Tree of Life QC: Species Report - Watsonalla cultraria

NCBI taxon id:	721166 NCBI; ENA; GoaT
Order:	Lepidoptera
Family:	Drepanidae
NCBI lineage:	Eukaryota;Metazoa;Ecdysozoa;Arthropoda;Hexapoda;Insecta;Pterygota;Neoptera;Endopterygota;Lepidoptera;Glossata;Ditrysia;Drepanoidea;Drepanidae;Drepaninae;Watsonalla;
GoaT genome size (M):	317 (ancestor)
GoaT asm span (M):	333 (ancestor)
GoaT chr no.:	62 (ancestor)
GoaT haploid no.:	31 (ancestor)
GoaT ploidy:	2 (ancestor)
ToLID prefix:	ilWatCult

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
ilWatCult1	Ox000407	UNIVERSITY OF OXFORD	NOT_COLLECTED	WHOLE_ORGANISM	SAMEA7520624	SAMEA7520529
ilWatCult2	Ox003068	UNIVERSITY OF OXFORD	NOT_COLLECTED	WHOLE_ORGANISM	SAMEA112775080	SAMEA112775017

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	ilWatCult2	31	33.24	326,320,060	20.56	0.07	98.53	0.08	histogram.txt
10x	ilWatCult1	31	31.92	617,602,827	43.03	1.87	98.06	0.44	histogram.txt
pacbio	ilWatCult1	31	7.33	1,740,930,242	39.32	1.31	98.51	0.17	histogram.txt
hic-arima2	ilWatCult1	31	91.19	296,231,433	15.51	0.49	97.16	0.58	histogram.txt

pipeline	specimen	date	run id	movie	well	tag	yield	N50	sample accession
PacBio - HiFi	ilWatCult1	2020-09-25	77509	m64089_200925_144141	B01	1009	5,412,902,172	12,850	SAMEA7520624
PacBio - HiFi	ilWatCult1	2020-09-27	77510	m64094_200927_153848	D01	1019	21,565,041,479	13,874	SAMEA7520624
PacBio - HiFi	ilWatCult2	2024-02-09	TRACTION-RUN-1121	m84047_240209_114632_s1	C01	2053	22,326,612,984	12,430	SAMEA112775080

id	taxon	similarity	seq	country	latitude	longitude
LON1292-14	Watsonalla cultraria	1	COI-5P	Norway	59.363	10.679
LON4823-16	Watsonalla cultraria	1	COI-5P	Norway	58.3882	8.71108
GWOR3790-09	Watsonalla cultraria	1	COI-5P	Germany	48.0431	11.1736
GWOR3960-09	Watsonalla cultraria	1	COI-5P	Germany	48.41	11.87
FBLMU926-09	Watsonalla cultraria	1	COI-5P	Germany	48.5349	13.4343
GWORK501-09	Watsonalla cultraria	1	COI-5P	Germany	47.8486	11.595
PHLAA244-09	Watsonalla cultraria	1	COI-5P	Austria	47.5578	14.1706
LEFIL543-10	Watsonalla cultraria	1	COI-5P	Germany	[object Object]	[object Object]
LENOA759-11	Watsonalla cultraria	1	COI-5P	France	49.4849	0.92396
LENOA760-11	Watsonalla cultraria	1	COI-5P	France	49.434	0.714

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 status	barcode
Chromium genome	ilWatCult1	2020-10-05	35148_4#3	96,906,192	14,632,834,992	SAMEA7520624	qc complete
Chromium genome	ilWatCult1	2020-10-05	35148_4#1	106,651,670	16,104,402,170	SAMEA7520624	qc complete
Chromium genome	ilWatCult1	2020-10-05	35148_4#2	121,383,888	18,328,967,088	SAMEA7520624	qc complete
Chromium genome	ilWatCult1	2020-10-05	35148_4#4	87,475,082	13,208,737,382	SAMEA7520624	qc complete
Hi-C - Arima v2	ilWatCult1	2020-10-08	35150_2#5	166,799,966	25,186,794,866	SAMEA7520624	qc complete	Watsonalla cultraria (1.00)
Hi-C - Arima v2	ilWatCult1	2020-10-08	35150_4#5	184,558,278	27,868,299,978	SAMEA7520624	qc complete	Watsonalla cultraria (1.00)
Hi-C - Arima v2	ilWatCult1	2020-10-08	35150_3#5	181,344,374	27,383,000,474	SAMEA7520624	qc complete	Watsonalla cultraria (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
0.999522	[120 seqs] NZ_JYPC01000001.1 Wolbachia endosymbiont of Operophtera brumata strain Ob_Wba WbOb01_Sc001, whole genome shotgun sequence [...]
0.962075	[50 seqs] NZ_MIKA01000001.1 Enterococcus plantarum strain LMG 26214, whole genome shotgun sequence [...]
0.934669	[64 seqs] NZ_JRFX01000001.1 Lactococcus lactis strain Bpl1 NODE_47, whole genome shotgun sequence [...]
0.91934	[608 seqs] NZ_MAYS01000001.1 Candidatus Erwinia dacicola strain IL contig_1, whole genome shotgun sequence [...]
0.907748	NC_018417.1 Candidatus Carsonella ruddii HT isolate Thao2000, complete genome
0.905028	[20 seqs] NZ_AYZL01000001.1 Lactobacillus floricola DSM 23037 = JCM 16512 strain DSM 23037 NODE_1, whole genome shotgun sequence [...]

