.5% (single = 66.4%, duplicated = 5.1%), using the poales_odb10 reference set ( n = 4,896).

Metadata for specimens, barcode results, spectra estimates, sequencing runs, contaminants and pre-curation assembly statistics are given at https://links.tol.sanger.ac.uk/species/59018.

Methods

Sample acquisition, genome size estimation and nucleic acid extraction

Luzula sylvatica (specimen ID EDTOL00071, ToLID lpLuzSylv1) was collected from Royal Botanic Garden Edinburgh (Inverleith), Scotland, UK (latitude 55.97, longitude –3.21) on 2020-08-12. The plant was originally collected in 1993 from the Scottish highlands (Glenmore, Coire na Ciste), at an altitude of 600 m. The specimen was collected and formally identified by Zoe Goodwin and David Bell (Royal Botanic Garden Edinburgh). Leaves were cut into segments using scissors and snap-frozen in liquid nitrogen. The herbarium specimen of the sequenced plant is kept at the Royal Botanic Garden Edinburgh (E) https://data.rbge.org.uk/herb/E01358005.

The genome size was estimated by flow cytometry using the fluorochrome propidium iodide and following the ‘one-step’ method as outlined in Pellicer et al. (2021). 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 Solanum lycopersicum ‘Stupiké polní rané’ with an assumed 1C-value of 968 Mb ( Doležel et al., 2007).

Protocols developed by the Wellcome Sanger Institute (WSI) Tree of Life core laboratory have been deposited on protocols.io ( Denton et al., 2023). The workflow for high molecular weight (HMW) DNA extraction at the WSI includes a sequence of core procedures: sample preparation; sample homogenisation, DNA extraction, fragmentation, and clean-up. In sample preparation, the lpLuzSylv1 sample was weighed and dissected on dry ice ( Jay et al., 2023). HMW DNA was extracted using the Automated Plant MagAttract v2 protocol ( Todorovic et al., 2023a). HMW DNA was sheared into an average fragment size of 12–20 kb in a Megaruptor 3 system with speed setting 30 ( Todorovic et al., 2023b). Sheared DNA was purified by solid-phase reversible immobilisation ( Strickland et al., 2023): in brief, the method employs a 1.8X ratio of AMPure PB beads to sample 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 and Qubit dsDNA High Sensitivity Assay kit. Fragment size distribution was evaluated by running the sample on the FemtoPulse system.

Sequencing

Pacific Biosciences HiFi circular consensus DNA sequencing libraries were constructed according to the manufacturers’ instructions. DNA sequencing was performed by the Scientific Operations core at the WSI on a Pacific Biosciences SEQUEL II instrument. Hi-C data were also generated from leaf tissue of lpLuzSylv1 using the Arima2 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). 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 using the gEVAL system ( Chow et al., 2016) as described previously ( Howe et al., 2021). Manual curation was performed using gEVAL, HiGlass ( Kerpedjiev et al., 2018) and Pretext ( Harry, 2022). The organelle genomes were assembled using MBG ( Rautiainen & Marschall, 2021).

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	
gEVAL	N/A	https://geval.org.uk/	
Hifiasm	0.16.1-r375	https://github.com/chhylp123/hifiasm	
HiGlass	1.11.6	https://github.com/higlass/higlass	
MBG	-	https://github.com/maickrau/MBG	
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	yahs-1.1.91eebc2	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: Luzula sylvatica. Accession number PRJEB50874; https://identifiers.org/ena.embl/PRJEB50874 ( Wellcome Sanger Institute, 2022). The genome sequence is released openly for reuse. The Luzula sylvatica 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.

Author information

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 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.23232.r95115
Reviewer response for version 1
Bouchenak-Khelladi Yanis 1Referee https://orcid.org/0000-0002-6412-864X

1 University of Bourgogne Franche-Comté, INRAE, Dijon, France, Dijon, France
6 9 2024 Copyright: © 2024 Bouchenak-Khelladi Y
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
This paper is well written, sufficiently detailed and the genome produced is of very good quality. All datasets are easily accessible and in useable format.

