Abstract
We present a genome assembly from a specimen of Hedera helix (common ivy; Streptophyta; Magnoliopsida; Apiales; Araliaceae). The genome sequence is 1,199.4 megabases in span. Most of the assembly is scaffolded into 24 chromosomal pseudomolecules. The mitochondrial and plastid genomes have also been assembled and are 609.2 and 162.2 kilobases in length respectively.
Keywords: Hedera helix, common ivy, genome sequence, chromosomal, Apiales
Species taxonomy
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae; asterids; campanulids; Apiales; Araliaceae; Hedera; Hedera helix (Linnaeus 1753) (NCBI:txid4052).
Background
The common ivy, Hedera helix L., is a vigorous self-clinging evergreen perennial vine that is one of the most familiar plant species in the British flora. Ivy is common across most of Britain, except parts of northern Scotland. It is much rarer in Ireland, but it is native to much of Europe from southern Scandinavia to Turkey. It forms dense ground cover, particularly in secondary woodland. Here, it acts as a keystone species, with the greenish-yellow flowers providing a rich source of nectar for insects in the autumn and the purplish-black berries being a source of food for birds in the spring ( Metcalfe, 2005). The common ivy, as well as other introduced ivy species, are widespread in and around gardens, where they are used as climbers to cover garden structures, particularly in shaded situations. Common ivy has widely escaped from gardens and is now frequently found as a non-native alien around the globe ( Biggerstaff & Beck, 2007), usually then known as English ivy. The species is also notable for its rich folklore, and is still widely used in wreaths and celebrated in Christmas songs.
The taxonomy of ivy is complex, with disagreement around the recognition of subspecific taxa and confusion around the European native status of some horticultural taxa. Here, we follow Stace (2010), with our specimen belonging to the widespread diploid Hedera helix (syn. Hedera helix subsp. helix) which has 2 n = 48, rather than the more westerly distributed tetraploid Hedera hibernica Poit. (syn. H. helix subsp. hibernica (Poit.) D.C.McClint.; 2 n = 96).
Here, we present the first high-quality ivy genome, which we anticipate being a valuable genomic resource for a range of future studies. These may include investigations into the biosynthetic pathway underlying the production of triterpenoid saponins, which has previously been studied in ivies using transcriptomic data ( Sun et al., 2017). The species is also of interest for its developmental genetics ( Schäffner & Nagl, 1979). The species undergoes a dramatic transition in leaf shape, with juveniles producing five-lobed leaves, while adults produce radially symmetrical ovate leaves ( Metcalfe, 2005). Finally, ivy is the host plant of the parasitic ivy broomrape ( Orobanche hederae Duby), and comparative genomic analyses could be used to investigate interactions in this obligate parasite-host system ( Twyford, 2018).
Genome sequence report
The genome was sequenced from one Hedera helix specimen ( Figure 1) collected from Petersham Common, Richmond, Surrey, UK (latitude 51.45, longitude –0.30). Using flow cytometry, the genome size (1C-value) was estimated to be 1.59 pg, equivalent to 1,550 Mb. A total of 29-fold coverage in Pacific Biosciences single-molecule HiFi long reads and 65-fold coverage in 10X Genomics read clouds were generated. Primary assembly contigs were scaffolded with chromosome conformation Hi-C data. Manual assembly curation corrected 276 missing joins or mis-joins and removed 15 haplotypic duplications, reducing the assembly length by 0.63% and the scaffold number by 79.25%, and increasing the scaffold N50 by 10.54%.
Figure 1. Example images of the common ivy Hedera helix (not the sampled specimen) growing in secondary woodland in Edinburgh.
a) juvenile foliage. b) mature foliage and fruits. Photos taken by Alex Twyford.
