Kleidocerys resedae
Birch Catkin Bug
Info
| NCBI taxon id: | 680436 |
|---|---|
| Order: | Hemiptera |
| Family: | Lygaeidae |
| NCBI lineage: | Eukaryota;Metazoa;Ecdysozoa;Arthropoda;Hexapoda;Insecta;Pterygota;Neoptera;Paraneoptera;Hemiptera;Heteroptera;Panheteroptera;Pentatomomorpha;Lygaeoidea;Lygaeidae;Ischnorhynchinae;Kleidocerys; |
| GoaT genome size (M): | 5,281 (ancestor) |
| GoaT asm span (M): | 1,099 (ancestor) |
| GoaT chr no.: | 16 (direct) |
| GoaT ploidy: | 2 (ancestor) |
| ToLID prefix: | ihKleRese |
Specimens
Below is information about specimens collected for this species retrieved from the Golden Record manifest.
public_name | specimen_id | gal | sex | organism_part | biosample | biospecimen |
|---|---|---|---|---|---|---|
| ihKleRese1 | Ox000313 | UNIVERSITY OF OXFORD | NOT_COLLECTED | WHOLE_ORGANISM | SAMEA7520434 | SAMEA7520350 |
| ihKleRese2 | Ox000314 | UNIVERSITY OF OXFORD | NOT_COLLECTED | WHOLE_ORGANISM | SAMEA7520435 | SAMEA7520351 |
| ihKleRese3 | NHMUK014439772 | NATURAL HISTORY MUSEUM | NOT_PROVIDED | WHOLE_ORGANISM | SAMEA111458295 | SAMEA111458196 |
| ihKleRese4 | Ox002526 | UNIVERSITY OF OXFORD | NOT_COLLECTED | WHOLE_ORGANISM | SAMEA112233213 | SAMEA112232722 |
Spectra estimates
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 (%) | histogram |
|---|---|---|---|---|---|---|---|---|---|
| pacbio | ihKleRese3 | 31 | 7.555 | 1,816,591,093 | 58.49 | 2.07 | 98.49 | 0.14 |   |
| hic-arima2 | ihKleRese3 | 31 | 198.5 | 1,627,896,338 | 55.12 | 3.35 | 96.28 | 0.39 |   |
| pacbio | ihKleRese2 | 31 | 22.66 | 96,447,421 | 96.59 | 3.88 | 81.02 | 2.32 |   |
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 | ihKleRese2 | 2021-08-03 | 85040 | m64178e_210803_125337 | D01 | 1002 | 9,087,492,511 | 10,217 | SAMEA7520435 | ||
| PacBio - HiFi | ihKleRese3 | 2023-01-10 | TRACTION-RUN-401 | m64229e_230110_104000 | E01 | 1018 | 28,699,114,793 | 13,254 | SAMEA111458295 |
Illumina run data
Illumina run stats.
pipeline | specimen | date | run id | read pairs | yield | sample accession | run accession | run status | barcode |
|---|---|---|---|---|---|---|---|---|---|
| Hi-C - Arima v2 | ihKleRese3 | 2023-02-01 | 46689_1#1 | 6,038,094,036 | 911,752,199,436 | SAMEA111458295 | qc complete | Kleidocerys resedae (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 |
|---|---|
| 0.988479 | [130 seqs] NZ_MUJL01000001.1 Wolbachia pipientis wUni gwu.contig.0_1, whole genome shotgun sequence [...] |
| 0.98062 | [426 seqs] NZ_AERW01000001.1 Wolbachia endosymbiont wVitB of Nasonia vitripennis Contig_0001, whole genome shotgun sequence [...] |
| 0.930437 | NC_018417.1 Candidatus Carsonella ruddii HT isolate Thao2000, complete genome |
| 0.909686 | [256 seqs] NZ_ACFP01000256.1 Wolbachia endosymbiont of Muscidifurax uniraptor Contig561, whole genome shotgun sequence [...] |
| 0.907748 | [28 seqs] NZ_LTBM01000001.1 Candidatus Phytoplasma oryzae isolate Mbita1 Pmin.contig.0_1, whole genome shotgun sequence [...] |
| 0.907083 | [2017 seqs] NW_004087753.1 Ichthyophthirius multifiliis unplaced genomic scaffold scaff_1120509249386, whole genome shotgun sequence [...] |
| 0.906409 | [2 seqs] NC_008513.1 Buchnera aphidicola BCc, complete genome [...] |
| 0.904677 | [3 seqs] NZ_LN890285.1 Buchnera aphidicola (Tuberolachnus salignus) strain BTs genome assembly, chromosome: 1 [...] |
| 0.904322 | NC_002520.1 Amsacta moorei entomopoxvirus 'L', complete genome |
| 0.901759 | NZ_AP013293.1 Candidatus Sulcia muelleri PSPU DNA, complete genome |
Species composition by small subunit (SSU) presence in the assembly.
specimen | contig | SSU length | attributed taxonomy by SSU |
|---|---|---|---|
| No matching records found | |||
Re-assembly of reads classified under each identified SSU Marker family.
specimen | family | classified reads | original assembly | re-assembly | |||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
count | (%) | BUSCO | BUSCO | contigs | contig length | reads | BUSCO | contigs | contig length | additional reads | circos | ||
| No matching records found | |||||||||||||
Visualisation of a classification of the PacBio reads using a variation autoencoder on the k-mer counts.
specimen | visualisation |
|---|---|
| ihKleRese2 |    |
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 MitoHiFi2.
specimen | asm | date | length | genes | frameshifts | is circular | reference |
|---|---|---|---|---|---|---|---|
| No matching records found | |||||||
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