I found one typo: "...sample preparation;..." use colon  instead of semicolon in the Methods_Sample acquisition section.

Nothing else to report, it is a nice data paper.

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:

Phylogenetics, evolution, comparative analyses, eco-evolutionary dynamics

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.23232.r89823
Reviewer response for version 1
Negawo Alemayehu Teressa 1Referee
1 Feed and Forage Development Program, International Livestock Research Institute Ethiopia, Addis Ababa, Addis Ababa, Ethiopia
9 8 2024 Copyright: © 2024 Negawo AT
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 paper reads well, and present a good contribution to reference genome development for the grass spp. 

Having said this, what is the main use of this grass? Please add a sentence or two on the importance of the crop in the introduction section. 

In the result section, the genome assembly was presented. No genome annotation and gene family analyses were done. If possible, for better completeness of the information, please add annotation analysis.

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:

genomic/genetic analysis, plant biotechnology, data analysis, genebank, quantitative genetics, field evaluation, phenotyping

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.
==== Refs
Abdennur N Mirny LA : Cooler: Scalable storage for Hi-C data and other genomically labeled arrays. Bioinformatics. 2020;36 (1 ):311–316. 10.1093/bioinformatics/btz540 31290943
Challis R Richards E Rajan J : BlobToolKit - interactive quality assessment of genome assemblies. G3 (Bethesda). 2020;10 (4 ):1361–1374. 10.1534/g3.119.400908 32071071
Cheng H Concepcion GT Feng X : Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm. Nat Methods. 2021;18 (2 ):170–175. 10.1038/s41592-020-01056-5 33526886
Chow W Brugger K Caccamo M : gEVAL - a web-based browser for evaluating genome assemblies. Bioinformatics. 2016;32 (16 ):2508–2510. 10.1093/bioinformatics/btw159 27153597
Dempsey RE Gornall RJ Bailey JP : Contributions to a cytological catalogue of the British and Irish flora. Watsonia. 1994;20 (1 ):63–66.
Denton A Yatsenko H Jay J : Sanger Tree of Life Wet Laboratory Protocol Collection V.1. protocols.io. 2023. 10.17504/protocols.io.8epv5xxy6g1b/v1
Di Tommaso P Chatzou M Floden EW : Nextflow enables reproducible computational workflows. Nat Biotechnol. 2017;35 (4 ):316–319. 10.1038/nbt.3820 28398311
Doležel J Greilhuber J Suda J : Estimation of nuclear DNA content in plants using flow cytometry. Nat Protoc. 2007;2 (9 ):2233–2244. 10.1038/nprot.2007.310 17853881
Gornall RJ Bailey JP : Cytological Catalogue of the British and Irish Flora Botanical Society of Britain and Ireland.1993; [Accessed 16 January 2024]. Reference Source
Guan D McCarthy SA Wood J : Identifying and removing haplotypic duplication in primary genome assemblies. Bioinformatics. 2020;36 (9 ):2896–2898. 10.1093/bioinformatics/btaa025 31971576
Harry E : PretextView (Paired REad TEXTure Viewer): A desktop application for viewing pretext contact maps.2022; [Accessed 19 October 2022]. Reference Source
Howe K Chow W Collins J : Significantly improving the quality of genome assemblies through curation. GigaScience. Oxford University Press,2021;10 (1 ): giaa153. 10.1093/gigascience/giaa153 33420778
Huang SQ Xiong YZ Barrett SCH : Experimental Evidence of Insect Pollination in Juncaceae, a Primarily Wind-Pollinated Family. Int J Plant Sci. 2013;174 (9 ):1219–1228. 10.1086/673247
Jay J Yatsenko H Narváez-Gómez JP : Sanger Tree of Life Sample Preparation: Triage and Dissection. protocols.io. 2023. 10.17504/protocols.io.x54v9prmqg3e/v1
