Tree of Life QC: Species Report

NCBI taxon id:	204328 NCBI; ENA; GoaT
Order:	Alcyonacea
Family:	Plexauridae
NCBI lineage:	Eukaryota;Metazoa;Cnidaria;Anthozoa;Octocorallia;Malacalcyonacea;Plexauridae;Muricea;
GoaT genome size (M):	625 (ancestor)
GoaT asm span (M):	453 (direct)
GoaT chr no.:	18 (ancestor)
GoaT haploid no.:	6 (ancestor)
GoaT ploidy:	12 (ancestor)
ToLID prefix:	jaMurMuri

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
jaMurMuri3	NSU0025901	NOVA SOUTHEASTERN UNIVERSITY	NOT_APPLICABLE	OTHER_SOMATIC_ANIMAL_TISSUE	SAMEA12927224	SAMEA12927197
jaMurMuri3	NSU0025901	NOVA SOUTHEASTERN UNIVERSITY	NOT_APPLICABLE	OTHER_SOMATIC_ANIMAL_TISSUE	SAMEA12927224	SAMEA12927197
jaMurMuri3	NSU0025901	NOVA SOUTHEASTERN UNIVERSITY	NOT_APPLICABLE	OTHER_SOMATIC_ANIMAL_TISSUE	SAMEA12927224	SAMEA12927197
jaMurMuri3	NSU0025901	NOVA SOUTHEASTERN UNIVERSITY	NOT_APPLICABLE	OTHER_SOMATIC_ANIMAL_TISSUE	SAMEA12927224	SAMEA12927197
jaMurMuri3	NSU0025901	NOVA SOUTHEASTERN UNIVERSITY	NOT_APPLICABLE	OTHER_SOMATIC_ANIMAL_TISSUE	SAMEA12927224	SAMEA12927197

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	jaMurMuri3	31	85.33	781,578,294	76.41	0.25	88.94	0.15	histogram.txt
illumina	jaMurMuri3	31	104.6	439,576,404	44.12	1.44	93.47	0.35	histogram.txt
hic-arima2	jaMurMuri4	31	61.69	453,985,297	49.57	1.95	98.35	0.58	histogram.txt

pipeline	specimen	date	run id	movie	well	tag	yield	N50	sample accession
PacBio - HiFi	jaMurMuri3	2022-06-21	TRACTION-RUN-144	m64229e_220621_162416	D01	1003	22,432,354,518	14,054	SAMEA12927224
PacBio - HiFi (ULI)	jaMurMuri3	2022-08-06	TRACTION-RUN-198	m64178e_220806_112901	C01	1016	26,433,163,265	11,041	SAMEA12927224
PacBio - HiFi (ULI)	jaMurMuri3	2025-01-23	TRACTION-RUN-1735	m84047_250123_113456_s1	A01	1016	47,062,527,687	11,618	SAMEA12927224
PacBio - HiFi	jaMurMuri3	2025-05-31	TRACTION-RUN-1929	m84093_250531_142937_s2	B01	2060	44,287,102,119	11,951	SAMEA12927224

id	taxon	similarity	seq	country	latitude	longitude
ABBAC197-12	Muricea muricata	1	COI-5P	Panama	9.35	-82.25
ABBAC187-12	Muricea muricata	1	COI-5P	Panama	9.35	-82.25
GBMNA12088-19	Muricea purpurea	1	COI-5P	[object Object]	[object Object]	[object Object]
GBCI10661-19	Muricea purpurea	1	COI-5P	[object Object]	[object Object]	[object Object]
GBCI4016-14	Muricea fruticosa	1	COI-5P	Panama	[object Object]	[object Object]
GBCI4017-14	Muricea sp. HMG81	1	COI-5P	Panama	[object Object]	[object Object]
GBMNA12087-19	Muricea crassa	1	COI-5P	[object Object]	[object Object]	[object Object]
GBCI10660-19	Muricea crassa	1	COI-5P	[object Object]	[object Object]	[object Object]
GBMNC22667-20	Muricea pendula	1	COI-5P	United States	27.931	-92.065
ABBAC057-10	Muricea laxa	1	COI-5P	Panama	9.35	-82.25

