Tree of Life QC: Species Report - Angelica archangelica

NCBI taxon id:	40949 NCBI; ENA; GoaT
Order:	Apiales
Family:	Apiaceae
NCBI lineage:	Eukaryota;Viridiplantae;Streptophyta;Embryophyta;Tracheophyta;Spermatophyta;Magnoliopsida;eudicotyledons;Gunneridae;Pentapetalae;asterids;campanulids;Apiales;Apiaceae;Apioideae;apioidsuperclade;Selineae;Angelica;
GoaT genome size (M):	3,246 (direct)
GoaT asm span (M):	2,077 (ancestor)
GoaT chr no.:	22 (ancestor)
GoaT haploid no.:	11 (direct)
GoaT ploidy:	2 (direct)
ToLID prefix:	drAngArch

Below is information about specimens collected for this species retrieved from the Sample Tracking System (STS).

tolid	specimen_id	gal	sex	organism_part	biosample	biospecimen
drAngArch1	EDTOL01367	ROYAL BOTANIC GARDEN EDINBURGH	HERMAPHRODITE_MONOECIOUS	LEAF	SAMEA9335195	SAMEA9335116
drAngArch1	EDTOL01367	ROYAL BOTANIC GARDEN EDINBURGH	HERMAPHRODITE_MONOECIOUS	LEAF	SAMEA9335200	SAMEA9335116
drAngArch1	EDTOL01367	ROYAL BOTANIC GARDEN EDINBURGH	HERMAPHRODITE_MONOECIOUS	LEAF	SAMEA9335198	SAMEA9335116
drAngArch1	EDTOL01367	ROYAL BOTANIC GARDEN EDINBURGH	HERMAPHRODITE_MONOECIOUS	LEAF	SAMEA9335197	SAMEA9335116
drAngArch1	EDTOL01367	ROYAL BOTANIC GARDEN EDINBURGH	HERMAPHRODITE_MONOECIOUS	LEAF	SAMEA9335199	SAMEA9335116

Below are estimates of genome size, repeat size, heterozygosity based on k-mer specta analysis with GenomeScope2.

source	specimen	k-mer	k-cov	haploid size	repeat (%)	heterozygosity (%)	model fit (%)	model error (%)	histogram
pacbio	drAngArch1	31	18.34	2,975,355,389	77.13	0.79	96.84	0.09	histogram.txt
hic-arima2	drAngArch1	31	40.16	3,896,875,215	129.29	0.69	97.64	0.33	histogram.txt

pipeline	specimen	date	run id	movie	well	tag	yield	N50	sample accession
PacBio - HiFi	drAngArch1	2021-08-23	85768	m64016e_210823_142624	D01	1016	5,117,071,432	10,991	SAMEA9335195
PacBio - HiFi	drAngArch1	2023-11-02	TRACTION-RUN-922	m84047_231102_174358_s4	B01	2052	75,006,934,201	14,290	SAMEA9335197
PacBio - HiFi	drAngArch1	2023-11-06	TRACTION-RUN-924	m84098_231106_154449_s2	B01	2052	32,523,059,863	14,400	SAMEA9335197

id	taxon	similarity	seq	country	latitude	longitude
GBVE1285-11	Angelica archangelica	1	matK	[object Object]	[object Object]	[object Object]
NNOR1809-15	Angelica archangelica litoralis	1	matK	[object Object]	[object Object]	[object Object]
NNOR1809-15	Angelica archangelica litoralis	1	ITS2	[object Object]	[object Object]	[object Object]
NNOR1839-15	Angelica archangelica archangelica	1	ITS2	[object Object]	[object Object]	[object Object]
GBVE1285-11	Angelica archangelica	1	matK	[object Object]	[object Object]	[object Object]
NNOR1809-15	Angelica archangelica litoralis	1	matK	[object Object]	[object Object]	[object Object]
BBYUK2742-18	Angelica archangelica	1	rbcLa	[object Object]	[object Object]	[object Object]
FBPL734-12	Angelica archangelica	1	rbcLa	[object Object]	[object Object]	[object Object]
FBPL735-12	Angelica archangelica	1	rbcLa	[object Object]	[object Object]	[object Object]
FBPL736-12	Angelica archangelica	1	rbcLa	[object Object]	[object Object]	[object Object]

pipeline	specimen	date	run id	flowcell	type	yield	N50	sample accession	report
No matching records found

