Supplemental Material for Hruska and Manthey, 2020

Supplemental File S1 contains information on the location and status of avesodb9 BUSCO gene sets. Supplemental File S2 contains a list of the missing avesodb9 BUSCO gene sets. Supplemental File S3 contains a summary of avesodb9 BUSCO gene sets. Supplemental File S4 contains information on the location and status of avesodb10 BUSCO gene sets. Supplemental File S5 contains a list of the missing avesodb10 BUSCO gene sets. Supplemental File S6 contains a summary of avesodb10 BUSCO gene sets.Supplemental File S7 contains information on the location and status of tetrapodsodb9 BUSCO gene sets. Supplemental File S8 contains a list of the missing tetrapodaodb9 BUSCO gene sets. Supplemental File S9 contains a summary of tetrapodaodb9 BUSCO gene sets. Supplemental File S10 contains information on the location and status of tetrapodsodb10 BUSCO gene sets. Supplemental File S11 contains a list of the missing tetrapodaodb10 BUSCO gene sets. Supplemental File S12 contains a summary of tetrapodaodb10 BUSCO gene sets. Supplemental File S13 contains the annotation information following the second round of MAKER. Supplemental File S14 contains the fasta sequences of CDS regions in the Caur_TTU_1.0 assembly discovered after the second round of MAKER. Supplemental File S15 contains the custom repeat library constructed using an earlier version of the Colaptes auratus genome and genomes from other songbird projects. File S16 contains the output from RepeatMasker, summarizing repetitive content in the Caur_TTU_1.0 assembly. File S17 contains information on the location and characteristics of the repetitive content in the Caur_TTU_1.0 assembly. .File S18_colaptes_reordered_filtered.txt is a tab-delimited text file that includes information on the position, percent identity, and length of each alignment that was produced using MUMMER’s show-coords module.