The final assembly has a total length of 1,199.4 Mb in 55 sequence scaffolds with a scaffold N50 of 50.5 Mb ( Table 1). Most (99.84%) of the assembly sequence was assigned to 24 chromosomal-level scaffolds. Chromosome-scale scaffolds confirmed by the Hi-C data are named in order of size ( Figure 2– Figure 5; Table 2). There is a region of low confidence on Chromosome 1 at 15–26.1 Mb consisting of several repetitive scaffolds with uncertain orientation and order. The Hi-C data indicate there is a nested heterozygous inversion on Chromosome 3 covering the approximate region 19.7–35.7 Mb. On Chromosome 20, there is a heterozygous inversion between approximately 1.6–4.4 Mb. The mitochondrial and chloroplast genomes were also assembled.
Figure 2. Genome assembly of Hedera helix, drHedHeli1.2: 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 1,199,358,263 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 (62,841,030 bp, shown in red). Orange and pale-orange arcs show the N50 and N90 scaffold lengths (50,454,882 and 40,242,199 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/drHedHeli1.2/dataset/CAMXCC02/snail.
Figure 5. Genome assembly of Hedera helix, drHedHeli1.2: Hi-C contact map.
Hi-C contact map of the drHedHeli1.2 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=RqLbs2mdRkulj0bOy5MAQw.
Table 1. Genome data for Hedera helix, drHedHeli1.2.
| Project accession data | ||
|---|---|---|
| Assembly identifier | drHedHeli1.2 | |
| Species | Hedera helix | |
| Specimen | drHedHeli1 | |
| NCBI taxonomy ID | 4052 | |
| BioProject | PRJEB47314 | |
| BioSample ID | SAMEA7522625 | |
| Isolate information | leaf tissue, drHedHeli1 (DNA sequencing and Hi-C) leaf
tissue, drHedHeli8 (RNA-Seq) |
|
| Assembly metrics * | Benchmark | |
| Consensus quality (QV) | 54.2 | ≥ 50 |
| k-mer completeness | 99.99% | ≥ 95% |
| BUSCO ** | C:99.2%[S:57.2%,D:42.0%],
F:0.1%,M:0.6%,n:2,326 |
C ≥ 95% |
| Percentage of assembly mapped
to chromosomes |
99.84% | ≥ 95% |
| Sex chromosomes | Not applicable. | localised homologous pairs |
| Organelles | Mitochondrial and plastid
genomes assembled. |
complete single alleles |
| Raw data accessions | ||
| PacificBiosciences SEQUEL II | ERR6907987, ERR6939262 | |
| 10X Genomics Illumina | ERR6688692–ERR6688695 | |
| Hi-C Illumina | ERR6688700 | |
| PolyA RNA-Seq Illumina | ERR9435019 | |
| Genome assembly | ||
| Assembly accession | GCA_947179155.2 | |
| Accession of alternate haplotype | GCA_947179205.2 | |
| Span (Mb) | 1,198.6 | |
| Number of contigs | 375 | |
| Contig N50 length (Mb) | 13.3 | |
| Number of scaffolds | 53 | |
| Scaffold N50 length (Mb) | 50.5 | |
| Longest scaffold (Mb) | 62.8 | |
* 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/drHedHeli1.2/dataset/CAMXCC02/busco.
Figure 3. Genome assembly of Hedera helix, drHedHeli1.2: 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/drHedHeli1.2/dataset/CAMXCC02/blob.
Figure 4. Genome assembly of Hedera helix, drHedHeli1.2: 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/drHedHeli1.2/dataset/CAMXCC02/cumulative.
Table 2. Chromosomal pseudomolecules in the genome assembly of Hedera helix, drHedHeli1.
