Tree of Life QC: Species Report

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

NCBI taxon id:	537462
Order:	Lepidoptera
Family:	Hepialidae
NCBI lineage:	Eukaryota;Metazoa;Ecdysozoa;Arthropoda;Hexapoda;Insecta;Pterygota;Neoptera;Endopterygota;Lepidoptera;Glossata;Exoporia;Hepialoidea;Hepialidae;Triodia;
GoaT genome size (M):	488 (ancestor)
GoaT asm span (M):	566 (ancestor)
GoaT chr no.:	56 (ancestor)
GoaT ploidy:	2 (ancestor)
ToLID prefix:	ilTriSylv

public_name	specimen_id	gal	sex	organism_part	biosample	biospecimen
ilTriSylv1	Ox000181	UNIVERSITY OF OXFORD	NOT_COLLECTED	THORAX	SAMEA7519964	SAMEA7519925
ilTriSylv1	Ox000181	UNIVERSITY OF OXFORD	NOT_COLLECTED	HEAD	SAMEA7519964	SAMEA7519925
ilTriSylv1	Ox000181	UNIVERSITY OF OXFORD	NOT_COLLECTED	ABDOMEN	SAMEA7519963	SAMEA7519925
ilTriSylv2	Ox000182	UNIVERSITY OF OXFORD	NOT_COLLECTED	THORAX	SAMEA7519965	SAMEA7519926
ilTriSylv2	Ox000182	UNIVERSITY OF OXFORD	NOT_COLLECTED	HEAD	SAMEA7519965	SAMEA7519926

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

source	specimen	k-mer	k-cov	haploid size	repeat (%)	heterozygosity (%)	model fit (%)	model error (%)
hic-qiagen	ilTriSylv1	31	21.45	2,105,914,757	0.00	20.26	5.57	0.27
10x	ilTriSylv1	31	16.46	2,630,644,776	46.94	1.35	98.87	0.34
pacbio	ilTriSylv1	31	14.53	668,006,093	64.22	12.38	70.59	1.69

pipeline	specimen	date	run id	movie	well	tag	yield	N50	sample accession	run accession	barcode
PacBio - HiFi	ilTriSylv1	2019-10-21	72393	m64089_191021_113836	C01	1012	10,606,738,705	13,642	SAMEA7519963
PacBio - HiFi	ilTriSylv1	2020-05-16	76089	m64097_200516_172809	B01	1011	22,421,698,231	10,373	SAMEA7519963

id	taxon	similarity	seq	country	latitude	longitude
LEPVM023-12	Triodia sylvina	1	COI-5P	Denmark	56.367	10.733
GMGMB010-14	Triodia sylvina	1	COI-5P	Germany	50.552	7.17
GMGMD242-14	Triodia sylvina	1	COI-5P	Germany	50.552	7.17
GMGMD018-14	Triodia sylvina	1	COI-5P	Germany	50.552	7.17
GMGMD020-14	Triodia sylvina	1	COI-5P	Germany	50.552	7.17
GMGMD040-14	Triodia sylvina	1	COI-5P	Germany	50.552	7.17
GMGMD243-14	Triodia sylvina	1	COI-5P	Germany	50.552	7.17
GMGMD034-14	Triodia sylvina	1	COI-5P	Germany	50.552	7.17
GMGMD033-14	Triodia sylvina	1	COI-5P	Germany	50.552	7.17
GMGMD021-14	Triodia sylvina	1	COI-5P	Germany	50.552	7.17

