Euphorbia peplus
Info
| NCBI taxon id: | 38846 NCBI; ENA; GoaT |
|---|---|
| Order: | Malpighiales |
| Family: | Euphorbiaceae |
| NCBI lineage: | Eukaryota;Viridiplantae;Streptophyta;Embryophyta;Tracheophyta;Spermatophyta;Magnoliopsida;eudicotyledons;Gunneridae;Pentapetalae;rosids;fabids;Malpighiales;Euphorbiaceae;Euphorbioideae;Euphorbieae;Euphorbia;Euphorbiasubgen.Esula;Euphorbiasect.Tithymalus; |
| GoaT genome size (M): | 391 (direct) |
| GoaT asm span (M): | 267 (direct) |
| GoaT chr no.: | 16 (direct) |
| GoaT haploid no.: | 11 (direct) |
| GoaT ploidy: | 2 (direct) |
| ToLID prefix: | ddEupPepu |
Specimens
Below is information about specimens collected for this species retrieved from the Sample Tracking System (STS).
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tolid | specimen_id | gal | sex | organism_part | biosample | biospecimen |
|---|---|---|---|---|---|---|
| ddEupPepu3 | KDTOL10012 | ROYAL BOTANIC GARDENS KEW | HERMAPHRODITE_MONOECIOUS | LEAF | SAMEA7521872 | SAMEA7521821 |
| ddEupPepu3 | KDTOL10012 | ROYAL BOTANIC GARDENS KEW | HERMAPHRODITE_MONOECIOUS | LEAF | SAMEA7521874 | SAMEA7521821 |
| ddEupPepu3 | KDTOL10012 | ROYAL BOTANIC GARDENS KEW | HERMAPHRODITE_MONOECIOUS | LEAF | SAMEA7521875 | SAMEA7521821 |
| ddEupPepu3 | KDTOL10012 | ROYAL BOTANIC GARDENS KEW | HERMAPHRODITE_MONOECIOUS | LEAF | SAMEA7521870 | SAMEA7521821 |
| ddEupPepu3 | KDTOL10012 | ROYAL BOTANIC GARDENS KEW | HERMAPHRODITE_MONOECIOUS | LEAF | SAMEA7521873 | SAMEA7521821 |
Spectra estimates
Below are estimates of genome size, repeat size, heterozygosity based on k-mer specta analysis with GenomeScope2.
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source | specimen | k-mer | k-cov | haploid size | repeat (%) | heterozygosity (%) | model fit (%) | model error (%) | histogram |
|---|---|---|---|---|---|---|---|---|---|
| 10x | ddEupPepu3 | 31 | 48.71 | 381,874,864 | 49.59 | 0.08 | 98.15 | 0.46 |   histogram.txt |
| pacbio | ddEupPepu3 | 31 | 29.87 | 355,397,449 | 46.13 | 0.07 | 96.80 | 0.17 |   histogram.txt |
| hic-arima2 | ddEupPepu3 | 31 | 116.9 | 295,141,779 | 51.24 | 1.14 | 96.12 | 0.42 |   histogram.txt |
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 | ddEupPepu3 | 2021-04-02 | 81042 | m64174e_210402_113844 | B01 | 1022 | 22,402,600,214 | 15,700 | SAMEA7521875 | ERR9630945 |
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ONT run data
Below are stats for each ONT seqeuncing run collected for this species.
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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.