| INSDC accession | Chromosome | Size (Mb) | GC% |
|---|---|---|---|
| OX359264.1 | 1 | 62.84 | 35.9 |
| OX359265.1 | 2 | 61.43 | 32.4 |
| OX359266.1 | 3 | 61.1 | 32.4 |
| OX359267.1 | 4 | 60.35 | 32.9 |
| OX359268.1 | 5 | 57.05 | 32.4 |
| OX359269.1 | 6 | 56.44 | 32.4 |
| OX359270.1 | 7 | 51.84 | 32.4 |
| OX359271.1 | 8 | 51.67 | 32.4 |
| OX359272.1 | 9 | 51.29 | 32.5 |
| OX359273.1 | 10 | 50.79 | 32.3 |
| OX359274.1 | 11 | 50.45 | 32.5 |
| OX359275.1 | 12 | 49.42 | 32.5 |
| OX359276.1 | 13 | 48.73 | 32.4 |
| OX359277.1 | 14 | 46.9 | 32.5 |
| OX359278.1 | 15 | 46.45 | 32.6 |
| OX359279.1 | 16 | 45.93 | 32.4 |
| OX359280.1 | 17 | 45.65 | 32.4 |
| OX359281.1 | 18 | 45.28 | 32.5 |
| OX359282.1 | 19 | 44.67 | 32.5 |
| OX359283.1 | 20 | 44.38 | 32.4 |
| OX359284.1 | 21 | 43.64 | 32.3 |
| OX359285.1 | 22 | 40.24 | 32.4 |
| OX359286.1 | 23 | 40.2 | 32.3 |
| OX359287.1 | 24 | 40.14 | 32.5 |
| OX381723.1 | mitochondrion | 0.61 | 45.1 |
| OX381724.1 | plastid | 0.16 | 38 |
| - | unplaced | 1.7 | 36.8 |
The assembly has a BUSCO v5.3.2 ( Manni et al., 2021) completeness of 99.2% (single 57.2%, duplicated 42.0%) using the eudicots_odb10 reference set. While not fully phased, the assembly deposited is of one haplotype. Contigs corresponding to the second haplotype have also been deposited.
The estimated Quality Value (QV) of the final assembly is 54.2 with k-mer completeness of 99.99%, and the assembly has a BUSCO v5.3.2 completeness of 99.2% (single = 57.2%, duplicated = 42.0%), 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/4052.
Methods
Sample acquisition, genome size estimation and nucleic acid extraction
A Hedera helix specimen (drHedHeli1) was collected from Petersham Common, Richmond, Surrey, UK (latitude 51.45, longitude –0.30) on 8 September 2020. The specimen was picked by hand from a beech woodland habitat by Maarten Christenhusz (Royal Botanic Gardens, Kew) collection number 9099. The specimen was identified by Maarten Christenhusz based on its morphology and preserved by freezing at –80°C.
A second specimen (drHedHeli8) was collected from the Royal Botanic Garden Edinburgh (Inverleith) (latitude 55.96, longitude –3.20) on 23 November 2020 by David Bell (Royal Botanic Garden Edinburgh). The specimen was identified by David Bell based on its morphology and flash-frozen in liquid nitrogen. This specimen was used for RNA sequencing.
The genome size was estimated by flow cytometry 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 drHedHeli1 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 Qiagen Plant MagAttract HMW DNA extraction kit. Low molecular weight DNA was removed from a 20 ng aliquot of extracted DNA using the 0.8X AMpure XP purification kit prior to 10X Chromium sequencing; a minimum of 50 ng DNA was submitted for 10X sequencing. 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 drHedHeli8 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 was 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 drHedHeli1 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 SALSA2 ( Ghurye et al., 2019). 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 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 |
| gEVAL | N/A | https://geval.org.uk/ |
| Hifiasm | 0.15.3-r339 | 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 |
| Merqury | MerquryFK | https://github.com/thegenemyers/MERQURY.FK |
| MBG | - | https://github.com/maickrau/MBG |
| PretextView | 0.2 | https://github.com/wtsi-hpag/PretextView |
| purge_dups | 1.2.3 | https://github.com/dfguan/purge_dups |
| SALSA | 2.2 | https://github.com/salsa-rs/salsa |
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.
Funding Statement
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.
[version 1; peer review: 2 approved]
Data availability
European Nucleotide Archive: Hedera helix. Accession number PRJEB47314; https://identifiers.org/ena.embl/PRJEB47314. ( Wellcome Sanger Institute, 2022)
The genome sequence is released openly for reuse. The Hedera helix 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 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.
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