pipeline	specimen	date	run id	read pairs	yield	sample accession	run status	barcode
Hi-C - Qiagen	ilTriSylv1	2020-03-04	33514_1#1	812,685,914	122,715,573,014	SAMEA7519964	qc complete	Triodia sylvina (1.00)
Chromium genome	ilTriSylv1	2020-01-13	32386_4#2	234,719,486	35,442,642,386	SAMEA7519963	qc complete	Triodia sylvina (1.00)
Chromium genome	ilTriSylv1	2020-01-13	32386_4#4	233,616,212	35,276,048,012	SAMEA7519963	qc complete	Triodia sylvina (1.00)
Chromium genome	ilTriSylv1	2020-01-13	32386_4#1	173,308,530	26,169,588,030	SAMEA7519963	qc complete	Triodia sylvina (1.00)
Chromium genome	ilTriSylv1	2020-01-13	32386_4#3	235,894,652	35,620,092,452	SAMEA7519963	qc complete	Triodia sylvina (1.00)
RNA PolyA	ilTriSylv6	2023-02-16	46781_2#23	71,437,164	10,787,011,764	SAMEA10979657	qc complete	Triodia sylvina (1.00)

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
0.995415	NC_021089.1 Wolbachia endosymbiont of Drosophila simulans wHa, complete genome
0.965939	[74 seqs] NZ_AGNS01000074.1 Carnobacterium maltaromaticum ATCC 35586 contig00099, whole genome shotgun sequence [...]
0.941977	NC_018417.1 Candidatus Carsonella ruddii HT isolate Thao2000, complete genome
0.932984	[256 seqs] NZ_ACFP01000256.1 Wolbachia endosymbiont of Muscidifurax uniraptor Contig561, whole genome shotgun sequence [...]
0.918041	[2 seqs] NC_008513.1 Buchnera aphidicola BCc, complete genome [...]
0.91616	[28 seqs] NZ_LTBM01000001.1 Candidatus Phytoplasma oryzae isolate Mbita1 Pmin.contig.0_1, whole genome shotgun sequence [...]
0.915329	[2017 seqs] NW_004087753.1 Ichthyophthirius multifiliis unplaced genomic scaffold scaff_1120509249386, whole genome shotgun sequence [...]
0.91333	[777 seqs] NC_033646.1 Plasmodium reichenowi strain SY57 chromosome 1, whole genome shotgun sequence [...]
0.912743	[3 seqs] NZ_LN890285.1 Buchnera aphidicola (Tuberolachnus salignus) strain BTs genome assembly, chromosome: 1 [...]
0.912148	NC_002520.1 Amsacta moorei entomopoxvirus 'L', complete genome

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

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specimen	contig	SSU length	attributed taxonomy by SSU
ilTriSylv1	ptg002732l	1902	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;
ilTriSylv1	ptg006773l	559	ENA: Eukaryota;Metazoa;Ecdysozoa;Arthropoda;Hexapoda;Insecta;Pterygota;Neoptera;Holometabola;Lepidoptera;Glossata; SILVA: Eukaryota;Amorphea;Obazoa;Opisthokonta;Holozoa;Choanozoa;Metazoa;Animalia;BCP clade;Bilateria;Protostomia;Ecdysozoa;Arthropoda;Hexapoda;Insecta;Pterygota;Neoptera;Amphiesmenoptera;Lepidoptera;
ilTriSylv1	ptg010894l	1551	ENA: Bacteria;Firmicutes;Bacilli;Lactobacillales;Carnobacteriaceae;Carnobacterium; SILVA: Bacteria;Firmicutes;Bacilli;Lactobacillales;Carnobacteriaceae;Carnobacterium;
ilTriSylv1	ptg012720l	1107	ENA: Eukaryota;Metazoa;Ecdysozoa;Arthropoda;Hexapoda;Insecta;Pterygota;Neoptera;Holometabola;Lepidoptera;Glossata; SILVA: Eukaryota;Amorphea;Obazoa;Opisthokonta;Holozoa;Choanozoa;Metazoa;Animalia;BCP clade;Bilateria;Protostomia;Ecdysozoa;Arthropoda;Hexapoda;Insecta;Pterygota;Neoptera;Amphiesmenoptera;Lepidoptera;
ilTriSylv1	ptg018260l	1500	ENA: Bacteria;Proteobacteria;Alphaproteobacteria;Rickettsiales;Anaplasmataceae;Wolbachieae;Wolbachia; SILVA: Bacteria;Proteobacteria;Alphaproteobacteria;Rickettsiales;Anaplasmataceae;Wolbachia;
ilTriSylv1	ptg018368l	1985	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;Diptera;