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
Standard	jaMurMuri3	2023-07-31	47686_1#4	848,179,780	128,075,146,780	SAMEA12927224	qc complete	Muricea muricata (1.00)
Hi-C - Arima v2	jaMurMuri4	2023-11-17	48086_3#1	555,223,164	83,838,697,764	SAMEA12927227	qc complete	Muricea muricata (1.00)
RNA PolyA	jaMurMuri4	2024-09-09	49387_3#62	94,280,656	14,236,379,056	SAMEA12927226	qc complete	Muricea muricata (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.

Loading, please wait

identity	info
0.907417	NC_027361.1 Propionibacterium phage PHL085N00, complete genome
0.903965	NC_018417.1 Candidatus Carsonella ruddii HT isolate Thao2000, complete genome

Showing 1 to 2 of 2 rows

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

Loading, please wait

specimen	contig	SSU length	attributed taxonomy by SSU
jaMurMuri3	atg000223l	886	ENA: Eukaryota;Metazoa;Cnidaria;Anthozoa;Octocorallia;Alcyonacea; SILVA: Eukaryota;Amorphea;Obazoa;Opisthokonta;Holozoa;Choanozoa;Metazoa;Animalia;BCP clade;Cnidaria;Anthozoa;Octocorallia;
jaMurMuri3	atg000328l	1295	ENA: Eukaryota;Metazoa;Cnidaria;Anthozoa;Octocorallia;Alcyonacea; SILVA: Eukaryota;Amorphea;Obazoa;Opisthokonta;Holozoa;Choanozoa;Metazoa;Animalia;BCP clade;Cnidaria;Anthozoa;Octocorallia;
jaMurMuri3	atg000581l	1477	ENA: Eukaryota;Metazoa;Cnidaria;Anthozoa;Octocorallia;Alcyonacea; SILVA: Eukaryota;Amorphea;Obazoa;Opisthokonta;Holozoa;Choanozoa;Metazoa;Animalia;BCP clade;Cnidaria;Anthozoa;Octocorallia;
jaMurMuri3	atg000985l	1783	ENA: Eukaryota;Metazoa;Cnidaria;Anthozoa;Octocorallia;Alcyonacea; SILVA: Eukaryota;Amorphea;Obazoa;Opisthokonta;Holozoa;Choanozoa;Metazoa;Animalia;BCP clade;Cnidaria;Anthozoa;Octocorallia;
jaMurMuri3	atg001695l	1830	ENA: Eukaryota;Metazoa;Cnidaria;Anthozoa;Octocorallia;Alcyonacea; SILVA: Eukaryota;Amorphea;Obazoa;Opisthokonta;Holozoa;Choanozoa;Metazoa;Animalia;BCP clade;Cnidaria;Anthozoa;Octocorallia;
jaMurMuri3	ptg000002l	1775	ENA: Eukaryota;Metazoa;Cnidaria;Anthozoa;Octocorallia;Alcyonacea; SILVA: Eukaryota;Amorphea;Obazoa;Opisthokonta;Holozoa;Choanozoa;Metazoa;Animalia;BCP clade;Cnidaria;Anthozoa;Octocorallia;
jaMurMuri3	ptg000005l	1826	ENA: Eukaryota;Metazoa;Cnidaria;Anthozoa;Octocorallia;Alcyonacea; SILVA: Eukaryota;Amorphea;Obazoa;Opisthokonta;Holozoa;Choanozoa;Metazoa;Animalia;BCP clade;Cnidaria;Anthozoa;Octocorallia;
jaMurMuri3	ptg000010l	1820	ENA: Eukaryota;Metazoa;Cnidaria;Anthozoa;Octocorallia;Alcyonacea; SILVA: Eukaryota;Amorphea;Obazoa;Opisthokonta;Holozoa;Choanozoa;Metazoa;Animalia;BCP clade;Cnidaria;Anthozoa;Octocorallia;
jaMurMuri3	ptg000012l	1698	ENA: Eukaryota;Metazoa;Cnidaria;Anthozoa;Octocorallia;Alcyonacea; SILVA: Eukaryota;Amorphea;Obazoa;Opisthokonta;Holozoa;Choanozoa;Metazoa;Animalia;BCP clade;Cnidaria;Anthozoa;Octocorallia;
jaMurMuri3	ptg000024l	1823	ENA: Eukaryota;Metazoa;Cnidaria;Anthozoa;Octocorallia;Alcyonacea; SILVA: Eukaryota;Amorphea;Obazoa;Opisthokonta;Holozoa;Choanozoa;Metazoa;Animalia;BCP clade;Cnidaria;Anthozoa;Octocorallia;