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pipeline | specimen | date | run id | read pairs | yield | sample accession | run accession | run status | barcode |
|---|---|---|---|---|---|---|---|---|---|
| Chromium genome | ddEupPepu3 | 2021-05-25 | 37883_2#33 | 94,946,420 | 14,336,909,420 | SAMEA7521875 | ERR9580480 | qc complete | Euphorbia peplus (1.00) |
| Chromium genome | ddEupPepu3 | 2021-05-25 | 37883_2#34 | 84,271,904 | 12,725,057,504 | SAMEA7521875 | ERR9580481 | qc complete | Euphorbia peplus (1.00) |
| Chromium genome | ddEupPepu3 | 2021-05-25 | 37883_2#36 | 101,304,416 | 15,296,966,816 | SAMEA7521875 | ERR9580483 | qc complete | Euphorbia peplus (1.00) |
| Chromium genome | ddEupPepu3 | 2021-05-25 | 37883_2#35 | 111,177,886 | 16,787,860,786 | SAMEA7521875 | ERR9580482 | qc complete | Euphorbia peplus (1.00) |
| Hi-C - Arima v2 | ddEupPepu3 | 2021-09-11 | 40666_1#6 | 647,755,518 | 97,811,083,218 | SAMEA7521873 | ERR9580485 | qc complete | Euphorbia peplus (1.00) |
| RNA PolyA | ddEupPepu3 | 2021-08-03 | 39723_6#9 | 44,378,600 | 6,701,168,600 | SAMEA7521875 | ERR9580484 | qc complete | Euphorbia peplus (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 |
|---|---|
| 0.916705 | NC_018417.1 Candidatus Carsonella ruddii HT isolate Thao2000, complete genome |
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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 |
|---|---|---|---|
| ddEupPepu3 | atg000164l | 1501 |
|
| ddEupPepu3 | atg000304l | 1499 |
|
| ddEupPepu3 | atg000359l | 1499 |
|
| ddEupPepu3 | atg000385l | 1492 |
|
| ddEupPepu3 | ptg000001l | 1809 |
|
| ddEupPepu3 | ptg000003l | 1803 |
|
| ddEupPepu3 | ptg000009l | 1755 |
|
| ddEupPepu3 | ptg000017l | 1807 |
|
| ddEupPepu3 | ptg000032l | 1808 |
|
| ddEupPepu3 | ptg000061l | 1497 |
|
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 | ||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
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.
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specimen | visualisation |
|---|---|
| ddEupPepu3 |    |
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
ddEupPepu3.hifiasm.20220213
Assemblies
In-progress assembly QC.
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specimen | asm | date | contig N50 | contigs | scaffold N50 | scaffolds | length | BUSCO | merqury |
|---|---|---|---|---|---|---|---|---|---|
| ddEupPepu3 | hicanu | 2021-09-14 | 13,314,894 | 2,479 | 363,865,673 | C:97.6%[S:94.3%,D:3.3%],F:0.6%,M:1.8%,n:2326 | - | ||
| ddEupPepu3 | hicanu.purging | 2021-09-14 | 16,667,389 | 567 | 288,923,437 | C:96.7%[S:93.6%,D:3.1%],F:0.6%,M:2.7%,n:2326 | - | ||
| ddEupPepu3 | hifiasm | 2022-02-13 | 30,534,274 | 1,368 | 339,021,863 | Q48.7-C96.7(10X); Q58.9-C98.6(HiFi) | |||
| ddEupPepu3 | hifiasm.purging | 2022-02-13 | 30,534,274 | 373 | 292,544,567 | Q53.7-C96.7(10X); Q64.4-C98.5(HiFi) | |||
| ddEupPepu3 | hifiasm.scaff.salsa | 2022-02-13 | 27,114,669 | 375 | 31,936,716 | 368 | 292,546,419 | - | |
| ddEupPepu3 | hifiasm.scaff.yahs | 2022-02-13 | 27,114,669 | 376 | 62,831,070 | 368 | 292,544,519 | - | |
| ddEupPepu3 | hifiasm.polishing | 2022-02-13 | 30,534,130 | 373 | 292,542,528 | - | |||
| ddEupPepu3 | hifiasm.scaffolding.salsa | 2022-02-13 | 27,114,682 | 375 | 31,936,718 | 368 | 292,546,028 | C:97.5%[S:94.1%,D:3.4%],F:0.6%,M:1.9%,n:2326 | Q53.7-C96.7(10X); Q52.9-C98.5(HiFi) |
| ddEupPepu3 | hifiasm.scaffolding.yahs | 2022-02-13 | 27,114,682 | 376 | 62,831,041 | 368 | 292,544,128 | C:97.5%[S:94.1%,D:3.4%],F:0.6%,M:1.9%,n:2326 | Q53.7-C96.7(10X); Q52.9-C98.5(HiFi) |
| ddEupPepu3 | hifiasm.scaffolding.yahs | 2022-02-13 | 30,534,130 | 388 | 36,975,123 | 381 | 292,543,928 | - |
Organelles
In-progress organelle results from MitoHiFi or Oatk.
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specimen | asm | organelle | date | length | genes | frameshifts | is circular | reference |
|---|---|---|---|---|---|---|---|---|
| ddEupPepu3 | oatk.reads | mito | 2021-09-14 | 723,827 | 9 | None | False | NC_045136.1; 682,840 bp; 52 genes |
| ddEupPepu3 | oatk.reads | pltd | 2021-09-14 | 159,599 | 105 | None | True | NC_058989.1; 159,466 bp; 129 genes |
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