The genome sequence of the chicken of the woods fungus, Laetiporus sulphureus (Bull.) Murrill, 1920

We present a genome assembly from an individual Laetiporus sulphureus (the chicken of the woods fungus; Basidiomycota; Agaricomycetes; Polyporales; Laetiporaceae). The genome sequence is 37.4 megabases in span. The complete assembly is scaffolded into 14 chromosomal pseudomolecules.


Background
Laetiporus sulphureus (chicken of the woods) is a poroid fungus that produces large, fleshy, orange to citric yellow, annual bracket-like sporocarps, with an undulating margin, which can grow up to 40 cm in size.A smooth, vivid yellow pore layer with 3-4 pores per millimetre can be observed in the underside.Sporocarps can occur individually or in large imbricate clusters.They have a dimitic hyphal structure and the generative hyphae lack clamps.Spores are ellipsoid to ovoid, smooth, hyaline, measuring 5-8 × 4-5 μm (Ryvarden & Melo, 2017).In culture, the hyphae are hyaline, clamped and sparingly branched, with some aerial growth.They produce large, thick-walled, terminal chlamydospores and smaller thin-walled conidia.Aging cultures appear dull yellow or orange, with a granular texture due to asexual spore production.
This species can form dense, vertical, rubbery sheets of mycelium along radial lines in well colonised heartwood, which are a distinctive identification feature when sporocarps are not present.
Laetiporus sulphureus has a distribution that includes Europe as well as North and South America (Song & Cui, 2017).Throughout Europe it is known to cause a brown-rot in the heartwood of a range of angiosperm trees, particularly Quercus, where it is a key engineer of hollowing, but it can also be found in species of Castanea, Fraxinus, Prunus, and Salix.It is also considered to occur on the gymnosperm Taxus baccata.In the UK, L .sulphureus is widespread and common wherever host trees are present.
Laetiporus sulphureus represents a group of cryptically diverse taxa that in recent years has undergone significant and ongoing revision (Song et al., 2018).The genome produced for this collection has the potential to help us resolve the cryptic diversity of this genus in the UK and to greatly expand our understanding of how these essential wood recyclers operate and interact in their environment.This information may be critical to our ability to protect the associated organisms that rely on dead wood and tree hollow habitats.

Genome sequence report
The genome was sequenced from a single L. sulphureus specimen (Figure 1) collected from Oldbury Court, Bristol, UK (latitude 51.4897, longitude -2.5253).A total of 106-fold coverage in Pacific Biosciences single-molecule HiFi long reads and 1853-fold coverage in 10X Genomics read clouds were  generated.Primary assembly contigs were scaffolded with chromosome conformation Hi-C data.Manual assembly curation corrected 7 missing/misjoins and removed 3 haplotypic duplications, reducing the assembly size by 2.87%, the scaffold number by 36.36% and the scaffold N50 by 0.88%.
The final assembly has a total length of 37.4 Mb in 14 sequence scaffolds with a scaffold N50 of 2.6 Mb (Table 1).
Of the assembly sequence, 100% was assigned to 14 chromosomal-level scaffolds (numbered by sequence length) (Figure 2-Figure 5; Table 2).The assembly has a BUSCO (Manni et al., 2021) completeness of 95.9% (single, 94.8%, duplicated 1.1%) using the polyporales_odb10 reference set (n=4464).While not fully phased, the assembly deposited is of one haplotype.Contigs corresponding to the second haplotype have also been deposited.

Sample acquisition and nucleic acid extraction
A L. sulphureus specimen (glLaeSulp1) was collected from Oldbury Court, Bristol, UK (latitude 51.4897, longitude -2.5253) by Richard Wright, Royal Botanic Gardens Kew, from a Quercus sp.trunk.The specimens were identified by the same individual and snap-frozen on dry ice.
DNA was extracted at the Tree of Life laboratory, Wellcome Sanger Institute.The gfLaeSulp1 sample was weighed and dissected on dry ice with tissue set aside for Hi-C sequencing.
Mycelium tissue was cryogenically disrupted to a fine powder using a Covaris cryoPREP Automated Dry Pulveriser, receiving multiple impacts.Fragment size analysis of 0.01-0.5 ng of DNA was then performed using an Agilent FemtoPulse.High molecular weight (HMW) DNA was extracted using the Qiagen Plant MagAttract HMW DNA extraction kit.Low molecular weight DNA was removed from a 200-ng aliquot of extracted DNA using 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 between 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 1.8X 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.