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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
ilWatCult2	ptg000046c	1499	ENA: Bacteria;Proteobacteria;Alphaproteobacteria;Rickettsiales;Anaplasmataceae;Wolbachieae;Wolbachia; SILVA: Bacteria;Proteobacteria;Alphaproteobacteria;Rickettsiales;Anaplasmataceae;Wolbachia;
ilWatCult2	ptg000061l	1898	ENA: Eukaryota;Metazoa;Ecdysozoa;Arthropoda;Hexapoda;Insecta;Pterygota;Neoptera; SILVA: Eukaryota;Amorphea;Obazoa;Opisthokonta;Holozoa;Choanozoa;Metazoa;Animalia;BCP clade;Bilateria;Protostomia;Ecdysozoa;Arthropoda;Hexapoda;Insecta;Pterygota;Neoptera;Amphiesmenoptera;Lepidoptera;
ilWatCult2	ptg000094l	1487	ENA: Eukaryota;Viridiplantae;Streptophyta;Embryophyta;Tracheophyta;Spermatophyta;Magnoliophyta;eudicotyledons;Gunneridae;Pentapetalae;rosids;fabids;Fagales;Fagaceae;Quercus; SILVA: Bacteria;Cyanobacteria;Cyanobacteriia;Chloroplast;
ilWatCult2	ptg000142l	1807	ENA: Eukaryota;Viridiplantae;Streptophyta;Embryophyta;Tracheophyta;Spermatophyta;Magnoliophyta;eudicotyledons;Gunneridae;Pentapetalae;rosids;fabids;Fagales; SILVA: Eukaryota;Archaeplastida;Chloroplastida;Charophyta;Phragmoplastophyta;Streptophyta;Embryophyta;Tracheophyta;Spermatophyta;Magnoliophyta;Fagales;
ilWatCult2	ptg000143l	1536	ENA: Bacteria;Proteobacteria;Gammaproteobacteria;Enterobacterales;Erwiniaceae; SILVA: Bacteria;Proteobacteria;Gammaproteobacteria;Enterobacterales;Erwiniaceae;Erwinia;
ilWatCult2	ptg000147l	1534	ENA: Unclassified; SILVA: Bacteria;Proteobacteria;Gammaproteobacteria;Enterobacterales;Orbaceae;
ilWatCult2	ptg000155l	1109	ENA: Eukaryota;Viridiplantae;Streptophyta;Embryophyta;Tracheophyta;Spermatophyta;Magnoliophyta;eudicotyledons;Gunneridae;Pentapetalae;rosids; SILVA: Bacteria;Proteobacteria;Alphaproteobacteria;Rickettsiales;Mitochondria;

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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
ilWatCult2	Anaplasmataceae	55,120	2.62	C:100.0%[S:0.0%,D:100.0%],F:0.0%,M:0.0%,n:364	C:99.8%[S:95.1%,D:4.7%],F:0.0%,M:0.2%,n:364	7	1.64Mb	55,019	C:99.8%[S:99.5%,D:0.3%],F:0.0%,M:0.2%,n:364	1	1.52Mb	54,960
ilWatCult2	Erwiniaceae	1,478	0.07	C:87.3%[S:27.3%,D:60.0%],F:6.1%,M:6.6%,n:440	C:57.1%[S:56.6%,D:0.5%],F:8.4%,M:34.5%,n:440	56	3.20Mb	1,092	C:50.5%[S:50.0%,D:0.5%],F:5.9%,M:43.6%,n:440	62	2.81Mb	1,017
ilWatCult2	Fagaceae	2,688	0.13	C:3.3%[S:3.2%,D:0.1%],F:1.8%,M:94.9%,n:1614	C:0.1%[S:0.1%,D:0.0%],F:0.0%,M:99.9%,n:1614	9	0.34Mb	188	C:0.1%[S:0.1%,D:0.0%],F:0.0%,M:99.9%,n:1614	9	0.24Mb	174
ilWatCult2	Orbaceae	371	0.02	C:63.4%[S:31.7%,D:31.7%],F:11.5%,M:25.1%,n:366	C:29.0%[S:28.7%,D:0.3%],F:6.3%,M:64.7%,n:366	17	0.61Mb	126	C:27.1%[S:26.8%,D:0.3%],F:6.0%,M:66.9%,n:366	18	0.57Mb	144

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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
ilWatCult1

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

ilWatCult2.hifiasm.20240213

specimen	asm	date	contig N50	contigs	scaffold N50	scaffolds	length	BUSCO	merqury
ilWatCult2	hifiasm.purging	2024-02-13	6,871,409	144			322,019,959	C:98.4%[S:98.0%,D:0.4%],F:0.7%,M:0.9%,n:1367	Q62.0-C99.4(HiFi)
ilWatCult2	hifiasm	2024-02-13	6,871,409	214			326,871,476	C:98.5%[S:98.0%,D:0.5%],F:0.7%,M:0.8%,n:1367	Q60.9-C99.8(HiFi)
ilWatCult2	hifiasm.scaffolding.yahs	2024-02-13	6,829,000	147	11,404,046	96	322,030,159	C:98.6%[S:98.2%,D:0.4%],F:0.7%,M:0.7%,n:1367	Q62.0-C99.4(HiFi)

specimen	asm	organelle	date	length	genes	frameshifts	is circular	reference
ilWatCult2	mitohifi.hifiasm	mito	2024-02-13	15,211	37	None	True	MH324504.1; 15,339 bp; 37 genes
ilWatCult2	mitohifi.reads	mito	2024-02-13	15,215	37	None	True	MH324504.1; 15,339 bp; 37 genes

Watsonalla cultraria

Info

Specimens

Spectra estimates

Sequence data

PacBio run data

ONT run data

Illumina run data

Cobionts

ilWatCult2.hifiasm.20240213

Assemblies

Organelles

Watsonalla cultraria

Mash screen

MarkerScan: species composition

MarkerScan: cobiont assembly

Readviz classification

Contigviz classification

ilWatCult2.hifiasm.20240213