Molothrus aeneus isolate:106 Genome sequencing and assembly

Background:The bronzed cowbird (family Icteridae) is an obligate brood parasitic songbird whose range spans much of North America. Cowbird DNA isolated for whole genome sequencing is derived from an adult female (bird sample id 106; collected in 2016 in Hidalgo County, Texas). High molecular weight DNA was used as input to generate long-reads on the Revio instrument (PacBio) according to the manufacturer's protocols. Total CCS coverage used for assembly was 82x using a genome size estimate of 1.2Gb. All sequence reads were assembled with Hifiasm using default parameter settings. HiC sequence data from a brown-headed female cowbird sample (see bioproject PRJNA523990) were aligned to the bronzed cowbird primary contigs using chromap v0.2.3-r407, and the resulting alignments were used to scaffold the assembly using YAHS v1.2a.1, followed by manual curation to chromosome format. As per the vertebrate genomes project guidelines all the expected chromosomes were numbered by size.This work was supported by NSF grants DBI 1754311, 1754397, 1754406, 1754643, 1940624.Molothrus aeneus 1.0 Sequence and Assembly Credits: University of Missouri, Columbia, MODNA source - Dr. Kathleen Lynch, Hofstra University, Long Island, NYGenome Sequence - Hudson Alpha Institute, Hunstville, AL.Sequence Assembly - University of Missouri, Columbia, MO.Citation upon use of this assembly in a manuscript:It is requested that users of this Molothrus aeneus 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 Drs. Michael Sorenson ([e-mail]) or Christopher Balakrishnan ([e-mail]) for the use of pre-publication data in accord with the Ft. Lauderdale and Toronto genomic data use agreements.