Sequencing
Pacific Biosciences HiFi circular consensus and 10X Genomics Chromium read cloud sequencing libraries were constructed according to the manufacturers' instructions.Sequencing was performed by the Scientific Operations core at the Wellcome Sanger Institute on Pacific Biosciences SEQUEL II (HiFi) and Illumina NovaSeq 6000 (10X) instruments.Hi-C data were generated in the Tree of Life laboratory from mycelium tissue of gfLaeSulp1 using the Arima v2 kit and sequenced on a NovaSeq 6000 instrument.

Genome assembly
Assembly was carried out with Hifiasm (Cheng et al., 2021).

Dilek Guldemir
National Parasitology Reference Laboratory, Saglik Mah, Ankara, Turkey In the relevant Data Note type study, "A genome assembly from an individual Laetiporus sulphureus (the chicken of the woods fungus; Basidiomycota; Agaricomycetes; Polyporales; Laetiporaceae).The genome sequence is 37.4 megabases in span.The complete assembly is scaffolded into 14 chromosomal pseudomolecules" is offered.
The methods used in the study are sufficient and the data obtained are useful.The study is suitable for publication as "Data Note".However, I recommend that the study be expanded and the number of Laetiporus sulphureus samples be increased to ensure regional representation, and that they be presented as the original article by comparing them with global WGS data and the reference genome as a representation of the species.
Is the rationale for creating the dataset(s) clearly described?

Miguel Naranjo-Ortiz
University of Oslo, Oslo, Norway The paper the protocols used to generate the reference genome of the fungus Laetiporus sulphureus.I consider that the methodology and results are sufficiently detailed.
There is a few very minor and optional suggested additions: I would suggest mentioning in the background that this species is a choice edible mushroom. 1.
Since there have been some taxonomic revision, it might be pertinent to disclose recent changes and perhaps even a rationale supporting that the sampled specimen corresponds to the species.For example, because it has a similar geographical range than the type specimen.

2.
Ideally the specimen used for data production or a culture derived from it would be available in a biological repository, be it a fungarium, a culture collection or a DNA bank.If that's the case, it should be mentioned.

3.
Is the rationale for creating the dataset(s) clearly described?Yes Are the protocols appropriate and is the work technically sound?Yes

Are sufficient details of methods and materials provided to allow replication by others? Yes
Are the datasets clearly presented in a useable and accessible format?Yes Competing Interests: No competing interests were disclosed.
Reviewer Expertise: Comparative genomics of fungi 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.

Figure 1 .
Figure 1.Images of the Laetiporus sulphureus specimen used for genome sequencing.(A) Laetiporus sulphureus spore producing bodies from which the culture for this genome was isolated, growing on the trunk of Quercus robur at Oldbury Court, Bristol.(B) An isolate of L. sulphureus at 10 days growth on 0.5% malt tannic acid agar.(C) An isolate of L. sulphureus at 30 days growth on 2 % malt extract agar.

Figure 2 .
Figure 2. Genome assembly of Laetiporus sulphureus, gfLaeSulp1.1:metrics.The main plot is divided into 1,000 size-ordered bins around the circumference with each bin representing 0.1% of the 37,410,216 bp assembly.The distribution of chromosome lengths is shown in dark grey with the plot radius scaled to the longest chromosome present in the assembly (4,563,458 bp, shown in red).Orange and pale-orange arcs show the N50 and N90 chromosome lengths (2,582,225 and 1,895,436 bp), respectively.The pale grey spiral shows the cumulative chromosome 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 polyporales_odb10 set is shown in the top right.An interactive version of this figure is available at https://blobtoolkit.genomehubs.org/view/gfLaeSulp1_1/dataset/gfLaeSulp1_1/snail.

Figure 3 .
Figure 3. Genome assembly of Laetiporus sulphureus, gfLaeSulp1.1: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/gfLaeSulp1_1/dataset/gfLaeSulp1_1/blob.

Figure 4 .
Figure 4. Genome assembly of Laetiporus sulphureus, gfLaeSulp1.1: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/gfLaeSulp1_1/dataset/gfLaeSulp1_1/cumulative.

Figure 5 .
Figure 5. Genome assembly of Laetiporus sulphureus, gfLaeSulp1.1:Hi-C contact map.Hi-C contact map of the gfLaeSulp1.2assembly, visualised in HiGlass.Chromosomes are given in size order from left to right and top to bottom.

Yes Are the protocols appropriate and is the work technically sound? Yes Are sufficient details of methods and materials provided to allow replication by others? Yes Are the datasets clearly presented in a useable and accessible format? Yes Competing Interests:
No competing interests were disclosed.

have read this submission and believe that I have an appropriate level of expertise to confirm that it is of an acceptable scientific standard.
This is an open access peer review report distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.