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IDs: 16181581 [UID] 41484108 [GenBank] 41609568 [RefSeq]
Agelaius phoeniceus (red-winged blackbird) Sequence Assembly Release Notes Background: The red-winged blackbird (family Icteridae), one of the most common songbirds in North America and an icterid with typical nesting behavior, was chosen for this study to serve as an outgroup to ... the obligate brood parasitic brown-headed cowbird (Molothrus ater). Red-winged blackbird DNA isolated for whole genome sequencing is derived from an adult female located in the state of Texas. High molecular weight DNA was used as input to generate long-reads using circular consensus sequence (CCS) base calling output from the Sequel II instrument (Pacific Biosciences) according to the manufacturer's protocols. Total CCS coverage was approx. 38x using a genome size estimate of 1.1Gb. All quality filtered sequence reads were assembled with HiFasm using default parameter settings and redundant contigs removed using purge_haplotigs. Assembled contigs were scaffolded with Hi-C data from the same individual using SALSA2, and then manually curated with JuiceBox. Chromosomes were numbered by size with the exception of 16 which was numbered based on alignment with chicken. This work was supported by NSF grants DBI 1754311, 1754397, 1754406, 1754643, 1940624. Agelaius phoeniceus 1.1 Sequence and Assembly Credits: DNA source - Hidalgo County, Texas (BioBank/Freezerworks ID: 100140; Name: 224; Unique Aliquot ID 101355; Developmental stage: Adult; Tissue type: brain; Date collected: 3/30/2018; Received from: Kathleen Lynch, Hofstra University, NY; Specimen ID: MCZ Ornithology 364415, collector Scott Edwards, link: https://mczbase.mcz.harvard.edu/guid/MCZ:Orn:364415). Genome Sequence - Hudson Alpha Institute, Hunstville, 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 Agelaius phoeniceus 1.1 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. The scaffolds and chromosomes for this genome were updated on October 2022. There was no change to the contigs. more
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