Tree of Life QC: Species Report - Pemphredon lugubris

Info

NCBI taxon id:	2495172
Order:	Hymenoptera
Family:	Crabronidae
NCBI lineage:	Eukaryota;Metazoa;Ecdysozoa;Arthropoda;Hexapoda;Insecta;Pterygota;Neoptera;Endopterygota;Hymenoptera;Apocrita;Aculeata;Apoidea;Spheciformes;Crabronidae;Pemphredoninae;Pemphredonini;Pemphredonina;Pemphredon;
GoaT genome size (M):	413 (ancestor)
GoaT asm span (M):	328 (direct)
GoaT chr no.:	16 (ancestor)
ToLID prefix:	iyPemLugu

Specimens

Below is information about specimens collected for this species retrieved from the Golden Record manifest.

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public_name	specimen_id	gal	sex	organism_part	biosample	biospecimen
iyPemLugu1	Ox000901	UNIVERSITY OF OXFORD	NOT_COLLECTED	HEAD	SAMEA8603434	SAMEA8603139
iyPemLugu1	Ox000901	UNIVERSITY OF OXFORD	NOT_COLLECTED	THORAX	SAMEA8603436	SAMEA8603139
iyPemLugu1	Ox000901	UNIVERSITY OF OXFORD	NOT_COLLECTED	ABDOMEN	SAMEA8603438	SAMEA8603139

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Spectra estimates

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

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source	specimen	k-mer	k-cov	haploid size	repeat (%)	heterozygosity (%)	model fit (%)	model error (%)
10x	iyPemLugu1	31	40.93	519,654,337	57.59	0.10	97.41	0.56
pacbio	iyPemLugu1	31	28.93	283,548,817	24.76	0.32	94.16	0.26
hic-arima2	iyPemLugu1	31	90.39	521,660,983	84.45	0.45	97.10	0.53

Sequence data

PacBio run data

Below are stats for each PacBio seqeuncing run collected for this species.

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pipeline	specimen	date	run id	movie	well	tag	yield	N50	sample accession	run accession	barcode
PacBio - HiFi	iyPemLugu1	2021-08-30	86005	m64178e_210830_172053	D01	1012	17,824,828,980	10,709	SAMEA8603436	ERR8575361

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id	taxon	similarity	seq	country	latitude	longitude
FBACA527-10	Pemphredon lugubris	1	COI-5P	Germany	48.776	12.948
NOSPH032-13	Hymenoptera	1	COI-5P	Norway	59.44	8.783
NOFOR166-14	Hymenoptera	1	COI-5P	Norway	63.347	10.227
NOFOR165-14	Hymenoptera	1	COI-5P	Norway	62.5726	11.4125
NOSPH029-13	Hymenoptera	0.9985	COI-5P	Norway	59.759	10.041
NOSPH031-13	Hymenoptera	0.9985	COI-5P	Norway	59.293	11.043
NOFOR164-14	Hymenoptera	0.9985	COI-5P	Norway	61.868	9.02
ARTNO181-17	Pemphredon lugubris	0.9984	COI-5P	Norway	59.8522	10.5474
NODRY083-14	Hymenoptera	0.9983	COI-5P	Norway	60.075	10.21
AMTPA2746-15	Pemphredon lugubris	0.9982	COI-5P	Germany	47.387	10.344

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Illumina run data

Illumina run stats.

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pipeline	specimen	date	run id	read pairs	yield	sample accession	run accession	run status	barcode
Chromium genome	iyPemLugu1	2021-06-28	38852_3#1	102,912,620	15,539,805,620	SAMEA8603436	ERR8571634	qc complete	Pemphredon lugubris (1.00)
Chromium genome	iyPemLugu1	2021-06-28	38852_3#2	110,313,082	16,657,275,382	SAMEA8603436	ERR8571635	qc complete	Pemphredon lugubris (1.00)
Chromium genome	iyPemLugu1	2021-06-28	38852_3#4	107,577,258	16,244,165,958	SAMEA8603436	ERR8571637	qc complete	Pemphredon lugubris (1.00)
Chromium genome	iyPemLugu1	2021-06-28	38852_3#3	141,137,388	21,311,745,588	SAMEA8603436	ERR8571636	qc complete	Pemphredon lugubris (1.00)
Hi-C - Arima v2	iyPemLugu1	2021-11-23	42033_2#3	916,220,052	138,349,227,852	SAMEA8603434	ERR8571639	qc complete	Pemphredon lugubris (1.00)
RNA PolyA	iyPemLugu1	2021-09-17	40838_7#6	34,726,128	5,243,645,328	SAMEA8603438	ERR8571638	qc complete	Pemphredon lugubris (1.00)

