Plant Pathogen, Genomics, PacBio HiFi, Sample ID 394855
Dataset size is: 880.36 GiB
Data and Resources
This data is made available openly under a Creative Commons Attribution license.
Please see the initiative
Data Policy
for attribution information.
Additional Info Show Blank Fields
| Field | Value |
|---|---|
| Resource Permissions | organization_member_after_embargo:date_of_transfer_to_archive:365:pp-prj043 |
| Access Control Date | 2024-02-24 |
| Access Control Mode | date |
| Sequence Data Type | pacbio-hifi |
| analysis_software | SMRTlink 11.0.0.144466 |
| ancillary_notes | Syzygium luehmannii (F.Muell.) L.A.S.Johnson (host plant) vouchered at The National Herbarium of New South Wales. Voucher number: 1124137. |
| bait_set_name | NA |
| bait_set_reference | NA |
| base_url | https://downloads-qcif.bioplatforms.com/bpa/pp_staging/pacbio-hifi/BPAOPS-1361/20230223_PP_AGRF_DA218825/ |
| bioplatforms_dataset_id | 102.100.100/399020 |
| bioplatforms_library_id | 102.100.100/397105 |
| bioplatforms_project | Plant Pathogen Initiative |
| bioplatforms_project_code | PP043_A_psidii_host |
| bioplatforms_sample_id | 102.100.100/394855 |
| ccg_jira_ticket | BPAOPS-1361 |
| cell_postion | A01 |
| class | Pucciniomycetes |
| collection_date | 2022-06-29 |
| collection_method | Sample taken at from controlled inoculation (14 June 2022) of plant. Diseased sample collected and stored in -80°C freezer 29th June 2022. |
| collector | Peri Tobias |
| common_name | Myrtle rust |
| country | Australia |
| data_context | Genomics |
| data_type | PacBio-HiFi |
| date_data_published | 03/03/2023 |
| date_of_transfer | 2023-02-24 |
| date_of_transfer_to_archive | 2023-02-27 |
| description | PacBio-HiFi |
| dna_treatment | shearing + DNA repair |
| download | https://data.bioplatforms.com/dataset?ext_search_by=&q=ticket%3ABPAOPS-1361 |
| experimental_design | NA |
| facility | AGRF |
| facility_sample_id | 394855 |
| family | Sphaerophragmiaceae |
| fast5_compression | NA |
| flowcell_id | DA218825 |
| flowcell_type | PacBio SMRTcell 8M |
| folder_name | 20230223_PP_AGRF_DA218825 |
| genus | Austropuccinia |
| host_common_name | Riberry |
| host_family | Myrtaceae |
| host_organ | Leaves |
| host_scientific_name | Syzygium luehmannii (F.Muell.) L.A.S.Johnson |
| host_status | Cultivated from myrtle rust screened experimental plants. Specific individual plant is highly susceptible to myrtle rust and given the specimen ID number 50. |
| host_symptom | Rust pustules |
| insert_size_range | 10-20kb |
| library_comments | NA |
| library_construction_protocol | Preparing whole genome and metagenome libraries using SMRTbell® prep kit 3.0 |
| library_id | 397105 |
| library_index_id | NA |
| library_index_id_dual | NA |
| library_index_seq_dual | NA |
| library_index_sequence | NA |
| library_layout | HiFi |
| library_location | AGRF |
| library_ng_ul | 120pM |
| library_oligo_sequence | NA |
| library_oligo_sequence_dual | NA |
| library_prep_date | 2023-01-16 |
| library_prepared_by | Trent Peters |
| library_selection | Diffusion |
| library_source | gDNA |
| library_strategy | HiFi |
| library_type | WGS |
| material_extracted_by | Jacob Downs - University of Sydney |
| material_extraction_date | 2022-12-15 |
| material_extraction_method | Sorbitol wash and CTAB |
| material_extraction_type | gDNA |
| metadata_revision_date | 2024-08-16 |
| metadata_revision_filename | 2024-08-12_Combined_Plant_Pathogen_sample_metadata_forQCIF_removelatlong.xlsx |
| model_base_caller | NA |
| movie_length | 30hrs |
| n_libraries_pooled | NA |
| order | Pucciniales |
| phylum | Basidiomycota |
| project_lead | Peri Tobias | University of Sydney |
| sample_collection_type | Infected Syzygium luehmannii plant |
| sample_custodian | University of Sydney, Plant Breeding Institute, Cobbitty, NSW |
| sample_id | 394855 |
| sample_type | Diseased plant |
| scientific_name | Austropuccinia psidii |
| scientific_name_authorship | (G. Winter) Beenken |
| sequencing_facility | AGRF |
| sequencing_kit_chemistry_version | Sequel II Sequencing Plate 2.0 |
| sequencing_model | Sequel Iie |
| sequencing_platform | PacBio |
| species | psidii |
| specimen_custodian | University of Sydney, Plant Breeding Institute, Cobbitty, NSW |
| specimen_id | Au_3, culture no. 622 and accession 115012 |
| specimen_id_description | Pandemic strain myrtle rust |
| state_or_region | NSW |
| taxon_id | 181123 |
| taxonomic_group | Fungi |
| ticket | BPAOPS-1361 |
| tissue | Leaf |
| tissue_preservation | Frozen |
| tissue_preservation_temperature | -80°C |