Below are stats for each Illumina run collected for this species. Click on a row to see associated plots from samtools stats.

pipeline	specimen	date	run id	read pairs	yield	sample accession	run accession	run status	barcode
Hi-C - Arima v2	drAngArch1	2021-09-21	41009_1#2	2,854,652,694	431,052,556,794	SAMEA9335195		qc complete	Angelica archangelica litoralis (1.00)

Cobionts

Below are results from a screen of the PacBio data using Mash screen against RefSeq assemblies. Only results with identity over 90% are displayed.

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identity	info
0.922553	NC_018417.1 Candidatus Carsonella ruddii HT isolate Thao2000, complete genome
0.91333	[2 seqs] NC_008513.1 Buchnera aphidicola BCc, complete genome [...]
0.909369	[2017 seqs] NW_004087753.1 Ichthyophthirius multifiliis unplaced genomic scaffold scaff_1120509249386, whole genome shotgun sequence [...]
0.909369	NC_002520.1 Amsacta moorei entomopoxvirus 'L', complete genome
0.908727	[3 seqs] NZ_LN890285.1 Buchnera aphidicola (Tuberolachnus salignus) strain BTs genome assembly, chromosome: 1 [...]
0.908403	NC_011047.1 Candidatus Phytoplasma mali strain AT complete chromosome
0.906067	[2 seqs] NC_004344.2 Wigglesworthia glossinidia endosymbiont of Glossina brevipalpis DNA, complete genome [...]
0.905028	[151 seqs] NZ_JICM01000001.1 Acinetobacter sp. ETR1 contig_1, whole genome shotgun sequence [...]
0.905028	NC_021246.1 Mythimna separata entomopoxvirus 'L', complete genome
0.905028	NZ_AP013293.1 Candidatus Sulcia muelleri PSPU DNA, complete genome

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Species composition by small subunit (SSU) presence in the assembly with MarkerScan.