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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
No matching records found

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

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specimen	contig	SSU length	attributed taxonomy by SSU
iyPemLugu1	ptg000103l	1859	ENA: Eukaryota;Fungi; SILVA: Eukaryota;Amorphea;Obazoa;Opisthokonta;Nucletmycea;Fungi;Zoopagomycota;Entomophthoromycotina;Entomophthoromycetes;Entomophthorales;Entomophthoraceae;Entomophthora;
iyPemLugu1	ptg001766l	1928	ENA: Eukaryota;Metazoa;Ecdysozoa;Arthropoda;Hexapoda;Insecta;Pterygota;Neoptera;Holometabola;Hymenoptera;Apocrita;Aculeata;Sphecoidea;Crabronidae; SILVA: Eukaryota;Amorphea;Obazoa;Opisthokonta;Holozoa;Choanozoa;Metazoa;Animalia;BCP clade;Bilateria;Protostomia;Ecdysozoa;Arthropoda;Hexapoda;Insecta;Pterygota;Neoptera;Hymenoptera;

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Re-assembly of reads classified under each identified SSU Marker family.

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specimen	family	classified reads			original assembly				re-assembly
specimen	family	count	(%)	BUSCO	BUSCO	contigs	contig length	reads	BUSCO	contigs	contig length	additional reads	circos
iyPemLugu1	Entomophthoraceae	222,352	10.45	Too many reads - NA	C:3.6%[S:3.6%,D:0.0%],F:0.8%,M:95.6%,n:758	78	0.68Mb	1,924	C:31.0%[S:29.8%,D:1.2%],F:5.7%,M:63.3%,n:758	347	9.69Mb	31,982

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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
iyPemLugu1

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

BTK datasets:

iyPemLugu1Pri_2

Assemblies

In-progress assembly QC.

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specimen	asm	date	contig N50	contigs	scaffold N50	scaffolds	length	BUSCO	merqury
iyPemLugu1	hifiasm	2021-11-25	21,615,749	2,178			327,420,272		-
iyPemLugu1	hifiasm	2021-11-25	21,615,749	2,453			334,992,788	C:99.5%[S:99.1%,D:0.4%],F:0.1%,M:0.4%,n:1367	-
iyPemLugu1	hifiasm.scaff.salsa	2021-11-25	21,417,186	2,466	24,038,185	2,347	335,047,114		-
iyPemLugu1	hifiasm.scaff.yahs	2021-11-25	21,417,186	2,482	29,616,010	2,474	334,989,214		-
iyPemLugu1	hicanu.purging	2021-11-24	21,414,988	2,834			318,768,655	C:99.3%[S:98.8%,D:0.5%],F:0.1%,M:0.6%,n:1367	Q29.5-C94.4(10X); Q65.6-C99.1(HiFi)
iyPemLugu1	hicanu	2021-11-24	19,395,268	4,437			354,982,500	C:99.3%[S:98.3%,D:1.0%],F:0.1%,M:0.6%,n:1367	Q29.1-C94.5(10X); Q64.8-C99.2(HiFi)
iyPemLugu1	hifiasm	2021-11-24	24,038,414	1,931			320,836,855	C:99.4%[S:99.0%,D:0.4%],F:0.1%,M:0.5%,n:1367	Q31.1-C94.4(10X); Q59.3-C99.0(HiFi)
iyPemLugu1	hifiasm.purging	2021-11-24	24,038,414	1,523			314,628,500	C:99.4%[S:99.0%,D:0.4%],F:0.1%,M:0.5%,n:1367	Q31.5-C94.4(10X); Q60.2-C98.9(HiFi)

Organelles

In-progress organelle results from MitoHiFi2.

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specimen	asm	date	length	genes	frameshifts	is circular	reference
iyPemLugu1	hicanu	2021-11-24	31,789	35	None		MW402864.1; 16,188 bp; 37 genes
iyPemLugu1	reads	2021-11-24	17,762	30	None	False	MW402864.1; 16,188 bp; 37 genes
iyPemLugu1	hifiasm	2021-11-24	31,707	35	None		MW402864.1; 16,188 bp; 37 genes

Pemphredon lugubris

Mash screen

SSU Marker species

SSU Marker re-assembly

Readviz classification

Contigviz classification

BlobToolKit