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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
ilTriSylv1	Anaplasmataceae	1,163	0.04	C:97.5%[S:4.9%,D:92.6%],F:1.4%,M:1.1%,n:364	C:94.2%[S:93.1%,D:1.1%],F:1.1%,M:4.7%,n:364	15	1.29Mb	1,033	C:97.8%[S:95.9%,D:1.9%],F:0.8%,M:1.4%,n:364	5	1.59Mb	80
ilTriSylv1	Carnobacteriaceae	456	0.01	C:49.7%[S:34.3%,D:15.4%],F:13.4%,M:36.9%,n:402	C:0.0%[S:0.0%,D:0.0%],F:0.0%,M:100.0%,n:402	1	0.01Mb	9	C:4.7%[S:4.7%,D:0.0%],F:1.0%,M:94.3%,n:402	11	0.27Mb	71

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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
ilTriSylv1

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

ilTriSylv1.hifiasm.20220915

Assemblies

specimen	asm	date	contig N50	contigs	scaffold N50	scaffolds	length	BUSCO	merqury
ilTriSylv1	hifiasm-hic	2022-09-15	265,540	19,555			2,828,661,927	C:97.0%[S:85.7%,D:11.3%],F:1.5%,M:1.5%,n:1367	Q37.9-C92.2(10X); Q52.6-C97.0(HiFi)
ilTriSylv1	hifiasm	2022-09-15	267,699	19,288			2,825,028,881	C:96.9%[S:86.1%,D:10.8%],F:1.5%,M:1.6%,n:1367	Q37.9-C92.1(10X); Q52.5-C97.0(HiFi)
ilTriSylv1	hifiasm.purging	2022-09-15	288,745	15,551			2,526,539,493	C:96.6%[S:92.9%,D:3.7%],F:1.7%,M:1.7%,n:1367	Q37.9-C91.8(10X); Q52.5-C96.7(HiFi)
ilTriSylv1	hifiasm.scaffolding.yahs	2022-09-15	266,576	17,292	898,819	12,811	2,527,435,693		-
ilTriSylv1	hicanu.purging	2022-09-15	109,802	37,917			2,735,586,838	C:93.0%[S:85.5%,D:7.5%],F:4.9%,M:2.1%,n:1367	Q38.7-C92.0(10X); Q61.6-C97.4(HiFi)
ilTriSylv1	hicanu	2022-09-15	85,666	74,740			4,465,784,699	C:95.9%[S:41.0%,D:54.9%],F:3.1%,M:1.0%,n:1367	Q38.4-C99.1(10X); Q61.6-C100.0(HiFi)

Organelles

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specimen	asm	date	length	genes	frameshifts	is circular	reference
ilTriSylv1	hifiasm-hic	2022-09-15	15,977	36	None	True	NC_040921.1; 15,040 bp; 37 genes
ilTriSylv1	hifiasm	2022-09-15	15,977	36	None	True	NC_040921.1; 15,040 bp; 37 genes
ilTriSylv1	hicanu	2022-09-15	15,979	36	None	True	NC_040921.1; 15,040 bp; 37 genes
ilTriSylv1	reads	2022-09-15	15,977	36	None	True	NC_040921.1; 15,040 bp; 37 genes

Triodia sylvina

Info

Specimens

Spectra estimates

Sequence data

PacBio run data

Illumina run data

Cobionts

ilTriSylv1.hifiasm.20220915

Assemblies

Organelles

Triodia sylvina

Mash screen

SSU Marker species

SSU Marker re-assembly

Readviz classification

Contigviz classification

ilTriSylv1.hifiasm.20220915