characteristics.text: SAMN31686289
characteristics.characteristic: External Id
characteristics.text: University of Missouri
characteristics.characteristic: INSDC center name
characteristics.text: 2022-11-10T00:00:00Z
characteristics.characteristic: INSDC first public
characteristics.text: 2023-02-01T22:15:18.690Z
characteristics.characteristic: INSDC last update
characteristics.text: SRS16649798
characteristics.characteristic: INSDC secondary accession
characteristics.text: live
characteristics.characteristic: INSDC status
characteristics.text: Model organism or animal
characteristics.characteristic: NCBI submission model
characteristics.text: Model.organism.animal.1.0
characteristics.characteristic: NCBI submission package
characteristics.text: SRS16649798
characteristics.characteristic: SRA accession
characteristics.text: Dr. Claire Spottiswoode
characteristics.characteristic: biomaterial_provider
characteristics.text: The Greater honeyguide (family Indicatoridae) is a near passerine bird residing in the southern regions of Africa with a typical nesting behavior that was chosen for this study to serve as an obligate brood parasitic bird. Honeyguide high molecular weight (HMW) DNA isolated for whole genome sequencing is derived from a adult female that originated in Zambia and was provided by Dr. Claire Spottiswoode. HMW DNA (from muscle) was used as input to generate long-reads using circular long reads (CLR) based calling output from the Sequel II instrument (Pacific Biosciences) according to the manufacturer's protocols. Total CLR coverage used for assembly was 254x using a genome size estimate of 1.1Gb. All quality filtered sequence reads were assembled with Flye v2.8.1-b1676 in pacbio-raw mode using default parameter settings. Haplotigs were then removed with purge_haplotigs using one of the flow cells of CLR reads and cutoffs 12,43,105. Next, contains were polished with alignment of 60x Illumina 150bp read data and the cextflow pipeline from the Warren Lab (shortread-polish-nf). Error corrected contains were scaffolded using HiC sequence data from a different individual but same sampling location using Salsa 2 and JuiceBox pipelines. As per the Vertebrate Genomes Project guidelines, all chromosomes were numbered by size. This work was supported by NSF grants DBI 1754311, 1754397, 1754406, 1754643, 1940624. Indicator indicator 1.0 Sequence and Assembly Credits: DNA source: Dr. Claire Spottiswoode Genome Sequence: Hudson Alpha Institute, Huntsville, AL. Sequence and Assembly: University of Missouri, Columbia, MO. Citation upon use of this assembly in a manuscript: It is requested that users of this Indicator indicator 1.0 sequence assembly acknowledge the brood parasitic bird genomes consortium in any publications that result from use of this sequence assembly prior to the publication of this resource. Any publications that propose to generate whole genome analyses using this resource should contact Dr. Michael Sorenson (msoren@bu.edu) or Chris Balakrishnan (balakrishnanc@ecu.edu) for the use of pre-publication data in accord with the Ft. Lauderdale and Toronto genomic data use agreements.
characteristics.characteristic: description
characteristics.text: Adult
characteristics.characteristic: dev_stage
characteristics.text: Zambia
characteristics.characteristic: geo_loc_name
characteristics.text: 239-I01
characteristics.characteristic: isolate
characteristics.text: Indicator indicator
characteristics.ontologyTerms: http://purl.obolibrary.org/obo/NCBITaxon_1002788
characteristics.characteristic: organism
characteristics.text: female
characteristics.characteristic: sex
characteristics.text: muscle
characteristics.characteristic: tissue
characteristics.text: Indicator indicator (honeyguide)
characteristics.characteristic: title