Kerpedjiev P Abdennur N Lekschas F : HiGlass: Web-based visual exploration and analysis of genome interaction maps. Genome Biol. 2018;19 (1 ): 125. 10.1186/s13059-018-1486-1 30143029
Loureiro J Rodriguez E Dolezel J : Two new nuclear isolation buffers for plant DNA flow cytometry: A test with 37 species. Ann Bot. 2007;100 (4 ):875–888. 10.1093/aob/mcm152 17684025
Manni M Berkeley MR Seppey M : BUSCO Update: Novel and Streamlined Workflows along with Broader and Deeper Phylogenetic Coverage for Scoring of Eukaryotic, Prokaryotic, and Viral Genomes. Mol Biol Evol. 2021;38 (10 ):4647–4654. 10.1093/molbev/msab199 34320186
Pellicer J Powell RF Leitch IJ : The application of flow cytometry for estimating genome size, ploidy level endopolyploidy, and reproductive modes in plants. In: Besse, P. (ed.) Methods Mol Biol. New York, NY: Humana,2021;2222 :325–361. 10.1007/978-1-0716-0997-2_17 33301101
Rao SSP Huntley MH Durand NC : A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping. Cell. 2014;159 (7 ):1665–1680. 10.1016/j.cell.2014.11.021 25497547
Rautiainen M Marschall T : MBG: Minimizer-based sparse de Bruijn Graph construction. Bioinformatics. 2021;37 (16 ):2476–2478. 10.1093/bioinformatics/btab004 33475133
Rhie A McCarthy SA Fedrigo O : Towards complete and error-free genome assemblies of all vertebrate species. Nature. 2021;592 (7856 ):737–746. 10.1038/s41586-021-03451-0 33911273
Rhie A Walenz BP Koren S : Merqury: Reference-free quality, completeness, and phasing assessment for genome assemblies. Genome Biol. 2020;21 (1 ): 245. 10.1186/s13059-020-02134-9 32928274
Simão FA Waterhouse RM Ioannidis P : BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics. 2015;31 (19 ):3210–3212. 10.1093/bioinformatics/btv351 26059717
Stace CA Preston CD Pearman DA : Hybrid flora of the British Isles. Bristol: Botanical Society of Britain and Ireland,2015. Reference Source
Stace CA Thompson H Stace M : New flora of the British Isles. 4th ed. C&M Floristics,2019.
Strickland M Cornwell C Howard C : Sanger Tree of Life Fragmented DNA clean up: Manual SPRI. protocols.io. 2023. 10.17504/protocols.io.kxygx3y1dg8j/v1
Stroh PA Walker KJ Humphrey TA : Plant Atlas 2020. Mapping changes in the distribution of the British and Irish flora. Durham: Botanical Society of Britain and Ireland,2023;2 . Reference Source
Surana P Muffato M Qi G : sanger-tol/readmapping: sanger-tol/readmapping v1.1.0 - Hebridean Black (1.1.0). Zenodo. 2023a; (Accessed: 17 April 2023). 10.5281/zenodo.7755665
Surana P Muffato M Sadasivan Baby C : sanger-tol/genomenote (v1.0.dev). Zenodo. 2023b, (Accessed: 17 April 2023). 10.5281/zenodo.6785935
Todorovic M Oatley G Howard C : Sanger Tree of Life HMW DNA Extraction: Automated Plant MagAttract v.2. Protocols.Io. 2023a. 10.17504/protocols.io.36wgq3n13lk5/v1
Todorovic M Sampaio F Howard C : Sanger Tree of Life HMW DNA Fragmentation: Diagenode Megaruptor ®3 for PacBio HiFi. protocols.io. 2023b. 10.17504/protocols.io.8epv5x2zjg1b/v1
Vasimuddin Md Misra S Li H : Efficient Architecture-Aware Acceleration of BWA-MEM for Multicore Systems. In: 2019 IEEE International Parallel and Distributed Processing Symposium (IPDPS). IEEE,2019;314–324. 10.1109/IPDPS.2019.00041
Wellcome Sanger Institute: The genome sequence of great wood-rush, Luzula sylvatica (Gaudin, 1811), European Nucleotide Archive, [dataset], accession number PRJEB50874.2022.
Zhou C McCarthy SA Durbin R : YaHS: yet another Hi-C scaffolding tool. Bioinformatics. 2023;39 (1 ): btac808. 10.1093/bioinformatics/btac808 36525368