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specimen	contig	SSU length	attributed taxonomy by SSU
drAngArch1	atg000104l	1186	ENA: Eukaryota;Viridiplantae;Streptophyta;Embryophyta;Tracheophyta;Spermatophyta;Magnoliophyta;eudicotyledons;Gunneridae;Pentapetalae;asterids;campanulids;Apiales; SILVA: Eukaryota;Archaeplastida;Chloroplastida;Charophyta;Phragmoplastophyta;Streptophyta;Embryophyta;Tracheophyta;Spermatophyta;Magnoliophyta;Apiales;
drAngArch1	atg001359l	1177	ENA: Eukaryota;Viridiplantae;Streptophyta;Embryophyta;Tracheophyta;Spermatophyta;Magnoliophyta;eudicotyledons;Gunneridae;Pentapetalae;asterids;campanulids;Apiales;Apiaceae;Apioideae; SILVA: Bacteria;Cyanobacteria;Cyanobacteriia;Chloroplast;
drAngArch1	atg001466l	1870	ENA: Eukaryota;Viridiplantae;Streptophyta;Embryophyta;Tracheophyta;Spermatophyta;Magnoliophyta;eudicotyledons;Gunneridae;Pentapetalae;asterids;campanulids;Apiales; SILVA: Eukaryota;Archaeplastida;Chloroplastida;Charophyta;Phragmoplastophyta;Streptophyta;Embryophyta;Tracheophyta;Spermatophyta;Magnoliophyta;Apiales;
drAngArch1	atg002981l	1480	ENA: Eukaryota;Viridiplantae;Streptophyta;Embryophyta;Tracheophyta;Spermatophyta;Magnoliophyta;eudicotyledons;Gunneridae;Pentapetalae;asterids;campanulids;Apiales;Apiaceae;Apioideae; SILVA: Bacteria;Cyanobacteria;Cyanobacteriia;Chloroplast;
drAngArch1	atg003829l	1143	ENA: Eukaryota;Viridiplantae;Streptophyta;Embryophyta;Tracheophyta;Spermatophyta;Magnoliophyta;eudicotyledons;Gunneridae;Pentapetalae;asterids;campanulids;Apiales; SILVA: Eukaryota;Archaeplastida;Chloroplastida;Charophyta;Phragmoplastophyta;Streptophyta;Embryophyta;Tracheophyta;Spermatophyta;Magnoliophyta;Apiales;
drAngArch1	atg003943l	1187	ENA: Eukaryota;Viridiplantae;Streptophyta;Embryophyta;Tracheophyta;Spermatophyta;Magnoliophyta;eudicotyledons;Gunneridae;Pentapetalae;asterids;campanulids;Apiales; SILVA: Eukaryota;Archaeplastida;Chloroplastida;Charophyta;Phragmoplastophyta;Streptophyta;Embryophyta;Tracheophyta;Spermatophyta;Magnoliophyta;Apiales;
drAngArch1	atg008476l	1807	ENA: Eukaryota;Viridiplantae;Streptophyta;Embryophyta;Tracheophyta;Spermatophyta;Magnoliophyta;eudicotyledons;Gunneridae;Pentapetalae;asterids;campanulids;Apiales; SILVA: Eukaryota;Archaeplastida;Chloroplastida;Charophyta;Phragmoplastophyta;Streptophyta;Embryophyta;Tracheophyta;Spermatophyta;Magnoliophyta;Apiales;
drAngArch1	atg009875l	1178	ENA: Eukaryota;Viridiplantae;Streptophyta;Embryophyta;Tracheophyta;Spermatophyta;Magnoliophyta;eudicotyledons;Gunneridae;Pentapetalae;asterids;campanulids;Apiales; SILVA: Eukaryota;Archaeplastida;Chloroplastida;Charophyta;Phragmoplastophyta;Streptophyta;Embryophyta;Tracheophyta;Spermatophyta;Magnoliophyta;Apiales;
drAngArch1	atg010059l	1491	ENA: Eukaryota;Viridiplantae;Streptophyta;Embryophyta;Tracheophyta;Spermatophyta;Magnoliophyta;eudicotyledons;Gunneridae;Pentapetalae;asterids;campanulids;Apiales;Apiaceae;Apioideae; SILVA: Bacteria;Cyanobacteria;Cyanobacteriia;Chloroplast;
drAngArch1	atg012416l	1186	ENA: Eukaryota;Viridiplantae;Streptophyta;Embryophyta;Tracheophyta;Spermatophyta;Magnoliophyta;eudicotyledons;Gunneridae;Pentapetalae;asterids;campanulids;Apiales; SILVA: Eukaryota;Archaeplastida;Chloroplastida;Charophyta;Phragmoplastophyta;Streptophyta;Embryophyta;Tracheophyta;Spermatophyta;Magnoliophyta;Apiales;

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MarkerScan cobiont assembly by read separation based on observed families (see above). These reads are both aligned to the assembly and independently re-assembled. The quality of these assemblies is assessed by their completeness according to BUSCO, their span and the number of reads they encompass. For more information here.

