Araneus diadematus
European garden spider
Info
| NCBI taxon id: | 45920 NCBI; ENA; GoaT |
|---|---|
| Order: | Araneae |
| Family: | Araneidae |
| NCBI lineage: | Eukaryota;Metazoa;Ecdysozoa;Arthropoda;Chelicerata;Arachnida;Araneae;Araneomorphae;Entelegynae;Araneoidea;Araneidae;Araneus; |
| GoaT genome size (M): | 2,513 (direct) |
| GoaT asm span (M): | 3,656 (ancestor) |
| GoaT chr no.: | 24 (ancestor) |
| GoaT haploid no.: | 12 (ancestor) |
| GoaT ploidy: | 6 (ancestor) |
| ToLID prefix: | qqAraDiad |
Specimens
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 |
|---|---|---|---|---|---|---|
| qqAraDiad1 | Ox000078 | UNIVERSITY OF OXFORD | FEMALE | ABDOMEN | SAMEA7519976 | SAMEA7519933 |
| qqAraDiad1 | Ox000078 | UNIVERSITY OF OXFORD | FEMALE | CEPHALOTHORAX | SAMEA7519977 | SAMEA7519933 |
| qqAraDiad2 | Ox000089 | UNIVERSITY OF OXFORD | MALE | CEPHALOTHORAX | SAMEA7519978 | SAMEA7519934 |
| qqAraDiad2 | Ox000089 | UNIVERSITY OF OXFORD | MALE | ABDOMEN | SAMEA7519979 | SAMEA7519934 |
| qqAraDiad3 | Ox000094 | UNIVERSITY OF OXFORD | FEMALE | CEPHALOTHORAX | SAMEA7519980 | SAMEA7519935 |
Spectra estimates
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 |
|---|---|---|---|---|---|---|---|---|---|
| 10x | qqAraDiad2 | 31 | 14.16 | 2,567,890,066 | 41.75 | 2.46 | 98.92 | 0.48 |   histogram.txt |
| pacbio | qqAraDiad2 | 31 | 37.05 | 7,698,614 | 78.18 | 3.82 | 89.99 | 5.54 |   histogram.txt |
| hic-arima2 | qqAraDiad4 | 31 | 50.2 | 2,944,208,912 | 65.48 | 5.12 | 98.63 | 0.33 |   histogram.txt |
Sequence data
PacBio run data
Below are stats for each PacBio seqeuncing run collected for this species.
pipeline | specimen | date | run id | movie | well | tag | yield | N50 | sample accession | run accession | barcode |
|---|---|---|---|---|---|---|---|---|---|---|---|
| PacBio - HiFi | qqAraDiad2 | 2020-10-10 | TRACTION-RUN-58 | m64094_201010_173420 | C01 | 1022 | 3,353,303,027 | 8,365 | SAMEA7519979 |
ONT run data
Below are stats for each ONT seqeuncing run collected for this species.
pipeline | specimen | date | run id | flowcell | type | yield | N50 | sample accession | report |
|---|---|---|---|---|---|---|---|---|---|
| No matching records found | |||||||||
Illumina run data
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 |
|---|---|---|---|---|---|---|---|---|---|
| Chromium genome | qqAraDiad2 | 2020-10-13 | 35188_8#3 | 226,669,040 | 34,227,025,040 | SAMEA7519979 | qc complete | Araneus diadematus (1.00) | |
| Chromium genome | qqAraDiad2 | 2020-10-13 | 35188_8#1 | 218,309,238 | 32,964,694,938 | SAMEA7519979 | qc complete | Araneus diadematus (1.00) | |
| Chromium genome | qqAraDiad2 | 2020-10-13 | 35188_8#4 | 213,861,922 | 32,293,150,222 | SAMEA7519979 | qc complete | Araneus diadematus (1.00) | |
| Chromium genome | qqAraDiad2 | 2020-10-13 | 35188_8#2 | 111,321,266 | 16,809,511,166 | SAMEA7519979 | qc complete | Araneus diadematus (1.00) | |
| Hi-C - Arima v2 | qqAraDiad4 | 2022-03-04 | 43892_1#2 | 2,705,768,916 | 408,571,106,316 | SAMEA8534491 | qc complete | Araneus diadematus (1.00) | |
| RNA PolyA | qqAraDiad5 | 2023-02-16 | 46781_2#63 | 68,406,476 | 10,329,377,876 | SAMEA8534492 | qc complete | Araneus diadematus (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.
identity | info |
|---|---|
| 0.977418 | NC_000935.1 Acyrthosiphon pisum bacteriophage APSE-1, complete genome |
| 0.940862 | NC_018417.1 Candidatus Carsonella ruddii HT isolate Thao2000, complete genome |
| 0.913621 | [28 seqs] NZ_LTBM01000001.1 Candidatus Phytoplasma oryzae isolate Mbita1 Pmin.contig.0_1, whole genome shotgun sequence [...] |
| 0.911545 | NZ_AP013293.1 Candidatus Sulcia muelleri PSPU DNA, complete genome |
| 0.910625 | [3 seqs] NZ_LN890285.1 Buchnera aphidicola (Tuberolachnus salignus) strain BTs genome assembly, chromosome: 1 [...] |
| 0.910001 | [2017 seqs] NW_004087753.1 Ichthyophthirius multifiliis unplaced genomic scaffold scaff_1120509249386, whole genome shotgun sequence [...] |
| 0.909686 | [2 seqs] NC_008513.1 Buchnera aphidicola BCc, complete genome [...] |
| 0.908403 | NC_011047.1 Candidatus Phytoplasma mali strain AT complete chromosome |
| 0.907748 | NC_002520.1 Amsacta moorei entomopoxvirus 'L', complete genome |
Species composition by small subunit (SSU) presence in the assembly with MarkerScan.
specimen | contig | SSU length | attributed taxonomy by SSU |
|---|---|---|---|
| No matching records found | |||
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.
specimen | family | classified reads | original assembly | re-assembly | ||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
count | (%) | BUSCO | BUSCO | contigs | contig length | number of reads | BUSCO | contigs | contig length | number of reads | ||
| No matching records found | ||||||||||||
Visualisation of a classification of the PacBio reads using a variation autoencoder on the k-mer counts.
specimen | visualisation |
|---|---|
| qqAraDiad2 |    |
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
Assemblies
In-progress assembly QC.
specimen | asm | date | contig N50 | contigs | scaffold N50 | scaffolds | length | BUSCO | merqury |
|---|---|---|---|---|---|---|---|---|---|
| No matching records found | |||||||||
Organelles
In-progress organelle results from MitoHiFi or Oatk.
specimen | asm | organelle | date | length | genes | frameshifts | is circular | reference |
|---|---|---|---|---|---|---|---|---|
| No matching records found | ||||||||
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