Showing 1 to 10 of 13 rows rows per page

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.

Loading, please wait

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
jaMurMuri3	Spirochaetaceae	290	0.02	-	-		0.00Mb		-		0.00Mb

Showing 1 to 1 of 1 rows

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

Loading, please wait

specimen	visualisation
No matching records found

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

jaMurMuri3.hifiasm.20220624

specimen	asm	date	contig N50	contigs	scaffold N50	scaffolds	length	BUSCO	merqury
jaMurMuri3	hifiasm.purging	2022-06-24	5,941,215	292			487,746,661	C:87.1%[S:85.4%,D:1.7%],F:6.7%,M:6.2%,n:954	Q60.6-C98.6(HiFi)
jaMurMuri3	hifiasm.scaffolding.yahs	2022-06-24	4,717,000	411	15,807,425	206	487,787,661	C:87.2%[S:85.7%,D:1.5%],F:6.6%,M:6.2%,n:954	Q60.7-C98.3(HiFi)
jaMurMuri3	hifiasm	2022-06-24	5,451,264	415			514,404,921	C:87.1%[S:85.2%,D:1.9%],F:6.7%,M:6.2%,n:954	Q59.9-C99.0(HiFi)
jaMurMuri3	hicanu.purging	2022-06-24	2,626,849	533			517,239,518	C:88.1%[S:84.0%,D:4.1%],F:6.6%,M:5.3%,n:954	Q61.8-C98.8(HiFi)
jaMurMuri3	hicanu	2022-06-24	2,221,127	1,990			930,801,240	C:88.8%[S:4.7%,D:84.1%],F:6.1%,M:5.1%,n:954	Q61.8-C100.0(HiFi)
jaMurMuri3	hifiasm.purging	2022-09-16	5,090,630	380			481,985,739		Q60.4-C98.8(HiFi)
jaMurMuri3	hifiasm.scaffolding.yahs	2022-09-16	4,238,000	508	15,020,843	299	482,027,539		-
jaMurMuri3	hifiasm	2022-09-16	4,879,003	767			525,335,688	C:85.8%[S:82.1%,D:3.7%],F:6.5%,M:7.7%,n:954	-

specimen	asm	organelle	date	length	genes	frameshifts	is circular	seqs	reference
jaMurMuri3	mitohifi.hifiasm	mito	2022-06-24	19,292	31	None	True	1	NC_029697.1; 19,586 bp; 17 genes
jaMurMuri3	mitohifi.reads	mito	2022-06-24	19,292	31	None	False	1	NC_029697.1; 19,586 bp; 17 genes
jaMurMuri3	mitohifi.hicanu	mito	2022-06-24	19,321	31	ND4	True	1	NC_029697.1; 19,586 bp; 17 genes
jaMurMuri3	mitohifi.hifiasm	mito	2022-09-16	19,358	30	None	False	1
jaMurMuri3	mitohifi.reads	mito	2022-09-16	19,292	31	None	True	1	NC_029698.1; 19,358 bp; 17 genes

Muricea muricata

Info

Specimens

Spectra estimates

Sequence data

PacBio run data

ONT run data

Illumina run data

Cobionts

jaMurMuri3.hifiasm.20220624

Assemblies

Organelles

Muricea muricata

Mash screen

MarkerScan: species composition

MarkerScan: cobiont assembly

Readviz classification

Contigviz classification

jaMurMuri3.hifiasm.20220624