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specimen	family	classified reads			original assembly				re-assembly
specimen	family	count	(%)	BUSCO	BUSCO	contigs	contig length	number of reads	BUSCO	contigs	contig length	number of reads
drAngArch1	Rosaceae	6,307	0.07	C:4.6%[S:4.0%,D:0.6%],F:1.8%,M:93.6%,n:1614	C:0.1%[S:0.1%,D:0.0%],F:0.0%,M:99.9%,n:1614	8	0.31Mb	183	C:0.2%[S:0.1%,D:0.1%],F:0.0%,M:99.8%,n:1614	61	1.87Mb	42,100

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Visualisation of a classification of the PacBio reads using a variation autoencoder on the k-mer counts.

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specimen	visualisation
drAngArch1

Canonical tetranucleotide counts for each contig or scaffold reduced to two dimensions with UMAP to allow visualisation.

Features (colours represent quantile bins):

Hexamer: Estimated coding density (expected to be higher in microbes than in animals).
FastK: The median number of times each 60-mer in the sequence occures across the whole assembly (illustrates repetitiveness)
Unique_15mers: Number of unique 15-mers per base pair (illustrates sequence diversity)
Is_Connected: Presence of at least one Hi-C connection to another scaffold (absence of connections can indicate contamination)
Connections_Base: Number of Hi-C connections per base pair

drAngArch1.hifiasm.20231111

specimen	asm	date	contig N50	contigs	scaffold N50	scaffolds	length	BUSCO	merqury
drAngArch1	hifiasm-hic	2023-11-11	2,058,394	2,924			2,926,159,539	C:97.3%[S:85.6%,D:11.7%],F:0.6%,M:2.1%,n:2326	-
drAngArch1	hifiasm-hic.purging	2023-11-11	2,274,209	1,724			2,208,514,128	C:84.0%[S:76.0%,D:8.0%],F:1.1%,M:14.9%,n:2326	Q62.2-C78.2(HiFi)
drAngArch1	hifiasm-hic	2023-11-11	1,958,175	3,796			2,891,706,157	C:96.3%[S:85.6%,D:10.7%],F:0.7%,M:3.0%,n:2326	Q60.3-C96.7(HiFi)
drAngArch1	hifiasm-hic	2023-11-11	2,962,088	2,987			3,168,107,011		-
drAngArch1	hifiasm-hic.scaffolding.yahs	2023-11-11	2,196,322	1,825	209,378,626	256	2,208,827,928	C:84.2%[S:76.3%,D:7.9%],F:1.1%,M:14.7%,n:2326	Q62.2-C78.2(HiFi)
drAngArch1	hifiasm.purging	2023-11-11	3,583,597	1,039			1,949,074,664	C:74.9%[S:67.5%,D:7.4%],F:1.1%,M:24.0%,n:2326	Q62.0-C77.7(HiFi)
drAngArch1	hifiasm	2023-11-11	2,981,441	2,940			3,157,844,079	C:98.7%[S:82.8%,D:15.9%],F:0.5%,M:0.8%,n:2326	Q60.1-C96.7(HiFi)
drAngArch1	hifiasm.scaffolding.yahs	2023-11-11	3,279,503	1,148	155,390,684	239	1,949,256,464	C:74.8%[S:67.6%,D:7.2%],F:1.1%,M:24.1%,n:2326	Q62.0-C77.7(HiFi)

specimen	asm	organelle	date	length	genes	frameshifts	is circular	reference
drAngArch1	oatk.reads	mito	2023-11-11	301,562	58	None	False	NC_082207.1; 281,432 bp; 55 genes
drAngArch1	oatk.reads	pltd	2023-11-11	145,653	108	rpoC1;rps16	True	OR209162.1; 146,811 bp; 128 genes

Angelica archangelica

Info

Specimens

Spectra estimates

Sequence data

PacBio run data

ONT run data

Illumina run data

Cobionts

drAngArch1.hifiasm.20231111

Assemblies

Organelles

Angelica archangelica

Mash screen

MarkerScan: species composition

MarkerScan: cobiont assembly

Readviz classification

Contigviz classification

drAngArch1.hifiasm.20231111